title: RNA Immunoprecipitation in macrophages using NLRC4 and Caspase11 and high-throughput sequencing of isolated lncRNA

status: Public on Apr 28 2021

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

summary: At the epigenetic level, lncRNAs play important roles in cell differentiation and function. We identified novel long-stranded non-coding RNA (GM1082) in BMDMs, which may play an important role in macrophage differentiation and function.To confirm the interaction between LNCRNA and NLRC4 and Caspase11, we performed RNA immunoprecipitation using NLRC4 and Caspase11 antibodies, and high-throughput sequencing of the obtained RNA.

overall_design: Mouse bone marrow cells were induced in vitro by adding 20ng/ml of M-csf in DMEM medium.After 6 days of M-CSF induction, BMDMs were exposed to flagellin.Cell lysates were incubated with normal rabbit IgG, NLRC4 and caspase11 antibody.RNAs were isolated from the Protein–RNA complexes with phenol-chloroform and subjected to library construction.

first: Ya

last: Wang


title: Genome-wide mapping of histone H3 Lysine 4 trimethylation (H3K4me3) and its Involvement in fatty acid biosynthesis in sunflower developing seeds.

city: Seville

first: Antonio J.

last: Moreno-Perez

address: Campus UPO. Building 4. Crta. Utrera Km 1

country: Spain

institute: Instituto de la Grasa (CSIC)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism as well as facilitates the identification of new functional regions in oil crop genomes. The present study characterized the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid related-genes and transcription factors in developing sunflower seeds.

overall_design: ChIP-seq experiment in sunflower developing seeds

first: Antonio

middle: J

last: Moeno-Pérez

first: José

middle: M

last: Santos-Pereira

first: Raquel

last: Martins-Noguerol

first: Cristinas

last: DeAndrés-Gil

first: M

middle: A

last: Troncoso-Ponce

first: Mónica

last: Venegas-Calerón

first: Rosario

last: Sánchez

first: Rafael

last: Garcés

first: Joaquín

last: Salas

first: Juan

last: Tena

first: Enrique

last: Martínez-Force


title: NLRC4 activation needs lncRNA LNCGM1082

country: China

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Preoperative exercise therapy triggers anti-inflammatory trained immunity of Kupffer cells through metabolic reprogramming

city: Columbus

first: Hai

last: Huang

state: OH

address: 486 Biomedical Research Tower, 460 West 12th Ave

department: Surgery

country: USA

institute: The Ohio State University

summary: Single-cell transcriptomics revealed that transcriptomic profile is shifted towards anti-inflammatory in Kupffer cells after pre-operative exercise therapy in mice.

overall_design: To investigate single cell transcriptomics on Kupffer cells, we obtained hepatic CD45+ leukocytes. Four-week exercise or sedentariness were performed, and liver tissue was harvested, followed by cell isolation, FACs sorting, and 10X Genomics Chromium Drop-Seq and library construction. Illumina Next-Seq sequencing of barcoded single nuclei libraries was performed and aligned to a pre-mrna genome with STAR/CellRanger. Gene/barcode matrices were merged and processed with the Seurat R package.

first: Hongji

last: Zhang

first: Meihong

last: Deng

first: Allan

last: Tsung

first: Tianmeng

last: Chen

first: Jinghua

last: Ren

first: Yujia

last: Xia

first: Amblessed

last: Onuma

first: Yu

first: Jiayi

last: He

first: Junru

last: Wu

first: Han

first: Ahmad

last: Hamad

first: Chengli

last: Shen

first: Jinxiang

first: John

last: Asara

first: Gregory

middle: K

last: Behbehani

first: Haitao

last: Wen


title: The hypothalamus predates the origin of vertebrates

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: The hypothalamus coordinates neuroendocrine functions in vertebrates, including circadian rhythm, metabolism, and appetite. To explore its evolutionary origin, we attempt to create integrated transcription/connectome brain maps for swimming tadpoles of the ascidian, Ciona intestinalis, which serves as an approximation of the ancestral proto-vertebrate. This map features several cell types related to different regions of the vertebrate hypothalamus, including coronet cells, magnocellular neurons and the arcuate nucleus.  Coronet cells express melanopsin and share additional properties with the saccus vasculosus, a specialized region of the hypothalamus that mediates photoperiodism in non-tropical fishes such as salmon. Comparative transcriptome analyses identified orthologous cell types for mechanosensory switch neurons, and VP+ and VPR+ relay neurons in different regions of the mouse hypothalamus. These observations provide evidence that the hypothalamus predates the evolution of the vertebrate brain.  We discuss the possibility that switch neurons, coronet cells, and FoxP+/VPR relay neurons comprise a behavioral circuit that helps trigger metamorphosis of Ciona larvae in response to twilight.

overall_design: After fertilization using gametes from the same individual, one-cell stage embryos were electroporated with Dmrt1>H2B:GFP and Dmrt1>LacZ (control condition) or Dmrt1>H2B:GFP and Dmrt1>NeuroD (NeuroD overexpression condition). At the late tailbud stage I, morphologically normal embryos were selected, and at late tailbud II, GFP+ embryos were dissociated as previously described in Cao et al, 2019. The dissociation was performed in duplicate. Single-cell suspensions were loaded onto The Chromium Controller (10x Genomics). For all of the samples, cells were lysed, cDNAs were barcoded and amplified with Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10x Genomics) following the instructions of the manufacturer. Illumina sequencing libraries were prepared from the cDNA samples using the Nextera DNA library prep kit (Illumina). All of the libraries were sequenced on Illumina NovaSeq 6000 with S1 reagent kit (300 cycles, paired-end) following standard Illumina protocols. Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only pass-filtered reads were used for further analysis. Reads that aligned to phix (using Bowtie version 1.1.1) were removed, as were reads that failed Illumina’s default chastity filter. We then combined the FASTQ files from each lane and separated the samples using the barcode sequences allowing one mismatch (using barcode_splitter version 0.18.2). In the read 2 of each sample, the rightmost bases after to position 100 were trimmed to keep only high-quality reads. Using 10x CellRanger version 3.0.2, the count pipeline was run with default settings on the trimmed FASTQ files to generate gene–barcode matrices for each sample. The reference sequence of Ciona intestinalis was obtained from the Ghost database (KH model 2012). The integration of scRNA-Seq data of NeuroD overexpressed embryos and the control embryos were performed with Seurat v3.0

first: Laurence

last: Lemaire


title: Long non-coding RNA CRNDE Involved in Resistance to EGFR tyrosine kinase inhibitor in EGFR-mutant Lung Cancer via eIF4A3/MUC1/EGFR Signal.

city: Bunkyo-ku Tokyo

first: Aya

last: Fukuizumi

address: 1-1-5 Sendagi

department: Department of Pulmonary Medicine and Oncology,

country: Japan

institute: Nippon Medical School

summary:
Introduction: Overcoming of acquired resistance to EGFR-tyrosine kinase inhibitors (EGFR-TKIs) is an intractable obstacle for many clinical oncologists. The mechanisms of resistance to EGFR-TKIs are very complex. Long non-coding RNAs (lncRNAs) may play an important role in cancer development and metastasis. However, the biological process between lncRNAs and drug resistance to EGFR mutated lung cancer largely unknown.
Methods: Osimertinib and afatinib-resistant EGFR-mutated lung cancer cells were established using by a stepwise method. Microarray analysis of non-coding and coding RNAs was performed using parental and resistant EGFR-mutant NSCLC cells.
Results: Microarray analysis was evaluated by bioinformatics analysis through medical-industrial collaboration. CRNDE and DGCR5 lncRNAs were highly expressed in EGFR-TKIs-resistant cells. CRNDE binds to eIF4A3 protein, down-regulates eIF4A3 and MUC1 expression, and down-regulates p-EGFR expression. CRNDE inhibition activated the eIF4A3/MUC1/EGFR signaling pathway and apoptotic activity and restored sensitivity to EGFR-TKIs.
Conclusions: We identified lncRNA CRNDE associated with resistance to EGFR-TKIs in EGFR-mutant NSCLC cells. CRNDE may be a novel therapeutic target for EGFR mutant NSCLC patients.

overall_design: We performed the microarray analysis of non-coding and coding RNAs using parental and resistant EGFR-mutant cell lines.

first: Satoshi

last: Takahashi

first: Rintaro

last: Noro

first: Masahiro

last: Seike


title: Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model

city: Belfast

first: Gary

last: Hardiman

state: Antrim

address: 19 Chlorine Gardens

department: Institute for Global Food Security

country: United Kingdom

institute: Queen's University Belfast

summary: We hypothesised that induction of a torpor-like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis, a torpor-like state was induced in zebrafish using melatonin treatment and cold temperature, and radiation exposure was administered twice over the course of 10 days. The protective effects of induced-torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation, torpor, and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor-like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response, including steroidal signalling and changes to metabolism, damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis, proliferation, cell survival signals and expression of genes involved in protection against the adverse effects of radiation, particularly in neurons, suggesting a radioprotective effect conferred by a torpor state. This proof-of-concept model provides compelling initial evidence for utilizing an induced torpor-like state as a potential countermeasure for radiation exposure.

