title: Khellin Modulates DDIT4 to Regulate Autophagy in Triple-Negative Breast Cancer

city: Guangzhou

first: YINING

last: ZHENG

address: No. 280, Waihuan East Road

institute: Guangdong Pharmaceutical University

summary: Objective: To investigate the potential anti-tumor mechanism and clinical impact of Khellin in triple-negative breast cancer (TNBC). Methodology: MDA-MB-231 cells were treated with 20 μM Khellin for 24 hours, and total RNA was extracted for transcriptome sequencing. Differentially expressed genes (DEGs) were screened, followed by functional and pathway enrichment analyses. Survival analysis, gene set enrichment analysis, and tumor immune microenvironment (TIME) analysis were employed to study the role of key genes. Subsequently, DDIT4 expression and changes in autophagy marker proteins were assessed using qRT-PCR and Western blot. Results: A total of 158 DEGs were discovered, with high enrichment in signaling pathways such as PI3K-Akt. DDIT4 was considerably elevated after Khellin treatment, and higher expression was associated with a better prognosis in TNBC patients. Immune infiltration and single-cell transcriptome analysis demonstrated that elevated DDIT4 expression improves anti-tumor immune activity in the tumor microenvironment. Khellin administration increased the LC3B-II/I ratio and decreased P62 protein production, which could be reversed by autophagy inhibitors. Conclusion: Khellin upregulates DDIT4 to activate autophagy in TNBC cells and remodel the tumor immune microenvironment. This study elucidates the critical function of DDIT4 in mediating Khellin-induced autophagy and immune modulation, laying the groundwork for a better understanding of its antitumor effects.

overall_design: RNA-seq of Human breast cancer cells: docetaxel-resistant group and Khellin-exp group


title: Dissecting the mechanism of circZNF827-mediated transcriptional regulation of neuronal differentiation (RNA-Seq)

status: Public on Mar 08 2026

city: Aarhus

first: Ivan

last: Zaporozhchenko

address: Universitetsbyen 83, 1874-356

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

type: Expression profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) originate from backsplicing of numerous genes in animals, but the functions of most circRNAs remain elusive. We previously demonstrated that circZNF827 forms a complex with hnRNPL/K and its host gene-encoded protein ZNF827 that acts in the nucleus to transcriptionally repress the nerve growth factor receptor (NGFR/p75NTR) gene during neuronal differentiation (Hollensen, 2020) [1]. To explore the mechanism of action, and to assess a potential role of the circZNF827-hnRNP complex on additional loci, we scrutinized the genome-wide consequences of circZNF827 and/or hnRNPL knockdown at the transcriptomic and epigenetic level. RNA-sequencing and CUT&RUN confirmed that NGFR and additional loci are transcriptionally repressed by the circZNF827-protein complex, and that these are primarily enriched for H3K27me3 signatures. Only a fraction of the massive transcriptomic changes could be ascribed a direct circZNF827 transcription-regulated phenotype, suggesting that initial key regulatory events elicited by the circZNF827-hnRNP complex likely lead to a secondary response, which further augments neuronal differentiation.

overall_design: RNA-Seq profiling of retinoic acid treated neuroblastoma L-AN-5 cells after circZNF827 and/or hnRNPL knockdown

middle: A

first: Anne

middle: K

last: Hollensen

first: Christian

last: Damgaard


title: Inflammatory arthritis immune related adverse events represent a unique autoimmune disease entity primarily driven by T cells, but likely not autoantibodies

status: Public on Mar 07 2026

city: Rochester

first: Hu

last: Zeng

state: MN

address: 209 Third Ave SW

department: Rheumatology

country: USA

institute: Mayo Clinic

summary: Immune checkpoint inhibitor (ICI)-induced inflammatory arthritis (IA) is an increasingly recognized immune-related adverse event (irAE), yet its underlying immunopathogenesis remains poorly understood. Unlike rheumatoid arthritis (RA), where autoantibodies and B cell dysfunction are central features, the contribution of humoral immunity to IA irAE is unclear. Here, we performed in-depth immunophenotyping of peripheral blood from patients with IA irAE, and compared them with seronegative RA patients, ICI-treated patients without irAE, and healthy controls. IA irAE was marked by a distinct T cell-dominated profile, with CD4+ T cells exhibiting reduced CXCR3 and CCR6 expression, and both CD4+ and CD8+ T cells showing increased cytotoxic molecule expression and metabolic activation. In contrast to seronegative RA, IA irAE patients displayed no significant elevation in autoantibody levels or atypical CD11c+CD21- B cells. IA irAE was further characterized by a proinflammatory cytokine milieu, with elevated levels of IL-6, IL-12, and type I IFN, which correlated with the observed T cell activation phenotypes. Altogether, our findings define IA irAE as an immunologically distinct entity from RA, representing a naturally occurring model of antibody-independent systemic autoimmunity in humans. These results suggest that pathogenic T cell responses, potentiated by specific inflammatory cytokines, may be sufficient to drive arthritis in the absence of humoral autoimmunity, offering new insights into immune tolerance breakdown and therapeutic targeting in irAEs.

overall_design: 4 groups of patients were recruited for this study, IA irAE (irAE) patients are cancer patients on PD-1 or PD-L1 inhibitors (pembrolizumab, nivolumab, cemiplimab, atezolimumab, durvalumab, or avelumab) therapy without pre-existing rheumatic diseases, who develop physician confirmed inflammatory arthritis; ICI-control (ICI) patients are cancer patients on PD-1 or PD-L1 inhibitors therapy without pre-existing rheumatic diseases, who have not developed any irAE; RA-control (RAC) patients are non-cancer patients with rheumatoid arthritis that match those with de novo rheumatic irAE; and heathy control (HC) are the sex- and age-matched healthy individuals.