overall_design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation

first: Thomas

last: Cahill

first: Willian

last: da Silveira

first: Ludivine

last: Renaud

first: Tucker

last: Williamson

first: Hao

last: Wang

first: Dongjun

last: Chung

first: Ian

last: Overton

first: Sherine

last: Chan


title: Identification of translated small open reading frames in lymphocytes

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

summary: Open reading frames (ORFs) are the genomic DNA sequences that have the potential to be translated. Genome annotation pipelines dismiss translation products of small ORFs (smORFs) of less than 100 codons (<300 nucleotides) as being unlikely to have a biological function. In this study, we systematically characterized smORFs in mouse B and T cells under different conditions and predicted a total of 5744 unique actively translated smORFs. We then extended our analysis to ORFs of 101-200 codons in length and predicted 945 of such longer translation products. Additionally, our results have suggested the existence of candidate secreted micropeptides. Furthermore, verifying their existence and identifying their functions will be essential and potentially lead to useful applications.

overall_design: Peripheral lymph nodes were isolated from 5 biological replicates of control C57BL/6 mice (Zfp36l1 floxed/floxed without Cre). Each sample was split to generate Ribosome profiling  and total RNA-seq libraries. Ribosome profiling data is submitted here; the corresponding total RNA-seq datasets are available in GSE146073.

first: Alexander

last: Saveliev

first: Fengyuan

last: Hu

first: Martin

last: Turner


title: Genome-wide occupancy of Acs2 in budding yeast

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

summary: Here, we performed a ChIP-seq of Acs2 from Acs2-FLAG cells with anti-FLAG antibody. As a control, the untagged BY4741 was used as a control. Acs2 can bind a significant amount of genes. Moreover, we also found Acs2 can bind subtelomere regions.

overall_design: ChIP Sequencing Analysis between Untagged and Acs2-FLAG in Saccharomyces cerevisiae

first: Wanping

last: Chen

first: Shanshan

last: Li


title: Mycobacterium abscessus biofilms have a distinct transcription profile and harbor long-chain mycolic acids

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Comparison of  transcriptional differences (RNA-seq) between biofilm and planktonic cultures of Mycobacterium abscessus

overall_design: For pellicle samples, cultures of Mycobacterium abscessus were grown in 75cm2 cap-vented culture flasks in a 37 degrees C static incubator for 5 (t1) or 7 (t2) days. For planktonic samples, M. abscessus was cultured with tyloxapol added to a final concentration of 0.05%. Samples were collected from pellicle and planktonic cultures from five independent experiments.  The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Epigenetics is implicated in the basis of gender incongruence. An epigenome-wide association analysis.

status: Public on Apr 27 2021

city: A Coruña

first: Rosa

last: Fernandez

state: None / N/A

address: Campus Elviña

department: Psychology

institute: University of A Coruña

type: Methylation profiling by genome tiling array

summary: The main objective was to carry out a global DNA methylation analysis in a population with gender incongruence before gender-affirming hormone treatment (GAHT), in comparison to a cisgender population.

overall_design: Methods: A global CpG (cytosine-phosphate-guanine) methylation analysis was performed on blood from 16 transgender people before GAHT vs. 16 cisgender people using the Illumina© Infinium Human Methylation 850k BeadChip, after bisulfite conversion. Changes in the DNA methylome in cisgender vs. transgender populations were analyzed with the Partek® Genomics Suite program (false discovery rate correction FDR p < 0.05; fold change ≥ ±2) by a 2-way ANOVA test comparing populations by group and their sex assigned at birth. Subsequently, we added two contrast interaction terms comparing populations: cis men vs. trans people with male assigned birth sex and cis women vs. trans people with female assigned birth sex. Finally, to interpret the list of significant genes, an enrichment analysis was performed with the Partek® Pathway program and the WebGestalt.

first: Karla

last: Ramirez

last: Fernández

first: Sarah

last: Collet

first: Meltem

last: Kiyar

first: Enrique

last: Delgado-Zayas

first: Esther

last: Gómez-Gil

first: Guy

last: T'Sjoen

first: Antonio

last: Guillamon

first: Sven

middle: C

last: Mueller

first: Eduardo

last: Pásaro


title: Morphological and genomic shifts in mole-rat queens increase fecundity but reduce skeletal integrity

city: Durham

first: Rachel

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

summary: We sequenced polyA-selected RNA from bone marrow derived cells from 47 bone samples collected from 16 captive, adult female Damaraland mole-rats (Fukomys damarensis). The 16 females were experimentally manipulated to either remain as nonbreeders (either as helpers or solitaires) or become breeders, and breeding status was maintained for over 1 year prior to tissue collection and cell culture. A subset of cultured cells were treated for 24 hours with 10 nM estradiol prior to sample collection.

overall_design: mRNA profiles (n = 47 total samples) of bone marrow derived cells from lumbar vertebrae and long bones of female breeding and female non-breeding Damaraland mole-rats (Fukomys damarensis).

first: Jenny

last: Tung


title: Aging-Induced Alterations in Gene Transcripts and Functional Activity of Mitochondrial Oxidative Phosphorylation Complexes in the Heart

city: Milwaukee

first: Arshad

last: Jahangir

state: WI

address: 2801 Kinnic Kinnic River Parkway, Suite 777

department: Cardiology

institute: Advocate Aurora Health

summary:
Aging is associated with progressive decline in energetic reserves compromising cardiac performance and tolerance to injury. Although deviations in mitochondrial functions have been documented in senescent heart, the molecular bases for the decline in energy metabolism are only partially understood.
High-throughput transcription profiles of genes coding for mitochondrial proteins in ventricles from adult and aged rats were compared using microarray analysis.

overall_design: The expression profile of genes encoding proteins for mitochondrial substrate metabolism and OxPhos, including subunits of the electron transport chain (ETC) complexes and mitochondrial F0F1 ATP synthase were characterized in ventricles from adult (6 month old) and aged (24 month old) rats using high throughput microarray (Rat Genome 230 2.0 arrays) and verified by RT-PCR.

first: Claudia

last: Preston


title: Acute detachment of hexokinase II from mitochondria modestly increases oxygen consumption of the intact mouse heart

city: New York

first: Sander

last: Houten

state: NY

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Cardiac hexokinase II (HKII) can translocate between cytosol and mitochondria and change its cellular expression with pathologies such as ischemia–reperfusion, diabetes and heart failure. The cardiac metabolic consequences of these changes are unknown. Here we measured energy substrate utilization in cytosol and mitochondria using stabile isotopes and oxygen consumption of the intact perfused heart for 1) an acute decrease in mitochondrial HKII (mtHKII), and 2) a chronic decrease in total cellular HKII.

overall_design: 12 samples from heart (6HKII+/+ and 6HKII+/-) were analyzed

first: Carmen

last: Argmann


title: Signatures of B cell receptor repertoire following Pneumocystis infection

city: Beijing

first: Zhaohui

last: Tong

state: Beijing

address: NO. 8, Gong Ti South Road

department: Department of Respiratory and Critical Care Medicine

institute: Beijing Chaoyang Hospital

summary: B cells play vital roles in host defense against Pneumocystis infection, however, the features of B cell receptor (BCR) repertoire in the disease progression remain unclear. Here we integrated single-cell RNA sequencing and single-cell BCR sequencing of immune cells from mice lung at uninfected state and 1-4 weeks postinfection, in order to illustrate the dynamic nature of B cell responses during Pneumocystis infection. We identified continuously increased plasma cells and an elevated ratio of (IgA+ IgG) to (IgD+ IgM) after infection. Moreover, Pneumocystis infection was associated with an increase of a naïve B subset characterized by elevated expression of the transcription factor ATF3. The proportion of clonal expanded cells progressively increased, with the BCR diversity decreased. Biased usage of V(D)J genes was observed, and the usage frequency of IGHV9-3 was elevated. Overall, these results present a detailed atlas of B cell transcriptional changes and BCR repertoire features in the context of Pneumocystis infection.

overall_design: Single-cell BCR profiles of wild type (WT) and mices  infected with Pneumocystis 1-4 weeks.

first: Zhao-Hui

first: Kan

last: Zhai

first: Han

last: Sun

first: Hu-Qin

last: Yang


title: A Whole Transcriptome Profiling of Uterine Leiomyoma Cells under the influence of Phenolic Environmental Estrogen

city: haikou

first: Feng

middle: Tao

last: Zhang

state: hainan

address: 58 Renmin Avenue, Meilan District

department: School of  Life and  Pharmaceutical Sciences

institute: Hainan University

summary:
Purpose:The study aimed to recognize potential molecular targets and signal pathways whereby phenolic environmental estrogen promotes the proliferation of uterine leiomyoma cells
Methods:Primary cultured cell lines were  treated with 0.1% DMSO, 10.0 μmol/L BPA, and 32.0 μmol/L NP for 48 h before RNA-seq was performed. Differentially expressed genes affected by BPA and NP were selected. Then, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and Protein-protein Interaction (PPI) analysis were performed. Quantitative real-time polymerase chain reaction (q-PCR) was used to verify the differentially expressed genes
Results:In comparison with the control group, 739 differentially expressed mRNAs were identified in the BPA intervention group and the NP intervention group. GO enrichment analysis results show that the most enriched GO terms were connective tissue development and G1/S transition of mitotic cell cycle, and extracellular matrix. The results of KEGG enrichment analysis showed that differentially expressed mRNA was enriched mainly in three primary pathways, including environmental information processing, human diseases, and cellular processes. The cell cycle, PI3K-Akt signaling pathway, pathways in cancer, and TGF-beta signaling pathway are significantly enriched.
Conclusions:Phenolic environmental estrogens may promote the proliferation and cell cycle progression of uterine leiomyoma cells through rapid non-genomic ER signaling, which leads to disordered cell cycle regulation and accelerates the transition of the cell cycle from G0/G1 phase to S phase. In addition, as an external harmful stimulant, phenolic estrogen promotes the upregulation of inflammatory factors in uterine leiomyomas.

overall_design: Examination the mRNA profile of uterine leiomyoma cell lines treated with 0.1% DMSO , 10.0 μmol/L BPA, and 32.0 μmol/L NP for 48 h under the influence of Phenolic Environmental Estrogen.the cells treated with the 32.0 μmol/L NP are the control group.

first: Zemin

last: Li

last: Yin

first: Yang

last: Shen


title: CDK19 regulates the proliferation of hematopoietic stem cells by suppressing p53-mediated transcription of p21

city: Chong Qing

first: zi hao

last: zhang

state: China/Chong Qing

address: Gaotanyan Street 30

department: College of Preventive Medicine

institute: Third Military Medical University

summary:
Aa an important component of mediator complex, CDK19 involved in various biological transcription processes .Interestingly, our results demonstrated that CDK19 participate in cell cycle regulation of HSCs.
We used microarrays to expolre differential gene expression between WT and CDK19-/- HSCs.

overall_design: Detection of CDK19-/- mouse hematopoietic phenotype by flow cytometry first,further verificate molecular mechanism by IP and CHIP-qPCR after analyze the bioinformatic results.

first: Zihao

first: Mengjia

last: Hu

first: Yukai

last: Lu

first: Yan

last: Qi


title: m6A modification in SARS-CoV-2 virus regulates host cell innate immune response

city: La Jolla

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

type: Methylation profiling by high throughput sequencing

summary: It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlying molecular mechanism. RNA modification landscape of SARS-CoV-2 and its functional relevance to host cell innate immune response remain unknown. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigated m6A modification of SARS-CoV-2 gene in regulating host cell innate immune response. Our data showed that SARS-CoV-2 virus has m6A modification enriched in 3' region of the viral genome. We also found that host cell m6A methyltransferase METTL3 depletion reduced viral load in infected cells, decreased m6A levels in SARS-CoV-2 and host genes, and m6A reduction in viral RNA increased RIG-1 binding and subsequently enhanced downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in severe COVID-19 patients. These findings will aid to understand the COVID-19 pathogenesis and help in designing future studies of regulating innate immunity for COVID-19 treatment.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: For RNA-Seq, total RNAs were extracted from SARS-CoV-2-infected shControl and shMETTL3 Caco-2 cells. Sequencing was performed by Illumina NovaSeq 6000 at the IGM Genomics Center, UCSD. For MeRIP-Seq, supernatant or cellular RNAs were purified from viral infected-Vero or Caco-2 cells. The RNAs were treated with DNaseI, concentrated and quantified. Purified RNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies) and the fragmented RNA purified by ethanol precipitation. An input sample (10% of total fragmented RNA) was reserved. Fragmented RNA was incubated with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C. The mixture was then incubated with 50 μl protein A/G magnetic beads (Thermo Fisher) for 2 h at 4°C, and the beads were collected and washed twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound RNA was eluted from the beads with m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4) and extracted with RNA Clean & Concentrator Kits (ZYMO). Input and m6A-containing viral RNA were dissolved in water and either reverse transcribed by iScript cDNA synthesis kit (Bio-Rad) and analyzed by qPCR or processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by Illumina NovaSeq 6000 at the IGM Genomics core, UCSD.

first: Hui

last: Hui

first: Tariq

last: Rana


title: Next Generation Sequencing Facilitates Quantitative Analysis of CHAA Transcriptomes

city: Dalian

first: Shuaijun

last: Zan

address: NO.2 of Linggong road

institute: Dalian university and technology

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived strain JSTW transcriptome profiling (RNA-seq) and to evaluate protocols for optimal high-throughput data analysis

overall_design: mRNA profiles of JSTW strain were generated by deep sequencing, in triplicate.

first: Zelong


title: Next Generation Sequencing (RNA-Seq) of stem cell-treated rats for quantitative analyses of retinal transcriptomes

city: Serdang

first: Pooi Ling

last: Mok

state: Selangor

address: Universiti Putra Malaysia

department: Department of Biomedical Sciences

country: Malaysia

institute: Universiti Putra Malaysia

summary:
Mesenchymal stem cell (MSC) heterogeneity can lead to variable treatment outcomes. Genetically modifying MSCs to express erythropoietin could confer additional therapeutic benefits that may enhance standalone MSC treatments. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) between healthy, retinal degenerated, and stem cell-treated rat retinal degeneration models for high-throughput data analysis. MSC, Wharton's jelly Mesecnhymal stem cells; MSCEPO, EPO-expressing MSC; DPSC, dental pulp MSC stem cells
Methods: Retinal mRNA profiles of 31-day-old healthy, sodium iodate-administered (retinotoxic inducer), DPSC-treated, MSC-treated, and MSCEPO-treated Sprague Dawley rats were generated by deep sequencing, in triplicate, using Illumina Nextseq 500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Salmon, and then converted to the gene level count matrices for quantification with DESeq2. The quant assay kit was used for qPCR amplification.
Results: Using the Salmon-DESeq2 pipeline, we mapped about 25-35 million sequence reads per sample to the rat genome (build Rnor 6.0) and identified 20,376 transcripts in the retinas of the control and experimental groups. Approximately 500-1000 genes were found to be differentially expressed using the arbitrary cutoff of Padj<.05 and fold change>±2.0. Hierarchical clustering of differentially expressed genes revealed profiles involved in cellular regeneration,cell death, and phototransduction, which indicated the therapeutic effectiveness of the stem cells on retinal survival. Gene set enrichment analysis and pathway topology analysis showed enrichment in the aforementioned processes, Padj<.05.
Conclusions: Our study represents the first detailed analysis of MSCEPO-treated retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for further investigations in MSC enhancement methods. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within the retina. We conclude that RNA-seq based retinal transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions, especially in regards to MSC-mediated tissue repair and phototransduction.

first: Pooi

middle: L

first: Kumar

middle: S

last: Suresh

first: Avin

middle: E

last: Koh


title: Responses to crowding stress in Atlantic salmon reared in different aquaculture systems

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Recirculation systems (RAS), which reduce water consumption and improve pathogen control are increasingly used in Atlantic salmon aquaculture. Performance and adaptation of fish to new farming environment is actively investigated. Here, responses to crowding stress were compared in salmon reared in two systems (RAS with brackish water and flowthrough with full salinity water) at low and high density.

overall_design: Salmon reared in RAS and flowthrough systems at low and high  densities (20-40 kg/m3 and (80-115 kg/m3) was exposed to crowding stress (300 kg/m3 for 30 min). Skin was sampled before (control) and 24 h after challenge.

first: Jelena

last: Kolarevic

first: Elisabeth

last: Ytteborg


title: Loss of function of MALAT1 on primary human OA osteoblast transcriptome

city: Birmingham

first: Archana

last: Sharma-Oates

address: Haworth Building

department: Centre for Computational Biology

institute: University of Birmingham

summary: Cells: Primary human osteoblasts from subchondral bone of osteoarthritis patients (n=3 patients). Treatments: Cells transfected using Lipofectamine 3000 (Qiagen) with either control LNA (NC) or MALAT1 LNA1 or MALAT1 LNA2 for 24 hours. Total RNA extracted by Qiagen RNeasy columns. RIN values >7 via Agilent Bioanalyser. Analysis: RNA subjected to Quantseq 3' RNA sequencing (Lexogen) and sequenced reads mapped to the hg38 reference human genome.

overall_design: 9 samples analysed in total. Primary OA subchondral bone osteoblasts from n=3 patients transfected for 24h with either (i) LNA control, (ii) MALAT1 LNA1 or (iii) MALAT1 LNA2.

first: Simon

middle: W

last: Jones

first: Fawzeyah

last: Alnajjar


title: Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia (RNA-Seq)

city: Heidelberg

first: Stefan

last: Gröschel

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ German Cancer Research Center

summary: Chromosomal aberrations in acute myeloid leukemia (AML), such as inv(3) and t(3;3), lead to deregulation of the EVI1 oncogene by the GATA2 distal hematopoietic enhancer (G2DHE). In this project, we aimed to study the transcription factor complexes involved in the regulation of the G2DHE sequence. We have identified PARPi as a member of the G2DHE complex. Here, we used RNA-Seq to analyze transcriptomic changes after PARP inhibition with olaparib and talazoparib and to compare those to EVI1 knockdown.