first: Xingxing

last: Zhu

first: Yue

last: Yu

first: Yanfeng

last: Li

first: Panwen

last: Wang

first: Ying

first: Chantal

last: McCabe

first: Shiju

last: Chen

first: Hannah

last: E. Langenfeld

first: Andrew

last: C Hanson

first: Brenna

last: E. Sharp

first: Amber

last: Woltzen

first: Cynthia

last: S. Crowson

first: Svetomir

last: N. Markovic

first: John

last: M. Davis III

first: Haidong

last: Dong

first: Uma

last: Thanarajasingam


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [scRNA-seq]

status: Public on Mar 09 2026

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

summary: Polycomb Repressive Complex 2 (PRC2) deposits H3K27me3 to recruit canonical PRC1 (cPRC1) that establishes repressive heterochromatin. Higher order cPRC1-mediated chromatin interactions characterize early development and resolve during cell differentiation. Here, we use two opposing models of H3K27me3 dysregulation to elucidate how these long-range loops affect gene expression and cellular phenotypes. Aggressive gliomas driven by histone H3 Lys-27-Met (H3K27M) mutations or EZH-Interacting Protein (EZHIP) expression confine H3K27me3 deposition to PRC2 nucleation sites, while loss of the H3K36 methyltransferase NSD1 in pluripotent stem cells leads to its unrestrained spread from these sites.  In H3K27M mutant tumours, focal H3K27me3 deposition concentrates chromatin occupancy of cPRC1 complexes, which results in long-range chromatin interactions anchored in polycomb bodies, mirroring patterns found in stem cells. Conversely, spread of H3K27me3 due to NSD1 loss dilutes cPRC1 deposition and disrupts polycomb body architecture. In H3K27M cells, H3K27me3 confinement sustains repression of genes tethered to the polycomb bodies, promoting self-renewing progenitor states required for tumour development. Maintenance of progenitor states depends on cPRC1 interaction with H3K27me3, as chemical allosteric modulation of chromodomains alleviates repression of transcription and promotes differentiation. These results suggest that H3K27me3 spread from CGIs modulates cPRC1 gene expression programs to orchestrate developmental transitions through the maintenance or dissolution of repressive 3D loop architecture at polycomb bodies. Imbalances in the spread of H3K27me3 altering chromatin architecture in disease including H3K27M-expressing neoplasms or following NSD1 loss contribute to explain pathogenic states.

overall_design: Hi-C, ChIP-seq, bulk and single-cell RNA-seq on model systems with altered H3K27me3 spread

first: Nada

last: Jabado

first: Chao

last: Lu


title: Epithelial sensing of vitamin A shapes intestinal antimicrobial defense

city: Dallas

first: Gabriella

last: Quinn

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Antimicrobial proteins form an essential chemical barrier that protects the intestinal epithelium from microbial invasion. REG3 family antimicrobial lectins are prominently induced by the microbiota, but how nutritional cues intersect with microbial signals to regulate their expression is poorly understood. Vitamin A plays a central role in mucosal adaptive immunity, but its contribution to epithelial innate immunity is unclear. Here, we show that dietary vitamin A promotes expression of REG3 antimicrobial lectins, including REG3G, in intestinal epithelial cells from both mice and humans. Vitamin A–dependent induction of REG3G expression is driven by retinoic acid and requires signaling through retinoic acid receptors (RARs). Mechanistically, RARs directly bind the Reg3g promoter adjacent to a binding site for STAT3, the transcription factor that transduces microbial signals, thereby integrating nutritional and microbial inputs at the level of REG3G transcription. Extending these findings, we demonstrate that vitamin A–retinoic acid signaling similarly promotes expression of α-defensin antimicrobial proteins. Together, these results define a transcriptional mechanism by which vitamin A enhances epithelial antimicrobial defenses to strengthen mucosal innate immunity.

overall_design: Pregnant C57BL/6 dams were placed on either a vitamin A sufficient (Vit.A+) or vitamin A deficient (Vit.A-) diet at ten days of gestation. Dietary conditions were continued post-weaning and mice were sacrificed at 8 weeks of age. Terminal small intestines were isolated and epithelial cell-enriched single cell suspensions were isolated via EDTA stripping. Live cells were filtered and analyzed with scRNA-seq.


title: DUX4.6 siRNA in vitro activity in FSHD patient-derived myotubes

city: San Diego

first: Barbora

last: Malecova

state: CA

address: 3020 Callan Rd

institute: Avidity Biosciences

summary: Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant muscular disease caused by the aberrant ectopic expression of DUX4 in skeletal muscle. There are no approved therapies for FSHD to date, and strategies aimed at reducing DUX4 expression in skeletal muscle of FSHD patients are promising therapeutic approaches. Here we demonstrate DUX4.6 siRNA activity in reducing DUX4-regulated gene expression in FSHD patient-derived myotubes in vitro.

overall_design:
FSHD (F1-MB02, F2-MB05, and F3-MB06) and control (H-MB07) primary myotubes were treated with DUX4.6 siRNA (B1), and gene expression profiles were evaluated by RNAseq. Treatment with a non-targeting siRNA (S) was used as control.
4 replicates per condition were analyzed.

first: David

last: Sala

first: Garineh

middle: M

last: Melikian

first: Sole

last: Gatto

first: Matthew

last: Onorato


title: Dual mechanisms for the antagonistic crosstalk between H3 glycation and H3K4me3

city: New York

first: Yael

last: David

state: NY

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer cells undergo profound metabolic reprogramming that elevates the intracellular levels of reactive byproducts. These include methylglyoxal (MGO), which can non-enzymatically modify macromolecules in a process known as glycation. Histones are particularly susceptible to glycation, resulting in substantial alterations to chromatin structure and the epigenetic landscape. However, the mechanism by which this impacts specific transcriptional outputs has been difficult to interrogate due to the lack of high-resolution tools. Here, we utilize adduct-, site-, and target-specific antibodies we developed against glycated histone H3 arginine 17 (H3R17MG-H1), one of the most abundant histone glycation marks, to determine its chromatin localization. We show that H3R17MG-H1 preferentially accumulates in euchromatin and directly crosstalks with H3K4me3, a key positive mark of activity at transcription start sites. Mechanistically, H3R17MG-H1 antagonizes global H3K4me3 through dual pathways: by preventing the local recruitment of WDR5-containing methyltransferases and by transcriptionally inducing KDM5 demethylases. The combined effects lead to a genome-wide depletion of H3K4me3 and reprogramming of cellular transcriptional networks. Overall, our findings reveal a distinct role for histone glycation as a potent modulator of the epigenetic landscape and transcriptional outputs, serving as a direct link between altered metabolism and epigenetic state.