overall_design: RNA-Seq in MUTZ-3 cells with PARP inhibition or EVI1 knockdown.

first: Carl

last: Herrmann

first: Sandra

last: Kiehlmeier


title: RNAseq data from ES and differentiated cells in Chd8 WT vs Chd8 KD and Chd8 KO cells

city: London

first: Andrea

last: Cerase

address: Newark st

institute: QMUL

summary: In this study, we compare the transcriptomic difference between WT and Chd8 depleted ES aand differentiating ES cells. We report significant differences between Chd8 WT and KD/KO cell lines.

overall_design: We used 2-3 matched WT and KO, we only used female ES lines.

first: Alex

last: Young

first: Sarah

last: Marzi


title: CRISPR genome editing of human dendritic cells (treatments of unedited dendritic cells)

city: Boston

first: Marco

last: Jost

state: MA

address: 77 Ave Louis Pasteur, NRB848

institute: Harvard Medical School

summary: Dendritic cells (DCs) are central regulators of both innate and adaptive immunity and play roles in processes ranging from antitumor immunity to host-microbiome communication at mucosal surfaces. It remains difficult, however, to genetically manipulate human DCs, limiting our ability to probe how DCs elicit specific immune responses and to deploy DCs for immunotherapy. Here, we develop a CRISPR/Cas9 genome editing method for human monocyte-derived DCs (moDCs) with a median knockout efficiency of >93% across >300 genes. Using this method, we perform arrayed genetic screens in moDCs, identifying mechanisms by which human immune cells tune responses to lipopolysaccharides (LPSs) from the human microbiome. In addition, we reveal donor-specific responses to LPSs, underscoring the importance of assessing immune phenotypes in donor-derived cells, and identify genes that control this specificity, highlighting the potential of our method to pick apart genetic determinants of inter-individual variation in immune responses.

overall_design: Treatment of 7-day old human monocyte-derived dendritic cells with different innate immune stimuli or PBS (negative control) for 2 hours. 3 replicate treatments for each stimulus.

first: Amy

middle: N

last: Jacobson

first: Michael

last: Fischbach

first: Jonathan

last: Weissman


title: Unsupervised analysis of flow cytometry data in a clinical setting captures cell diversity and allows population discovery

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

summary: In our study, MegaClust - an unsupervised, data-driven algorithm - barely described mDCs and pDC subsets were identified. To confirm these findings we performed RNA sequencing Facs sorted of mDCs (CD123-CD11c+CD4+HLA-DR+), pDCs (CD123+CD11c-CD4+HLA-DR+) and monocytes (CD14+) from healthy donors and compared these with publicly available data.

overall_design: mDC, pDC and CD14 from 3 donors.

first: Petra

last: Baumgaertner

first: Nicolas

last: Guex

first: Alexandre

last: Harari


title: Non-canonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

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

sample_organism: Campylobacter jejuni subsp. jejuni CG8421

overall_design: Refer to individual Series


title: Non-canonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9 [RIP-seq]

summary: RIP-seq analysis to identify CjCas9 bound RNAs using co-immunoprecipitation and sequencing in CG84-21.

platform_organism: Campylobacter jejuni subsp. jejuni CG8421

overall_design: Cas9 was chromosomally tagged using 3xFLAG epitope at the C-terminus in Campylobacter jejuni CG84-21 wild-type cells and immunoprecipitated using anti-FLAG antibody,  untagged version of the wild-type CG84-21 strain was used as a control.  Lysates for immunoprecipitation for both untagged and Cas9-3xFLAG samples were prepared from  60 O.D. of bacteria grown to mid-log phase ( OD600 ≈ 0.6) . RNA was eluted from both untagged and Cas9-3xFLAG  samples to use for cDNA library preparation and sequencing.

first: Chunlei

last: Jiao

first: Sahil

last: Sharma

first: Gaurav

last: Dugar

first: Natalia

last: Peeck

first: Thorsten

last: Bischler

first: Franziska

last: Wimmer

first: Cynthia

first: Chase

last: Beisel


title: Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia (4C-Seq)

first: Stefan

last: Gröschel

summary: Chromosomal aberrations in acute myeloid leukemia (AML), such as inv(3) and t(3;3), lead to deregulation of the EVI1 oncogene by the GATA2 distal hematopoietic enhancer (G2DHE). In this project, we aimed to study the transcription factor complexes involved in the regulation of the G2DHE sequence. We identified PARP1 as an interactor of G2DHE-associated transcription factors. In this dataset, we studied the interaction of genomic loci between the EVI1 promoter and G2DHE by 4C-Seq in the 3q-rearranged AML cell line MUTZ-3 treated with the PARP1 inhibitors olaparib, talazoparib or the DMSO vehicle control for 24 h.

overall_design: MUTZ-3 cells were treated with PARP1 inhibitors and the genomic interactors of the EVI1 promoter locus were captured by 4C-Seq.

first: Sandra

last: Kiehlmeier

first: Mahmoud-Reza

last: Rafiee

first: Jagoda

last: Mika

first: Sabrina

last: Kruse

first: Judith

last: Müller

last: Schweiggert

first: Carl

last: Herrmann

first: Gianluca

last: Sigismondo

first: Jeroen

last: Krijgsveld


title: Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia


title: Analysis of genome occupancy of Chd8 and H3K4me3 peaks in embryonic stem cells and differentiaing ESCs and associated ATAC-seq profiles in the presence and absence of Chd8

first: Andrea

last: Cerase

summary: In this work, we show a role for Chd8 in the regulation of Xist RNA, the master regulator of X chromosome inactivation (XCI)

overall_design: ES cells and differentiang ES cells (3 day differentiated cella, Neuronal Progenitor cells (NPCs))

first: Andreas

last: Buness


title: System-wide analysis of Dhx36 function in skeletal muscle satellite cells reveals its binding with 5’UTR G4 structure to promote Gnai2 RNA translation

city: HONG KONG

first: Jie

last: Yuan

state: HONG KONG

address: Prince of Wales Hospital

department: Orthopaedics and Traumatology

institute: The Chinese University of Hong Kong

summary:
In this study, we deciphered the functions of Dhx36 and related molecular mechanisms in muscle stem cells and muscle regeneration. We found Dhx36 was highly induced in activated muscle stem cells during regeneration induced by injury. Conditional inactivation of Dhx36 in mouse muscle stem cells caused significant impaired regeneration, which was due to the dramatically decreased cell proliferation. Dhx36 was a well-known RNA helicase for binding/unwinding DNA/RNA G-quadruplexes and it was dominantly expressed in cytoplasm of proliferating myoblast. CLIP-seq was conducted to identify the mRNAs interacting with Dhx36 in myoblast cells. To examine whether Dhx36 regulates translation process, we also conducted polysome profiling followed by RNA-seq in WT and Dhx36 KO myoblast cells.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
2 Dhx36 CLIP-seq, 6 polysome profiling experiments performed.

Refer to individual Series

first: Huating

last: Wang

first: Hao

last: Sun

first: Xiaona

last: Chen


title: System-wide analysis of Dhx36 function in skeletal muscle satellite cells reveals its binding with 5’UTR G4 structure to promote Gnai2 RNA translation [Polysome profiling]

summary: In this study, we deciphered the functions of Dhx36 and related molecular mechanisms in muscle stem cells and muscle regeneration. We found Dhx36 was highly induced in activated muscle stem cells during regeneration induced by injury. Conditional inactivation of Dhx36 in mouse muscle stem cells caused significant impaired regeneration, which was due to the dramatically decreased cell proliferation. Dhx36 was a well-known RNA helicase for binding/unwinding DNA/RNA G-quadruplexes and it was dominantly expressed in cytoplasm of proliferating myoblast. To examine whether Dhx36 regulates translation process, we conducted polysome profiling followed by RNA-seq in WT and Dhx36 KO myoblast cells.

overall_design: 6 polysome profiling experiments performed.


title: System-wide analysis of Dhx36 function in skeletal muscle satellite cells reveals its binding with 5’UTR G4 structure to promote Gnai2 RNA translation [CLIP-seq]

summary: In this study, we deciphered the functions of Dhx36 and related molecular mechanisms in muscle stem cells and muscle regeneration. We found Dhx36 was highly induced in activated muscle stem cells during regeneration induced by injury. Conditional inactivation of Dhx36 in mouse muscle stem cells caused significant impaired regeneration, which was due to the dramatically decreased cell proliferation. Dhx36 was a well-known RNA helicase for binding/unbinding DNA/RNA G-quadruplexes and it was dominantly expressed in cytoplasm of proliferating myoblast. Therefore CLIP-seq was conducted to identify the mRNAs interacting with Dhx36 in myoblast cells.

overall_design: 2 Dhx36 CLIP-seq experiments performed.


title: CRISPR genome editing of human dendritic cells (treatments of knockout dendritic cells)

first: Marco

last: Jost

overall_design: Treatment of human monocyte-derived dendritic cells with knockouts of TLR4, LY96, CD14, or RPE65 (neutral gene control) with LPS from E. coli or B. theta or PBS (negative control) for 2 hours. 2 replicate treatments for each stimulus.

first: Amy

last: Jacobson

first: Michael

last: Fischbach

first: Jonathan

last: Weissman


title: Non-canonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9 [dRNA-seq]

first: Tom

last: Gräfenhan

summary: Differential RNA sequencing using terminator exonuclease (TEX) to identify processed versus unprocessed transcripts in Campylobacter jejuni strain CG84-21

overall_design: Total RNA was purified from Campylobacter jejuni CG84-21 cells harvested at mid-log (OD600 ≈ 0.6) and used for TEX treatment.

first: Chunlei

last: Jiao

first: Sahil

last: Sharma

first: Gaurav

last: Dugar

first: Natalia

last: Peeck

first: Thorsten

last: Bischler

first: Franziska

last: Wimmer

first: Cynthia

first: Chase

last: Beisel


title: Tumor microenvironment impairs Th1 cell differentiation through alternative splicing modifications

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL


title: Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

status: Public on Apr 26 2021

city: Wooloongabba

first: Seth

last: Cheetham

state: QLD

address: Level 4, 37 Kent St

country: Australia

institute: Mater Research Institute-University of Queensland

summary: Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. When transcribed, pseudogenes may encode proteins or enact RNA-intrinsic regulatory mechanisms. However, the extent, characteristics and functional relevance of the human pseudogene transcriptome are unclear. Short-read sequencing platforms have limited power to resolve and accurately quantify pseudogene transcripts owing to the high sequence similarity of pseudogenes and their parent genes. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes. Pseudogene transcripts are expressed in tissue-specific patterns, exhibit complex splicing patterns and contribute to the coding sequences of known genes. We survey pseudogene transcripts encoding intact open reading frames (ORFs), representing potential unannotated protein-coding genes, and demonstrate their efficient translation in cultured cells. To assess the impact of noncoding pseudogenes on the cellular transcriptome, we delete the nucleus-enriched pseudogene PDCL3P4 transcript from HAP1 cells and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the transcriptional landscape underpinning human biology and disease.

overall_design: Identification of full-length pseudogene transcripts

first: Robin

last: Troskie

first: Yohaann

last: Jafrani

first: Tim

middle: R

last: Mercer

first: Adam

middle: D

last: Ewing

first: Geoffrey

last: Faulkner


title: Sensitivity of transcription factor mutants of Aspergillus fumigatus to  Congo Red

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Inhibition of fungal growth by Congo Red (CR) has been known for a long time and claimed to be associated to a specific binding to fibrillar chains of β-1,3-glucans which blocks cell wall polysaccharide synthesis. It has also been suggested that the effect of CR could be pleiotropic, especially because of its oxido-reductive properties. One way to elucidate the mechanism of action of CR is to identify transcription factors (TF) which regulate the response to CR and interrogate their regulon. The analysis of TF mutants with differential sensitivity to CR would be also a way to identify new regulatory pathways involved in cell wall biosynthesis. During the investigation of the sensitivity to CR of a TF mutant library, several mutants either sensitive or resistant to CR were analysed . The morphology of the conidial germination was affected differently by CR in the parental strain and TF mutants. Abnormal distorted swollen conidia called Quasimodo cells were seen in presence of the CR. The size of the Quasimodo cells in the resistant mutants are bigger and adsorb more CR than the germinating conidia of the sensitive or parental strain. This is associated to a difference in permeability of the mutants. The clearing of the drug from the medium by the resistant strain was mainly responsible for the survival and later growth of some of resting conidia of these mutants which did not adsorb intracellularly the drug whereas in the sensitive mutants all conidia adsorbed the drug and were consequently killed. Although there are some modifications of the composition of the cell wall, a transcriptomic analysis of the mutant showed that CR affected many different pathways, including iron and calcium metabolism. Accordingly, the susceptibility to other cell wall drugs of the sensitive and the resistant TF mutants varied with the mutants and not always in connexion with their sensitivity to CR. Interestingly, a new paradoxical effect of the CR was discovered in the resistant mutant since the growth of one of them could be stimulated after recovering from the CR stress.

overall_design: Examination of mRNA patterns of 4 transcription factor mutants of Aspergillus fumigatus and its parental strains in presence of 2 concentrations of Congo Red

first: Shriya

last: Raj

first: Odile

last: Sismeiro

first: Hugo

last: Varet

first: Mike

last: Bromley

first: Jean-Paul

last: Latgé


title: Overexpression of a histone-like nucleoid structuring protein in Burkholderia multivorans affects several traits dependent on the cell envelope

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

summary: Burkholderia cepacia complex bacteria comprise opportunistic pathogens causing chronic respiratory infections in cystic fibrosis (CF) patients. These microorganisms produce exopolysaccharides which are considered virulence determinants. Here, we report the isolation of an evolved nonmucoid variant (17616nmv) after the ancestor, Burkholderia multivorans ATCC 17616, was subjected to prolonged stationary phase. Lack of exopolysaccharide cepacian biosynthesis in the variant was correlated with downregulation of bce genes expression. Furthermore, genome sequence of the variant identified the transposition of a mobile element of the IS406 family into the promoter region of an hns-like gene (Bmul_0158) encoding a histone-like nucleoid structuring protein, a known global transcriptional repressor. This IS element upregulated the expression of Bmul_0158 gene. Transcriptome analysis identified the global effects of this mutation on gene expression, with major changes in motility, pili synthesis, type VI secretion, and chromosome associated functions. Concomitant with these differences, the nonmucoid variant displays reduced adherence to a CF lung bronchial cell line, reduced surface hydrophobicity, forms smaller cellular aggregates, but has an increase in swimming and swarming motilities. Finally, bioinformatic analysis led to the identification of various genomic regions, possibly acquired by horizontal gene transfer, which were transcriptionally repressed by the increased expression of hns gene in the nonmucoid variant. Taken together, our results revealed a significant role for this H-NS protein in the regulation of B. multivorans persistence- and virulence-associated genes.

platform_organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616

overall_design: For expression profiling, overnight cultures of the Burkholderia multivorans ATCC 17616 and its nonmucoid variant 17616nmv were grown in SM medium and diluted to an initial OD640 nm of 0.1 into  the same medium. Triplicate samples were cultured at 37ºC with 250 r.p.m. agitation for 10 h and RNA extracted.

first: Inês

last: Silva

first: Jorg

last: Becker


title: Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

summary:
Purpose: Myocardial infarction (MI) promotes a range of systemic effects, many of which are unknown. Here, we investigated the alterations associated with MI progression in heart and other metabolically active tissues (liver, skeletal muscle, and adipose) in a mouse model of MI (induced by ligating the left ascending coronary artery) and sham-operated mice.
Results: By generating tissue-specific biological networks, we observed: (1) dysregulation in multiple biological processes (including immune system, mitochondrial dysfunction, fatty-acid beta-oxidation, and RNA and protein processing) across multiple tissues post MI; and (2) tissue-specific dysregulation in biological processes in liver and heart post MI.
Conclusions: Overall, our integrative analysis highlighted both common and specific biological responses to MI across a range of metabolically active tissues.

overall_design: We performed a genome-wide transcriptomic analysis on tissue samples obtained from 10-week-old male C57B1/6N mice at 6- and 24-hours post MI or sham operation (as control).

first: Martina

last: Klevstig

first: Rui

last: Benfeitas

first: Stephen

last: Doran

first: Hasan

last: Turkez

first: Mathias

last: Uhlén

first: Johannes

last: Wikström

first: Cheng

last: Zhang

first: Malin

last: Levin

first: Adil

last: Mardinoglu

first: Jan

last: Boren


title: DNase-seq from coronary artery (ENCSR999TSD)

status: Public on Apr 22 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

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: Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance

status: Public on Apr 30 2021

city: Beijing

first: Dali

last: Han

state: 北京

address: Da-Tun Road

institute: Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences

summary: Ever-increasing understanding about the complexity of factors and regulatory layers that contribute to immune evasion facilitates the development of immunotherapies. However, the diversity of malignant tumors limits many known mechanisms in specific genetic and epigenetic contexts, manifesting the need to discover general driver genes. Here, we have identified the m6A demethylase FTO as an essential epitranscriptomic regulator utilized by tumors to escape immune surveillance through regulation of glycolytic metabolism. We show that FTO-mediated m6A demethylation in tumor cells elevates transcription factors c-Jun, JunB, and C/EBPβ, which allows the rewiring of glycolytic metabolism. Fto knockdown impairs the glycolytic activity of tumor cells, which restores the function of CD8+ T cells, thereby inhibiting tumor growth. Furthermore, we developed a small-molecule compound Dac51 that can inhibit the activity of FTO, block FTO-mediated immune evasion, and synergize with checkpoint blockade for better tumor control, suggesting reprogramming RNA epitranscriptome as a potential strategy for immunotherapy.

overall_design: B16-OVA-shNC and shFto cells were used to generate libraries of RNA-seq and ATAC-seq. B16-OVA-shNC, shFto and Dac51 treated shNC cells were used to generate libraries of m6A-seq. OTI CD8+ T cells co-cultured with B16-OVA-shNC or B16-OVA-shFto were sorted to generate libraries for RNA-seq.