overall_design: ChIP-seq profiling (H3K4me3, WDR5, KDM5B) of HEK293T GLO1KO cells (-/+ 0.2 mM MGO, overnight).

first: Yang

last: Xiao

first: Yujin

last: Choi

first: Richard

last: Koche


title: Single-neuron sequencing of PBN-projecting Sp5C neurons in CION or Sham mice

city: SHANGHAI

first: Liting

last: Sun

state: SHANGHAI

address: 131 DONG'AN ROAD, XUHUI DISTRICT

country: China

institute: Fudan University

summary: Parabrachial (PBN)-projecting the caudal part of spinal trigeminal nucleus (Sp5C) neurons are essential for trigeminal neuralgia-induced pain hypersensitivity, but the molecular identities of PBN-projecting Sp5C neurons remain unclear.  We have employed single-neuron sequencing by Smart-seq3  to study  PBN-projecting Sp5C neurons in chronic constriction injury of the infraorbital nerve(CION）model or Sham mice.  This study suggest that the Tac1 gene serve as a specific marker for PBN-projecting Sp5C neurons and demonstrate transcriptional reprogramming induced by CION in PBN-projecting Sp5C Tac1 neurons.

overall_design: RetroAAV2/2-EGFP virus was injected into the right PBN of WT CION/Sham mice to express EGFP in PBN-projecting Sp5C neurons. Manually selected EGFP-labeled neurons and constructed Smart-seq3 library for each neuron and performed the sequencing and data analysis.

first: Jia-Jia

last: Wang

first: Xiang-yu

last: Li

first: Xin-Yi

last: Lin

first: Juan

first: Qiu-Tong

last: Yu

first: Zi-Han

first: Xue-Ping

last: Gao

first: Lei

last: Jin

first: Wei-Ke

first: Tian-Lin

last: Cheng

last: Deng


title: Dual mechanisms for the antagonistic crosstalk between H3 glycation and H3K4me3 [CUT&Tag]

summary: Cancer cells undergo profound metabolic reprogramming that elevates the intracellular levels of reactive byproducts such as methylglyoxal (MGO), which can non-enzymatically modify macromolecules in a process known as glycation. Histones are particularly susceptible to glycation, resulting in substantial alterations to chromatin structure and the epigenetic landscape. However, the mechanism by which histone glycation alters epigenetic landscape and impacts specific transcriptional output in vivo has remained unclear due to the lack of high-resolution tools. Here, we utilize adduct-, site-, and target-specific antibodies we developed against histone H3 glycation at arginine 17 (H3R17MG-H1), one of the most abundant histone glycation marks, to perform precise detection and enrichment of this mark. With these, we show that H3 glycation preferentially accumulates in euchromatin and directly crosstalks with a key active transcription-associated mark, H3K4me3, at transcription start sites. Mechanistically, H3 glycation antagonizes global H3K4me3 through dual pathways: by preventing the recruitment of WDR5-containing methyltransferase complexes to glycated H3 and by transcriptionally inducing KDM5 demethylases expression. The combined effects lead to genome-wide depletion of H3K4me3 and reprogramming of cellular transcriptional networks. Our findings reveal a distinct role for histone glycation as a potent modulator of epigenetic landscape and transcriptional output, serving as a direct link between altered metabolism and cell fate.

overall_design: CUT&Tag profiling (H3R17MG-H1, H3K4me3, H3K9me3, H3K27me3, H3K36me3, IgG) of HEK293T GLO1KO cells (-/+ 0.2 mM MGO, overnight).

first: John

last: Pettingill

first: Tessa

last: Firestone

first: Alli

last: Hickman

first: Lu

first: Michael

last: Keogh


title: CCAAT‐enhancer binding protein delta functions as a tumor suppressor gene in acute myeloid leukemia

city: Charlottesville

first: Subhash

last: Prajapati

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: There is a continued need for identification of novel disease drivers of acute myeloid leukemia (AML) as many patients experience relapse and have poor clinical outcomes. Using genomic analyses of a study dataset of paired diagnosis and relapse specimens (n = 59), we identified recurrent downregulation of CCAAT-enhancer binding protein delta (CEBPD) expression at relapse and inferred CEBPD as one of the key regulators of gene transcription in a subset of relapse patients. Three independent public datasets validated downregulation of CEBPD expression at relapse and predicted it as a candidate tumor suppressor gene in AML. To evaluate CEBPD’s tumor suppressor function, we performed complementary loss- and gain-of-function experiments in human AML cell lines OCI-AML2 and OCI-AML5. Consistent with the prediction, knockdown of CEBPD expression led to activation of MAPK signaling and upregulation of downstream effectors cyclin D1 and TNFα expression with concomitant increase in leukemic growth, while CEBPD overexpression resulted in induction of myeloid differentiation marker CD14 expression in the cell lines. Consistent with prior reports, our integrative genomic analyses and azacytidine treatment experiments further suggest a role for DNA methylation in downregulation of CEBPD expression during AML progression. Collectively, our results provide direct functional evidence for a tumor suppressor function of CEBPD in human cell lines and support prior studies implicating its epigenetic silencing in human AML.

overall_design: RNA-Seq of CRISPR-mediated CEBPD knockdown and control OCI-AML5 samples

first: Francine

last: Garrett-Bakelman


title: BASIC PENTACYSTEINE 1 (BPC1) is involved in the epigenetic suppression of camalexin biosynthesis in Arabidopsis

city: Anseong

first: Eojin

last: Cho

address: Seodong-daero, Daedeok-myeon

department: Plant Science and Technology

country: South Korea

institute: College of Biotechnology, Chung-Ang University

summary: Camalexin is one of indolic phytoalexins protecting plants against biotic challenges like pathogen attack. However, molecular mechanism on how camalexin accumulation is modulated is not fully understood. In our study, we found that a plant specific transcription factor, BASIC PENTACYSTEINE 1 (BPC1) play a negative role in the camalexin biosynthesis. The bpc1-1 mutant has more accumulated amount of camalexin than level of Col-0. In a consistency, expression of genes involved in the camalexin biosynthesis was upregulated in the bpc1-1 mutant in comparison to Col-0. ChIP-qPCR analysis showed that BPC1 directly binds to promoter region of MYB51, CYP79B2, and CYP79B3 via the recognition of GA-rich motif. In addition, we found that BPC1 is required for the PRC2-medidated enrichment of H3K27me3 on many of camalexin biosynthetic genes. Amount of camalexin was significantly increased in knock-out mutants of components of PRC2 complex like CLF, SWN, and EMF1. Overall, our study demonstrated that BPC1 is required for the epigenetic suppression of camalexin biosynthesis by coordinating the PRC2-mediated enrichment of H3K27me3 in Arabidopsis.

overall_design: RNA-seq profiling of wildtpe Col-0 and BPC1 knockout derivaties (BPC1, BPC2) at 2-week.

first: Adji Baskoro Dwi

last: Nugroho

first: Dasom

last: Choi

first: Heewon

last: Moon

first: Dong-Hwan

last: Kim


title: Characterization of the effect of hepatocyte nuclear factor 4 (Hnf4) silencing in enterocytes on gene expression in the developing Drosophila larval midgut

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

country: Germany

institute: University of Cologne

summary: The main objective of this study was to characterize the effects of Hnf4 silencing in enterocytes (ECs) on the Drosophila midgut during larval development. Larval midguts from control animals and animals expressing Hnf4 RNAi in ECs were collected on day three and four after egg laying, corresponding to the late L2 and early L3 stages, respectively. Midguts were then processed for RNA extraction and mRNA sequencing. Our mRNA-seq study reveals significant changes in the transcriptome of control midguts between days three and four of larval development, with increased expression of numerous genes involved in lipid metabolism. Silencing Hnf4 largely suppresses this transcriptional switch, highlighting the role of this nuclear receptor in inducing intestinal lipid metabolism during larval development.

overall_design: Hnf4 silencing in ECs was achieved by expressing a UAS-Hnf4 RNAi transgene using the EC-specific mex-GAL4 driver. To do this, mex-GAL4 females (RRID:BDSC_ 91368) were crossed with UAS-Hnf4 RNAi males (RRID:BDSC_64988), and the resulting offspring (“mex_Hnf4i”) were used in the experiments. The progeny of the cross between mex-GAL4 females and attP40 males (RRID:BDSC_36304) were used as controls (“mex_attp40”). Embryos were collected after an overnight egg-laying period, and transferred in batches of 40 to polystyrene vials containing a yeast-only diet. Larvae were then collected three and four days later for midgut dissection (“D3” and “D4”, respectively). These time points correspond to the late L2 and early L3 stages, respectively. Total RNA was extracted from 30 midguts for the D3 larvae, and 10 midguts for the D4 larvae. mRNA sequencing was performed on four biological replicates per genotype and time point.

first: Clara

last: Lefranc

first: Arnaud

last: Fichant


title: Longitudinal analysis of lipid changes in the sciatic nerve caused by overexpression of PMP22 in models of CMT1A.

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: Charcot-Marie-Tooth type 1A (CMT1A), a prevalent progressive demyelinating peripheral neuropathy is caused by a duplication of the peripheral myelin protein (PMP22) gene. PMP22 is crucial for formation of compact myelin, but the mechanism by which PMP22 overexpression results in CMT1A pathogenesis remains elusive. To investigate these mechanisms, we analyzed the C3 and C22 mouse models, carrying 5 and 10 additional copies of the human PMP22 gene, at five developmental stages (3, 5, 7, 9, and 12 weeks of age). We focused on alterations in lipid synthesis associated with PMP22 overexpression and disease progression, and found a clear gene-dosage effect. In addition, we examined mice on the C3 background with a Schwann cell–specific c-Jun knockout. Our findings suggest potential avenues for dietary interventions, to improve myelination in CMT1A.

overall_design: RNA-seq was performed on whole sciatic nerves from two mouse models of CMT1A, the C22 (10 additional copies of human PMP22) and C3 (5 additional copies of human PMP22) and their respective controls at five time points (3, 5, 7, 9, and 12 weeks). In addition, we also collected th esciatic nerve and conducted RNA-seq on the whole sciatic nervest for C3-PMP22 c-JunP0Cre mice, these have in addition to increased hPMP22 copies also a schwann cell specific knock-out of cs-Jun.

first: Tom

middle: P

last: Hellings

first: Naima

last: Lamzira-Arichi

first: Jeroen

last: Vreijling

first: Davy

last: Cats

middle: B

last: Kuipers

first: Rico

last: J E Derks

first: Marieke

last: Heijink

first: Niek

last: Blomberg

first: Iulia

last: Sidorov

first: Martin

last: Giera

first: Frank

last: Baas

first: Kees

last: Fluiter


title: Transcriptomic study of the Drosophila midgut during larval development

summary: The main goal of this study was to characterize the transcriptome of the Drosophila midgut during larval development. Larval midguts were collected on three different days during development for RNA extraction and mRNA-seq. Our data show that a drastic transcriptomic change occurs in the midgut between the third and fourth day of larval life, corresponding to the entry into the third instar.