first: Meng

last: Xu

first: Cai-Guang

last: Yang


title: ATAC-seq from prostate gland (ENCSR999NKW)

summary:
ATAC-seq on human prostate gland

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: Transcriptome analysis of Th1 cells from spleen, lymph nodes, draining lymph nodes and B16-F10 tumor

first: Romain

last: Boidot

summary:
It is now clearly established that immune system can affect cancer response to therapy.
However, the influence of tumor microenvironment on immune cells is not completely understood.
In this respect, alternative splicing is increasingly described to affect immune system biology.
Here, we showed that tumor microenvironment, by increasing alternative splicing events, induced the expression of an alternative isoform of the IRF1 transcription factor in Th1 cells. Furthermore,
we also shown, in both mice and humans, that IRF1 alternative isoform alters IRF1 full form transcriptional activity on Il12rb1 promotor, resulting in decreased IFN-? secretion in Th1 cells.
Thus, IRF1-short isoform increases in tumor microenvironment and to prevent this isoform appearance could potentiate Th1 cell antitumor effect.

overall_design:
We report that tumor microenvironnement impacts alternative splicing and genes expression
Examination of the expression profile of CD4+ T cells

first: Antoine

last: Bernard


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR536VAY)


title: ATAC-seq from HG03045 (ENCSR249FXU)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR135XMY)


title: Transcriptome analysis of CD4+ T cells from spleen and MC38 tumor

overall_design:
We report that tumor microenvironnement impacts alternative splicing and gene expression
Examination of the expression profile and alternative splicing events of CD4+ T cells

first: Corentin

last: Richard


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR252NVI)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR250GDW)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR987GUS)


title: DNase-seq from cerebellum (ENCSR983KOM)


title: ATAC-seq from liver (ENCSR465PYP)

summary:
ATAC-seq on embryonic e15.5 mouse liver

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: ATAC-seq from neural tube (ENCSR983JWA)

summary:
ATAC-seq on embryonic e15.5 mouse neural tube

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: ATAC-seq from K562 (ENCSR465IDZ)

summary:
ATAC-seq on human cell line K562

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: DNase-seq from sigmoid colon (ENCSR462XTM)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR245AXW)


title: ATAC-seq from K562 (ENCSR243BXK)


title: ATAC-seq from K562 (ENCSR978HFU)


title: ATAC-seq from kidney (ENCSR732OTZ)

summary:
ATAC-seq on embryonic e16.5 mouse kidney

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: ATAC-seq from limb (ENCSR460BUL)

summary:
ATAC-seq on embryonic e14.5 mouse limb

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: ATAC-seq from GM18502 (ENCSR241VGH)


title: ATAC-seq from GM21723 (ENCSR233HSC)


title: ATAC-seq from GM19452 (ENCSR454UTH)


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR732IFV)


title: ATAC-seq from GM19351 (ENCSR231BZU)


title: DNase-seq from testis (ENCSR978QUT)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR731DJH)


title: ATAC-seq from megakaryocyte progenitor cell (ENCSR229QKB)

summary:
PSU mouse CFU-M 50,000 cells ATAC-seq

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: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR452RAX)


title: ATAC-seq from hematopoietic stem cell (ENCSR453AWR)

summary:
PSU mouse HSC 50,000 cells ATAC-seq

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR971MMF)


title: ATAC-seq from right cardiac atrium (ENCSR452OSK)

summary:
ATAC-seq on human right cardiac atrium

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: ATAC-seq from K562 (ENCSR974QYY)


title: Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia (ChIP-Seq)

first: Stefan

last: Gröschel

summary: Chromosomal aberrations in acute myeloid leukemia (AML), such as inv(3) and t(3;3), lead to deregulation of the EVI1 oncogene by the GATA2 distal hematopoietic enhancer (G2DHE). In this project, we aimed to study the transcription factor complexes involved in the regulation of the G2DHE sequence. In silico and in vitro analyses revealed that binding sites for CEBPA are critical for G2DHE function. Here, we used ChIP-Seq to show association of the CEBPA transcription factor with the G2DHE sequence in the 3q-rearranged cell line MOLM-1

overall_design: CEBPA ChIP-Seq in MOLM-1

first: Sandra

last: Kiehlmeier

first: Mahmoud-Reza

last: Rafiee

first: Jagoda

last: Mika

first: Sabrina

last: Kruse

first: Judith

last: Müller

last: Schweiggert

first: Carl

last: Herrmann

first: Gianluca

last: Sigismondo

first: Jeroen

last: Krijgsveld


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR724QTW)

last: DCC


title: DNase-seq from activated CD4-positive, alpha-beta memory T cell (ENCSR720TCN)


title: ATAC-seq from K562 (ENCSR966ZCL)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR998IXQ)


title: DNase-seq from inflammatory macrophage (ENCSR226JLK)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR226LVB)


title: ATAC-seq from GM19463 (ENCSR712ZRY)


title: ATAC-seq from GM19455 (ENCSR706GDQ)


title: DNase-seq from activated T-cell (ENCSR223KKX)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR703AYZ)


title: ATAC-seq from heart (ENCSR451NAE)

summary:
ATAC-seq on postnatal p0 mouse heart

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: ATAC-seq from K562 (ENCSR446UJL)


title: ATAC-seq from intestine (ENCSR966ORC)

summary:
ATAC-seq on embryonic e16.5 mouse intestine

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: DNase-seq from activated T-cell (ENCSR219KTW)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR442SDV)


title: ATAC-seq from GM18517 (ENCSR442OAV)


title: ATAC-seq from neural tube (ENCSR700QBR)

summary:
ATAC-seq on embryonic e14.5 mouse neural tube

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: ATAC-seq from neural tube (ENCSR217NOA)

summary:
ATAC-seq on embryonic e13.5 mouse neural tube

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: ATAC-seq from K562 (ENCSR442DWQ)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR438USP)

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR698VDM)


title: DNase-seq from vagina (ENCSR437AYW)


title: ATAC-seq from GM18499 (ENCSR700HPA)


title: ATAC-seq from K562 (ENCSR217QAB)


title: ATAC-seq from K562 (ENCSR214SFA)


title: ATAC-seq from K562 (ENCSR214QZO)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR696LPC)


title: ATAC-seq from K562 (ENCSR962TDN)


title: ATAC-seq from GM21619 (ENCSR214EIV)


title: ATAC-seq from HG03108 (ENCSR962ITF)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR436JRE)


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR692PKU)


title: ATAC-seq from neural tube (ENCSR690VOH)

summary:
ATAC-seq on embryonic e12.5 mouse neural tube

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: ATAC-seq from intestine (ENCSR961SMM)

summary:
ATAC-seq on embryonic e15.5 mouse intestine

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: DNase-seq from T-helper 9 cell (ENCSR433WOV)


title: DNase-seq from ZHBTc4 (ENCSR434TGY)


title: ATAC-seq from gastrocnemius medialis (ENCSR689SDA)

summary:
ATAC-seq on human gastrocnemius medialis

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: ATAC-seq from midbrain (ENCSR211OCS)

summary:
ATAC-seq on postnatal p0 mouse midbrain

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: ATAC-seq from GM19324 (ENCSR425WQW)


title: ATAC-seq from G1E-ER4 (ENCSR428BSK)

summary:
PSU mouse G1E-ER4+E2 50,000 cells ATAC-seq

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR688OIJ)


title: ATAC-seq from testis (ENCSR210NKB)

summary:
ATAC-seq on human testis

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: ATAC-seq from GM21515 (ENCSR960KGO)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR688DKY)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR424MWH)


title: DNase-seq from embryo (ENCSR687JCD)


title: ATAC-seq from GM21447 (ENCSR424KQH)


title: ATAC-seq from breast epithelium (ENCSR955JSO)

summary:
ATAC-seq on human mammary gland

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: ATAC-seq from GM21717 (ENCSR422RPD)


title: ATAC-seq from HG02981 (ENCSR208HAP)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR210JVF)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR960EVM)


title: DNase-seq from cortex (ENCSR432XZX)


title: 5-hydroxymethylcytosine is Dynamically Regulated During Forebrain Organoid Development and Prematurely Altered in Forebrain Organoids of Alzheimer’s Disease Patients

city: Atlanta

first: Janise

middle: Nichole

last: Kuehner

state: GA

address: 615 Michael St NE

department: Human Genetics

institute: Emory University

summary: 5-hydroxymethylcytosine (5hmC) endures dynamic changes during mammalian brain development and its aberrant regulation is known to be associated with numerous neurological diseases such as Alzheimer’s Disease (AD). Recent evidence suggests that key epigenetic changes could occur during neural development long before the onset of neurodegenerative disorders. However, the dynamics of 5hmC during early human brain development and how that contributes to pathogenesis of neurodegeneration, particularly AD pathologies, remain largely unexplored. To investigate this, we utilized the human iPSC-derived organoid model. We derived the 5hmC and transcriptome profiles across healthy forebrain-organoid developmental time points, as well as a patient derived AD organoid time point, allowing us to study brain development at the cellular and molecular levels. In the present study, we identified stage specific differentially hydroxymethylated regions that demonstrated unique acquisition and depletion of 5hmC modifications across development stages. In addition, genes bearing concomitant increases or decreases in both 5hmC and gene expression were enriched in neurobiological processes or early developmental processes respectively. Our AD organoids corroborate both cellular and epigenetic phenotypes previously observed in human AD brains. Importantly, in AD organoids, we identified significant 5hmC alterations at key neurodevelopmental and AD-risk genes, consequently downregulating genes involved in neurodevelopmental and immune response pathways. Collectively our data indicates that, during human fetal neurodevelopment, the precise temporal regulation of 5hmC could modulate key gene expression patterns ensuring that critical neurodevelopmental milestones are achieved. Further, we also demonstrate that premature epigenetic dysregulation of the 5hmC landscape during neuronal development may predispose AD pathogenesis.