overall_design: w1118 embryos were collected after overnight egg laying and transferred in batches of 40 to polystyrene vials containing a yeast-only diet (“day zero”). Larvae were then collected on days two, three and four for midgut dissection. Total RNA was extracted from 60, 30 or 10 midguts for larvae aged two, three or four days, respectively. mRNA sequencing was performed on five biological replicates per time point.

first: Ali

last: Abdallah


title: Connecting HTT intermediate alleles and microRNA dysregulation to enhanced tauopathy in Late-Onset Alzheimer's Disease

city: Oviedo

first: Sergio

middle: Pérez

last: Oliveira

state: Asturias

address: Avenida roma s/n

department: Investigación Clínica-Básica en Neurología

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Late-onset Alzheimer´s disease (LOAD) is a heterogeneous disorder influenced by complex genetic factors. We previously described intermediate alleles (IAs; 27-35 CAG repeats) in the huntingtin (HTT) gene as potential modifiers in around 6% of AD population. The caudate nucleus, the most affected region in Huntington's disease, is highly sensitive to these HTT CAG repeats. We hypothesized that HTT IAs induce gene expression deregulation, including altered microRNA (miRNA) profiles, leading to altered disease progression.
Methods: We investigated the impact of HTT IAs on LOAD progression by genotyping HTT CAG repeats in a cohort of 323 LOAD patients and 335 healthy controls. Comprehensive histopathological and molecular analyses were performed on caudate nucleus samples from a matched subcohort (6 healthy controls, 14 LOAD non-HTT IA carriers, and 13 LOAD HTT IA carriers).
Results: HTT IAs carriers patients exhibited decreased survival after disease onset compared to non-carriers. Histopathologically, while LOAD patients showed increased soluble HTT levels and altered tau pathology compared to controls, these changes were consistently and markedly exacerbated in HTT IA carriers. This phenotype was characterized by heightened diffuse HTT immunoreactivity and an advanced maturation of tau pathology, specifically a pronounced increase in neuronal tau 3R burden and 3R tau-enriched ghost tangles. Interestingly, this pathological state was associated with alterations in key splicing factors, including decreased SRSF6 levels and increased nuclear FUS-SFPQ complex assembly. Analysis of microRNA (miRNA) profiling in the caudate nucleus revealed that the LOAD-associated miRNA dysregulation was significantly amplified in HTT IA carriers, identifying a signature of five miRNAs (miR-100-5p, miR-218-5p, miR-27b-3p, miR-487-3p, and miR-9-3p). In silico modeling and target validation demonstrated that these miRNAs target components of the nuclear spliceosome machinery, such as SRSF family, along with MAPT and HTT genes, suggesting a direct link to the observed tauopathy.
Conclusions: Our findings underscore that HTT IAs as critical modifiers in LOAD progression through an miRNA-mediated dysregulation of splicing and proteostasis. Thus, identifying HTT IAs through routine blood genetic screening offers a practical, non-invasive biomarker for patient stratification, taking a step forward to personalized therapeutic strategies in LOAD.

overall_design: miRNA-seq profiling of  33 human caudate tissue samples divided into three groups: 6 cognitively healthy controls, 14 LOAD patients without HTT intermediate alleles, and 13 LOAD patients with HTT intermediate alleles. The main variable is HTT genotype status within Alzheimer's disease. Control samples serve as a reference. No technical replicates are included.

last: Pérez-Oliveira

first: Juan

last: Castilla-Silgado

first: Paola

last: Pinto-Hernandez

first: Manuel

last: Fernandez-Sanjurjo

first: María Daniela

last: Corte-Torres

first: Olaya

last: Fernandez-Alvarez

first: Eduardo

last: Iglesias-Gutierrez

last: Menéndez-González

first: Cristina

last: Tomas-Zapico

first: Victoria

last: Álvarez


title: CRIPTO regulates EV uptake and fibroblast activation in breast cancer [scRNAseq]

city: Salt Lake City

first: David

last: Freeman

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Inhibition of CRIPTO blocks the serial passage capacity of breast cancer organoids. Here, we sequenced control MDA-MB-468 organoids and organoids expressing a CRIPTO inhibitor, A4Fc, at the time of passaging to determine the effects of CRIPTO blockade of discrete cell populations.

overall_design: MDA-MB-468 control and A4-Fc expressing organoids were isolated from 3D cultures and analyzed by single-cell seq using the chromium 10x protocols

middle: W

first: Brooke

last: Gates

first: Mauri

middle: D

last: Spendlove

first: H

middle: E

last: Gulbahce

first: Ben

middle: T

last: Spike


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [sgLif_CITEseq]

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: Single Cell RNA-seq analysis (5' CITE-seq) of immune Cells from Murine Lkb1 mutant KP Lung Tumors  with deletion of Lif or Lifr (Figure 3 and Figure 4)

overall_design: 11 weeks after tumor initiation, immune cells from the lungs of KP GEMM mice were isolated (sorted live, CD45 positive, extravascular CD45 negative). 10% sorted tumor cells were spiked in (GFP positive CD45 negative). 2 samples per lane individually hashed. N=2 per tumor genetic condition.

first: Ray

last: Pillai

last: Rashidfarrokhi

first: Aristotelis

last: Tsirigos

first: Sergei

last: Koralov

first: Thales

last: Papagiannakopoulos


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [RNA-seq]

summary: Bulk RNA-seq of sorted Lkb1 wildtype (sgNeo) and Lkb1 mutant (sgLkb1) tumor cells

overall_design: 11 weeks after tumor initiation, tumors were sorted (GFP positive CD45 negative) and Bulk RNA-seq was performed.

first: Ali


title: Dual mechanisms for the antagonistic crosstalk between H3 glycation and H3K4me3 [RNA-Seq]

first: Yael

last: David

overall_design: PolyA-RNA-seq profiling of HEK293T GLO1KO cells (-/+ 0.2 mM MGO, overnight).

first: Yang

last: Xiao

first: Yujin

last: Choi

first: Richard

last: Koche


title: Study on isochromosomes: clinical experience from a tertiary referral center

city: Fuzhou

first: Xiaoqing

last: Wu

address: 18 daoshan road, Gulou district

institute: Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University

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

summary: Isochromosomes are structural chromosomal abnormalities associated with diverse clinical phenotypes. This retrospective study analyzed 99 cases of isochromosomes, including 69 postnatal and 30 prenatal cases, to investigate chromosomal distribution, parental inheritance, and risk factors. Karyotyping and cytogenetic analyses identified that isochromosomes predominantly involved the X chromosome (86.7%, 86/99). Among postnatal cases, 99.6% (68/69) exhibited sex chromosomal isochromosomes, with the most common karyotypes being 45,X/46,X,i(X)(q10) (40.5%) and 46,X,i(X)(q10) (39.1%). In prenatal cases, 63.3% (19/30) involved sex chromosomal isochromosomes, while 36.7% (11/30) involved autosomal isochromosomes. Parental chromosomal analysis for 69.0% (20/29) of fetuses showed normal results, suggesting that isochromosomes are predominantly de novo mutations. Advanced maternal age was significantly associated with autosomal isochromosomes (63.6% vs. 31.6% in sex chromosomal cases, p < 0.05). Ultrasound abnormalities were detected in 90.9% of autosomal cases, while non-invasive prenatal testing (NIPT) was the primary detection method for sex chromosomal isochromosomes (47.4%). These findings highlight the significant role of advanced maternal age in autosomal isochromosomes and underscore the importance of ultrasound for autosomal cases and NIPT for sex chromosomal isochromosomes in prenatal screening.

overall_design:
A retrospective analysis was conducted on 99 cases of isochromosomes, including 69 postnatal and 30 prenatal cases. Karyotyping and cytogenetic analyses were performed to identify chromosomal involvement. Parental chromosomal analysis was conducted for available fetal cases.

**Submitters indicated that some CEL files were lost and thus this submission includes 11 CEL files only**

last: Lin


title: Multiple defects in mouse stem cell based embryo models lacking all Hox function [ChIP-Seq]

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

summary: Mammals have four genomic copies of an ancestral Hox cluster, with a total of 39 genes. While gene inactivation approaches and full cluster deletions have revealed their critical functions during early development, the effect of removing all Hox function has remained elusive due to both biological and technological challenges. We have used mouse gastruloids, an ES cells-derived embryo model where Hox genes are properly activated in time and space, to assess the effect of their complete absence. We report that gastruloids lacking Hox function can still elongate and reach a general shape resembling their control counterparts, with a well-established AP polarity. However, unlike controls, they fail to produce any endoderm and are unable to properly segment their presomitic mesoderm into persistent somite-like structures. Instead, they produce a type of mesoderm with a more anterior identity. We thus propose that, in this system at least, HOX proteins are necessary to posteriorize an existing anterior ‘ground-state’ structure, in part by promoting and/or maintaining the epithelialization of cellular condensations. Multiomes analysis revealed range of modifications in chromatin accessibility in the absence of any HOX proteins, involving in particular variations in the binding of the co-factor PBX1. In contrast, neuro-mesodermal progenitor (NMP) cells are not overtly affected in mutant gastruloids, even though they normally initiate strong Hox gene transcription, suggesting that these cells are used as vehicles to translate a temporal sequence of activation into an AP colinear transcript distribution, which becomes functional at a later stage only.

overall_design: PBX1 ChIPmentation data of wt and Hox-/- gastruloids

first: Lucille

last: Lopez-Delisle

first: Alexandre

last: Mayran

first: Yuliia

last: Romaniuk

first: Cynthia

last: Diabanza

first: Anne-Catherine

last: Cossy

first: Denis

last: Duboule


title: DNase-seq from hypothalamus (ENCSR991AEE)

status: Public on Mar 06 2026

city: Stanford

first: ENCODE

last: DCC

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: DNase-seq from substantia nigra (ENCSR995IED)


title: CRIPTO regulates EV uptake and fibroblast activation in breast cancer [Bulk RNAseq]

first: David

last: Freeman

summary: To investigate the role of CRIPTO-laden extracellular vesicles in the regulation of fibroblast cell-state

overall_design: 3T3 murine fibroblasts were either untreated or treated with extracellular vesicles were isolated from MDA-MB-468 control (shCon), CRIPTO knockdown (shCr) and CRIPTO overexpressing (CrOE) for 24 hours. RNA was isolated from the fibroblasts and subjected to bulk RNAseq

first: Brooke

last: Gates

first: Mauri

last: Spendlove

first: H

last: Gulbahce

first: Ben

last: Spike


title: IRE1 drives a homeostatic response to reduced protein influx into the endoplasmic reticulum

city: Redwood City

first: Altos Labs

last: Bioinformatics Hub

address: 2600 Island Dr.

department: Institute of Technology

institute: Altos Labs

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

overall_design: Refer to individual Series

first: Francesca

last: Zappa

first: Advait

last: Subramanian

first: Benjamin

last: Yang

first: Julia

last: Conrad

first: Tsan-Wen

last: Lu

first: Nicolas

last: Debeaubien

first: Rose

last: Yan

first: Renato

last: Minopoli

first: Tristan

last: Croll

first: Stefka

last: Tyanova

first: Mauro

last: Costa-Mattioli

first: Peter

last: Walter

first: Diego

last: Acosta-Alvear


title: DNase-seq from nucleus accumbens (ENCSR990LQJ)

first: ENCODE

last: DCC


title: DNase-seq from amygdala (ENCSR993RWL)


title: Epigenetic Regulation During Flatfish Metamorphosis: Integrative Omics Analysis of DNA Methylation and Gene Expression in Turbot Brain