overall_design: Examine the dynamics of 5hmC during early human brain development and how alterations in those dynamics may contribute to Alzheimer's Disease

first: Junyu

last: Chen


title: ATAC-seq from HG02870 (ENCSR420RVW)

first: ENCODE


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR207CQH)


title: ATAC-seq from GM18870 (ENCSR684KUG)


title: ATAC-seq from GM19025 (ENCSR419UYY)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR679EFH)


title: ATAC-seq from limb (ENCSR204ZTY)

summary:
ATAC-seq on embryonic e15.5 mouse limb

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: ATAC-seq from K562 (ENCSR680XOP)

summary:
ATAC-seq on human cell line K562

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR419CKG)


title: DNase-seq from activated T-cell (ENCSR416QNA)


title: ATAC-seq from K562 (ENCSR685YMG)


title: ATAC-seq from K562 (ENCSR199HSR)


title: ATAC-seq from adrenal gland (ENCSR414DVK)

summary:
ATAC-seq on human adrenal gland

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR950YTI)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR205ECC)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR943BCO)


title: ATAC-seq from HG03159 (ENCSR940YDN)


title: ATAC-seq from excitatory neuron (ENCSR187VKR)


title: ATAC-seq from GM21529 (ENCSR954BDA)


title: ATAC-seq from HG02763 (ENCSR404OEO)


title: ATAC-seq from K562 (ENCSR420NIU)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR953UJL)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR457JOG)


title: ATAC-seq from GM21526 (ENCSR408IVU)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR965ZWZ)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR951MYM)


title: ATAC-seq from HG02571 (ENCSR400ISH)


title: DNase-seq from sigmoid colon (ENCSR391YAV)


title: DNase-seq from activated CD4 positive, naive alpha-beta T cell (ENCSR396EWH)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR408GYQ)


title: ATAC-seq from HG02588 (ENCSR189VFC)


title: ATAC-seq from HG03025 (ENCSR673ZMQ)


title: DNase-seq from mesothelial cell of epicardium (ENCSR945KSP)


title: ATAC-seq from forebrain (ENCSR976LWP)

summary:
ATAC-seq on embryonic e15.5 mouse forebrain

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR669NQZ)


title: ATAC-seq from K562 (ENCSR197GOQ)


title: ATAC-seq from transverse colon (ENCSR668VCT)

summary:
ATAC-seq on human transverse colon

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: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR940UEK)


title: ATAC-seq from GM21528 (ENCSR939EVW)


title: ATAC-seq from kidney (ENCSR389CLN)

summary:
ATAC-seq on postnatal p0 mouse kidney

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: DNase-seq from gamma-delta T cell (ENCSR676GAW)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR935HEI)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR388NOI)


title: ATAC-seq from lung (ENCSR668EIA)

summary:
ATAC-seq on embryonic e15.5 mouse lung

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: DNase-seq from tibial nerve (ENCSR401ESD)


title: ATAC-seq from K562 (ENCSR676UFY)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR180KMR)


title: ATAC-seq from SK-N-SH (ENCSR182EZJ)

summary:
ATAC-seq on human cell line SK-N-SH (RA treated)

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: ATAC-seq from K562 (ENCSR935JVI)


title: ATAC-seq from K562 (ENCSR934FTO)


title: ATAC-seq from transverse colon (ENCSR386HAZ)


title: ATAC-seq from K562 (ENCSR390UVH)


title: ATAC-seq from HG02678 (ENCSR180HEL)

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR933VOY)


title: DNase-seq from H9 (ENCSR662RIZ)


title: DNase-seq from MCF 10A (ENCSR385SZQ)


title: DNase-seq from T-helper 1 cell (ENCSR932OSG)


title: ATAC-seq from K562 (ENCSR180IJO)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR177GYC)


title: ATAC-seq from hindbrain (ENCSR662KNY)

summary:
ATAC-seq on embryonic e15.5 mouse hindbrain

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: ATAC-seq from midbrain (ENCSR384JBF)

summary:
ATAC-seq on embryonic e14.5 mouse midbrain

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: ATAC-seq from GM18498 (ENCSR924SDV)


title: DNase-seq from neural tube (ENCSR661GMU)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR173HPQ)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR175OHT)


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR173BJC)


title: DNase-seq from T-helper 1 cell (ENCSR384GGJ)


title: DNase-seq from progenitor cell of endocrine pancreas (ENCSR169KNO)


title: ATAC-seq from midbrain (ENCSR382RUC)

summary:
ATAC-seq on embryonic e11.5 mouse midbrain

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR167VIP)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR933HFM)


title: ATAC-seq from DND-41 (ENCSR660WSB)

summary:
ATAC-seq on human cell line DND-41

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: ATAC-seq from K562 (ENCSR179IAC)


title: ATAC-seq from K562 (ENCSR920YDG)


title: ATAC-seq from hindbrain (ENCSR176BYZ)

summary:
ATAC-seq on embryonic e13.5 mouse hindbrain

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: ATAC-seq from K562 (ENCSR165JXS)


title: ATAC-seq from HG02938 (ENCSR920FQJ)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR920JUM)


title: DNase-seq from activated T-cell (ENCSR660FSU)


title: DNase-seq from stomach (ENCSR163PKT)


title: DNase-seq from intestine (ENCSR655WKX)


title: ATAC-seq from GM18909 (ENCSR917WJS)


title: ATAC-seq from HG03469 (ENCSR163KRG)


title: ATAC-seq from K562 (ENCSR163VQD)


title: ATAC-seq from breast epithelium (ENCSR654UYP)

summary:
ATAC-seq on human breast epithelium

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: ATAC-seq from NCI-H929 (ENCSR382LBS)

summary:
ATAC-seq on human cell line 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: ATAC-seq from common myeloid progenitor (ENCSR914PYX)

summary:
PSU mouse CMP 50,000 cells ATAC-seq

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR171APM)


title: ATAC-seq from thyroid gland (ENCSR914DTI)

summary:
ATAC-seq on human thyroid gland

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: ATAC-seq from GM19328 (ENCSR383RDZ)


title: DNase-seq from activated T-cell (ENCSR653OVF)


title: ATAC-seq from GM19043 (ENCSR409YCK)


title: ATAC-seq from HG02610 (ENCSR905PWV)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR653ISV)


title: ATAC-seq from HG03039 (ENCSR381LJX)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR658NVL)


title: ATAC-seq from HG03439 (ENCSR376YMU)


title: DNase-seq from liver (ENCSR158YXM)


title: DNase-seq from omental fat pad (ENCSR154OUQ)


title: DNase-seq from yolk sac (ENCSR894HWV)


title: ATAC-seq from GM21423 (ENCSR902CFR)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR380TXB)


title: ATAC-seq from midbrain (ENCSR154BXN)

summary:
ATAC-seq on embryonic e12.5 mouse midbrain

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: ATAC-seq from forebrain (ENCSR903GMO)

summary:
ATAC-seq on embryonic e13.5 mouse forebrain

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: ATAC-seq from limb (ENCSR377YDY)

summary:
ATAC-seq on embryonic e11.5 mouse limb

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: ATAC-seq from heart (ENCSR652CNN)

summary:
ATAC-seq on embryonic e12.5 mouse heart

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: ATAC-seq from K562 (ENCSR644KPP)

summary:
ATAC-seq on human cell line K562

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: ATAC-seq from limb (ENCSR896XIN)

summary:
ATAC-seq on embryonic e13.5 mouse limb

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR377CRU)


title: DNase-seq from limb (ENCSR380VCU)


title: DNase-seq from inflammatory macrophage (ENCSR643ZGR)


title: ATAC-seq from GM19395 (ENCSR372IGW)


title: ATAC-seq from body of pancreas (ENCSR152PSA)

summary:
ATAC-seq on human body of pancreas

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: ATAC-seq from frontal cortex (ENCSR889WQX)

summary:
mouse frontal cortex

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: DNase-seq from stomach (ENCSR641ZPF)