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

institute: CSIC

type: Methylation profiling by high throughput sequencing

summary: The regulation of gene expression plays a pivotal role in the complex metamorphic process of flatfishes, which oversees the dynamic alterations that occur during their transition from a pelagic to a benthic way of life. Flatfish metamorphosis is characterized by substantial modifications in both form and function, which are initiated by thyroid hormones. Epigenetic mechanisms play a vital role in the regulation of gene expression during this transformative process. This study examines the molecular mechanisms underlying flatfish metamorphosis by integrating multi-omics data that provide information on chromatin status, DNA methylation profile, and gene expression at three key stages (pre-metamorphosis, climax and post-metamorphosis) in the turbot (Scophthalmus maximus) brain, a complex organ that plays a critical role in the regulation of this intricate process. The analysis of DNA methylation patterns revealed major epigenetic dynamic changes during the different metamorphosis stages. Specifically, the methylation levels exhibited a typical bimodal distribution in the pre-metamorphic stage, transitioned to intermediate levels of methylation (around 50%) during the climax stage, and reverted to a bimodal distribution in the post-metamorphic stage. Notably, DMRs were identified in regions of open chromatin that colocalized with CpG islands. Moreover, our results indicate an inverse relationship between DNA methylation and transcriptional activity in regions near the transcription start sites (TSSs), where high levels of methylation correspond to low expression and low levels of methylation corresponds to high gene transcription. This study thereby elucidates the regulatory impact of methylation on gene expression during the metamorphosis process in the flatfish brain.

overall_design: Methylation profiling (RRBS-seq) of turbot brain samples from the pre-metamorphic, climax of metamorphosis and post-metamorphic stages.

last: Guerrero-Peña

first: Paula

last: Suarez-Bregua

first: Núria

last: Sánchez-Baizán

first: Francesc

last: Piferrer

first: Juan

middle: J

last: Tena

first: Josep

last: Rotllant


title: DNase-seq from hypothalamus (ENCSR990VCR)


title: An integrated approach reveals synergistic effects of jasminoidin combined with ursodeoxycholic acid against cerebral ischemia-reperfusion injury

city: Beijing

first: danli

last: hao

address: 16 Baixincang, Dongzhimennei

institute: China Academy of Chinese Medical Sciences

summary: To investigate synergistic mechanism of JA and UA in cerebral ischemia

overall_design: We then performed gene expression profiling analysis using data obtained from mRNA-seq of sham, vehicle,JA, UA and JU.

first: Peng-Qian

last: Wang

first: Dan-Li

last: Hao

first: Yi-Lin

last: Zhong

first: Feng

last: Sui


title: Mettl8 programs Tcf1+CXCR5+ T cells in autoimmune disease and tumor by mediating Tcf1 mRNA m3C modification and Tcf1-bound chromatin loops

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: In the tumor microenvironment (TME), the active tertiary lymphoid structure (TLS) plays a crucial role in fostering the reactivation of naïve or memory cells, leading to the expansion of effector cells. However, an excessive reinvigoration of T cells can result in autoimmune-like diseases, such as those observed in immune checkpoint blockade (ICB) therapy. Here, we have identified that the gene encoding RNA methyltransferase Mettl8 is highly expressed in inflammatory CD4+ CXCL13+ TFH cells of autoimmune patients. Surprisingly, the genetic deletion of Mettl8 in mice resulted in a reduced autoimmune phenotype in helper CD4 cells and slowed tumor growth through increased activation/effector response in CD8+ T cells. Mechanistically, Mettl8 is found to imprint m3C modification, stabilizing Tcf1 mRNA, and simultaneously interacts with Tcf1 protein to co-bind specific genome loops for genomic reorganization, as revealed by Hi-C analysis. These findings suggest that targeting Mettl8 promotes antitumor immunity while preventing the occurrence of autoimmune diseases. Notably, pharmacological inhibition of sumoylation-stabilizing Mettl8 protein has shown efficacy in compromising autoimmune CXCL13+ TFH specialization and function. In conclusion, these findings underscore the dual regulatory elements of the Mettl8-Tcf1 complex as a promising target for tumor immunotherapy, offering protection against autoimmune diseases.

overall_design: To investigate whether Mettl8 deficiency causes alterations in Tcf1 binding sites and chromatin accessiblity, we performed Mettl8 and Tcf1 CUT&Tag, and ATAC-seq in WT and Mettl8 KO CD8+ T cells.Given that Tcf1 regulates genomic organization to maintain CD8+ T cell identity, we next examined whether Mettl8 deficiency disrupts Tcf1-mediated 3D genome organization by HiC.To comprehensively understand the impact of Mettl8 deficiency on CD8+ T cells, we conducted RNA sequencing on sorted tumor-infiltrating CD8+ T cells. Considering the heterogeneous expression of these markers across T cell subsets, we further performed RNA sequencing on sorted Ly108+ Tim3− TPEX, Tim3+ CX3CR1+ Ly108− Int-TEX, and Tim3+ CX3CR1− Ly108− TEX subsets. To investigate the molecular mechanism of Mettl8 regulating TPEX cell transition, we conducted m3C-seq and Mettl8-RIP-seq using sorted tumor-infiltrating CD8+ T cells.