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: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR152FWD)


title: ATAC-seq from heart (ENCSR371KFW)

summary:
ATAC-seq on embryonic e16.5 mouse heart

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR152AVY)


title: ATAC-seq from HG02852 (ENCSR368FYV)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR154NOT)


title: ATAC-seq from K562 (ENCSR888JRM)


title: ATAC-seq from embryonic facial prominence (ENCSR150RMQ)

summary:
ATAC-seq on embryonic e11.5 mouse embryonic facial prominence

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR885AWF)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR889YWJ)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR884ODJ)


title: ATAC-seq from GM21825 (ENCSR641KNU)


title: DNase-seq from T-helper 1 cell (ENCSR635QIZ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR635VQU)


title: DNase-seq from astrocyte (ENCSR146KFX)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR883WDW)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR881CRY)


title: ATAC-seq from GM19468 (ENCSR635AIF)


title: ATAC-seq from GM19035 (ENCSR637MUF)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR642BXP)


title: ATAC-seq from intestine (ENCSR150EOO)

summary:
ATAC-seq on embryonic e14.5 mouse intestine

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR147QLU)


title: ATAC-seq from GM19467 (ENCSR635CAC)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR634ZYB)


title: ATAC-seq from embryonic facial prominence (ENCSR876SYO)

summary:
ATAC-seq on embryonic e14.5 mouse embryonic facial prominence

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: ATAC-seq from HG02759 (ENCSR144ZXR)


title: ATAC-seq from K562 (ENCSR874GAJ)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR144NXI)


title: ATAC-seq from K562 (ENCSR366CEQ)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR139PLJ)


title: ATAC-seq from stomach (ENCSR363SKQ)

summary:
ATAC-seq on embryonic e16.5 mouse stomach

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR141RSN)


title: ATAC-seq from hematopoietic stem cell (ENCSR366VBB)


title: ATAC-seq from GM18861 (ENCSR628PLS)


title: ATAC-seq from monocyte (ENCSR862JVD)


title: ATAC-seq from erythroid progenitor cell (ENCSR136XSY)

summary:
PSU mouse CFU-E 50,000 cells ATAC-seq

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: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR363LUK)


title: ATAC-seq from K562 (ENCSR632VDU)


title: ATAC-seq from right lobe of liver (ENCSR373TDL)

summary:
ATAC-seq on human right lobe of liver

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR874DUP)


title: ATAC-seq from HG03095 (ENCSR359HFH)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR860IDO)


title: ATAC-seq from GM19438 (ENCSR134OSR)


title: ATAC-seq from lung (ENCSR627OCR)

summary:
ATAC-seq on embryonic e16.5 mouse lung

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR134CIY)


title: DNase-seq from regulatory T cell (ENCSR133OSO)


title: ATAC-seq from HG03520 (ENCSR624CTU)


title: ATAC-seq from HG02970 (ENCSR857MCZ)


title: ATAC-seq from GM18508 (ENCSR357WQH)


title: ATAC-seq from embryonic facial prominence (ENCSR358MOW)

summary:
ATAC-seq on embryonic e13.5 mouse embryonic facial prominence

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: DNase-seq from cardiac fibroblast (ENCSR856NXV)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR124PXN)


title: ATAC-seq from HG03442 (ENCSR858GTE)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR130HIE)


title: ATAC-seq from HG02943 (ENCSR123WME)


title: ATAC-seq from heart left ventricle (ENCSR117PYB)

summary:
ATAC-seq on human heart left ventricle

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: ATAC-seq from GM21576 (ENCSR122NDR)


title: ATAC-seq from stomach (ENCSR851SBY)

summary:
ATAC-seq on human stomach

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: ATAC-seq from hindbrain (ENCSR623GSD)

summary:
ATAC-seq on embryonic e16.5 mouse hindbrain

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: ATAC-seq from sigmoid colon (ENCSR355SGJ)

summary:
ATAC-seq on human sigmoid colon

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR121BSW)


title: ATAC-seq from K562 (ENCSR121GEL)

summary:
ATAC-seq on human cell line K562

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: ATAC-seq from HG02885 (ENCSR621JYI)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR618HFT)


title: ATAC-seq from HG02840 (ENCSR854ZBA)


title: ATAC-seq from heart left ventricle (ENCSR851EBF)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR111WTE)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR115YPI)


title: ATAC-seq from stomach (ENCSR618HDK)

summary:
ATAC-seq on embryonic e14.5 mouse stomach

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: ATAC-seq from neutrophil (ENCSR351YUI)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR841UCZ)


title: DNase-seq from GM23338 (ENCSR108PUO)


title: DNase-seq from activated T-cell (ENCSR617NTY)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR107XZC)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR840QLA)


title: ATAC-seq from GM21360 (ENCSR105SCQ)


title: ATAC-seq from HG03432 (ENCSR839UOB)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR616AEG)


title: ATAC-seq from HG03139 (ENCSR615YIL)


title: DNase-seq from gamma-delta T cell (ENCSR104QUE)


title: ATAC-seq from HG03460 (ENCSR345NVR)


title: ATAC-seq from lung (ENCSR102NGD)

summary:
ATAC-seq on postnatal p0 mouse lung

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR840USW)

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: ATAC-seq from esophagus muscularis mucosa (ENCSR609GST)

summary:
ATAC-seq on human esophagus muscularis mucosa

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: DNase-seq from CD4-positive naive resting alpha-beta T cell (ENCSR100OSB)


title: ATAC-seq from liver (ENCSR609OHJ)

summary:
ATAC-seq on postnatal p0 mouse liver

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: ATAC-seq from forebrain (ENCSR836PUC)

summary:
ATAC-seq on embryonic e16.5 mouse forebrain

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: ATAC-seq from liver (ENCSR343TXK)

summary:
ATAC-seq on embryonic e13.5 mouse liver

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: ATAC-seq from HG03565 (ENCSR835WBW)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR605SQL)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR607HIL)


title: ATAC-seq from midbrain (ENCSR096JCC)

summary:
ATAC-seq on embryonic e16.5 mouse midbrain

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: ATAC-seq from HG03135 (ENCSR096VEO)


title: ATAC-seq from K562 (ENCSR343TQX)


title: DNase-seq from activated T-cell (ENCSR343MCI)


title: ATAC-seq from HG02884 (ENCSR604YEQ)


title: ATAC-seq from HG03103 (ENCSR833ACP)


title: ATAC-seq from K562 (ENCSR342GFK)


title: ATAC-seq from tibial nerve (ENCSR831KAH)

summary:
ATAC-seq on human tibial nerve

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR604FER)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR336QAO)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR832THJ)


title: ATAC-seq from heart (ENCSR603MWL)

summary:
ATAC-seq on embryonic e15.5 mouse heart

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: ATAC-seq from esophagus squamous epithelium (ENCSR096BPX)

summary:
ATAC-seq on human esophagus squamous epithelium

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: DNase-seq from neural crest cell (ENCSR826URD)


title: ATAC-seq from HG03378 (ENCSR824DUE)


title: ATAC-seq from K562 (ENCSR096HVF)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR335LOQ)


title: ATAC-seq from stomach (ENCSR597BGP)

summary:
ATAC-seq on postnatal p0 mouse stomach

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: ATAC-seq from gastrocnemius medialis (ENCSR823ZCR)

summary:
ATAC-seq on human gastrocnemius medialis

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: ATAC-seq from lung (ENCSR335VJW)

summary:
ATAC-seq on embryonic e14.5 mouse lung

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: ATAC-seq from HG03575 (ENCSR331JFZ)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR335EYA)


title: ATAC-seq from K562 (ENCSR091YVK)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR324OTS)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR323TXQ)


title: ATAC-seq from WTC11 (ENCSR089KIJ)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR323PWV)


title: ATAC-seq from GM19372 (ENCSR335JVB)


title: ATAC-seq from HG02642 (ENCSR821QHC)


title: ATAC-seq from K562 (ENCSR822IYG)


title: ATAC-seq from hindbrain (ENCSR088UYE)

summary:
ATAC-seq on embryonic e12.5 mouse hindbrain

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: ATAC-seq from HG02623 (ENCSR821JHD)


title: DNase-seq from T-helper 1 cell (ENCSR595THL)


title: ATAC-seq from HG03457 (ENCSR322SBN)


title: ATAC-seq from HG03521 (ENCSR594TMY)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR322BYN)


title: DNase-seq from CD4-positive naive resting alpha-beta T cell (ENCSR593OUE)


title: ATAC-seq from heart (ENCSR820ACB)

summary:
ATAC-seq on embryonic e11.5 mouse heart

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR315WAC)


title: DNase-seq from R1 (ENCSR319PWR)


title: ATAC-seq from midbrain (ENCSR819QOJ)

summary:
ATAC-seq on embryonic e13.5 mouse midbrain

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: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR314IBN)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR314IOV)


title: ATAC-seq from sigmoid colon (ENCSR086OGH)

summary:
ATAC-seq on human sigmoid colon

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: ATAC-seq from GM21737 (ENCSR315QWI)


title: ATAC-seq from K562 (ENCSR314EDO)

summary:
ATAC-seq on human cell line K562

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: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR312ZTS)

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: DNase-seq from Right ventricle myocardium inferior (ENCSR085MZL)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR819EPD)


title: ATAC-seq from coronary artery (ENCSR584AXZ)

summary:
ATAC-seq on human coronary artery

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: ATAC-seq from GM18519 (ENCSR312UCH)


title: ATAC-seq from SK-N-SH (ENCSR587TRP)

summary:
ATAC-seq on human cell line SK-N-SH

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: ATAC-seq from GM18505 (ENCSR084FHK)