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR985SKP)


title: DNase-seq from putamen (ENCSR987WIW)


title: DNase-seq from anterior cingulate cortex (ENCSR984VJY)


title: DNase-seq from cerebellum (ENCSR986SNR)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR982XHY)


title: DNase-seq from hypothalamus (ENCSR980PSM)


title: DNase-seq from amygdala (ENCSR984UNI)


title: DNase-seq from hypothalamus (ENCSR982BCS)


title: DNase-seq from amygdala (ENCSR982NZD)


title: DNase-seq from anterior cingulate cortex (ENCSR975CBO)


title: DNase-seq from caudate nucleus (ENCSR971MCN)


title: DNase-seq from putamen (ENCSR978NIK)


title: DNase-seq from cerebellum (ENCSR972WHM)


title: DNase-seq from substantia nigra (ENCSR969JSD)


title: Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability

city: Guangzhou

first: Dai

last: ranran

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou, Guangdong Province

institute: Sun Yat-Sen University

summary: The aim of this project is to investigate the role of N-glycosylation in the regulation of H3K9me3.

overall_design:
CUT-RUN in inhibition of N-glycosylation and the N-glycosylation-defective mutant of INM Protein
ChIP-seq in inhibition of N-glycosylation and the N-glycosylation-defective mutant of INM Protein

first: Xiuxiao

last: Tang

first: Ranran

last: Dai


title: DNase-seq from anterior cingulate cortex (ENCSR972QAI)

last: DCC


title: DNase-seq from hypothalamus (ENCSR966JUL)


title: DNase-seq from cerebellum (ENCSR966ZIA)


title: DNase-seq from caudate nucleus (ENCSR966BPO)


title: DNase-seq from anterior cingulate cortex (ENCSR968GKJ)


title: DNase-seq from caudate nucleus (ENCSR965IUZ)


title: DNase-seq from hypothalamus (ENCSR955JER)


title: DNase-seq from putamen (ENCSR966NTE)


title: DNase-seq from Ammon's horn (ENCSR970TQP)


title: DNase-seq from hypothalamus (ENCSR949TRE)


title: DNase-seq from caudate nucleus (ENCSR946ORZ)


title: DNase-seq from Ammon's horn (ENCSR955BCT)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR936FGZ)


title: DNase-seq from nucleus accumbens (ENCSR951HRO)


title: DNase-seq from caudate nucleus (ENCSR947VPM)


title: DNase-seq from hypothalamus (ENCSR939WEH)


title: DNase-seq from Ammon's horn (ENCSR932MFK)


title: DNase-seq from caudate nucleus (ENCSR935RGG)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR964HOO)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR929ESM)


title: DNase-seq from hypothalamus (ENCSR927TTG)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR935QVH)


title: DNase-seq from putamen (ENCSR933MOK)


title: DNase-seq from cerebellum (ENCSR918UPX)


title: DNase-seq from Ammon's horn (ENCSR921HYQ)


title: DNase-seq from cerebellum (ENCSR925FLT)


title: DNase-seq from amygdala (ENCSR922NIB)


title: DNase-seq from substantia nigra (ENCSR913YDD)


title: DNase-seq from putamen (ENCSR922FCQ)


title: DNase-seq from anterior cingulate cortex (ENCSR911UFI)


title: DNase-seq from hypothalamus (ENCSR910TVN)


title: DNase-seq from amygdala (ENCSR918QYG)


title: DNase-seq from nucleus accumbens (ENCSR909XMW)


title: DNase-seq from nucleus accumbens (ENCSR913TJG)


title: DNase-seq from hypothalamus (ENCSR909HJB)


title: DNase-seq from putamen (ENCSR907NES)


title: DNase-seq from nucleus accumbens (ENCSR907ZGE)


title: DNase-seq from amygdala (ENCSR927NAP)


title: DNase-seq from anterior cingulate cortex (ENCSR951HGM)


title: DNase-seq from anterior cingulate cortex (ENCSR904APY)


title: DNase-seq from amygdala (ENCSR907FQX)


title: DNase-seq from caudate nucleus (ENCSR902OAY)


title: DNase-seq from cerebellum (ENCSR904VLC)


title: DNase-seq from anterior cingulate cortex (ENCSR898IWL)


title: DNase-seq from amygdala (ENCSR884QQY)


title: DNase-seq from Ammon's horn (ENCSR905ECO)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR880FFK)


title: DNase-seq from anterior cingulate cortex (ENCSR895HXW)


title: DNase-seq from caudate nucleus (ENCSR880DGB)


title: DNase-seq from caudate nucleus (ENCSR895LDY)


title: DNase-seq from hypothalamus (ENCSR897EQJ)


title: DNase-seq from caudate nucleus (ENCSR891YFU)


title: DNase-seq from anterior cingulate cortex (ENCSR872OJT)


title: DNase-seq from cerebellum (ENCSR883SFD)


title: DNase-seq from hypothalamus (ENCSR878UCC)


title: DNase-seq from anterior cingulate cortex (ENCSR870FVK)


title: DNase-seq from putamen (ENCSR869YMF)


title: DNase-seq from substantia nigra (ENCSR870YMP)


title: DNase-seq from anterior cingulate cortex (ENCSR868ZXQ)


title: DNase-seq from substantia nigra (ENCSR865YJP)


title: DNase-seq from Ammon's horn (ENCSR861HOD)


title: DNase-seq from putamen (ENCSR856ZNO)


title: DNase-seq from nucleus accumbens (ENCSR850CID)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR855LVD)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR864BXZ)


title: DNase-seq from caudate nucleus (ENCSR848LNH)


title: DNase-seq from putamen (ENCSR846QAF)


title: DNase-seq from cerebellum (ENCSR838MVE)


title: DNase-seq from nucleus accumbens (ENCSR844XQO)


title: DNase-seq from caudate nucleus (ENCSR846VDO)


title: DNase-seq from hypothalamus (ENCSR849IAY)


title: DNase-seq from amygdala (ENCSR854XDD)


title: DNase-seq from anterior cingulate cortex (ENCSR830UKQ)


title: DNase-seq from cerebellum (ENCSR828JEX)


title: DNase-seq from cerebellum (ENCSR821TKQ)


title: DNase-seq from hypothalamus (ENCSR844ANY)


title: DNase-seq from putamen (ENCSR860FLB)


title: DNase-seq from anterior cingulate cortex (ENCSR835OQW)


title: DNase-seq from putamen (ENCSR846NLY)


title: DNase-seq from substantia nigra (ENCSR821KTM)


title: DNase-seq from Ammon's horn (ENCSR850BMG)


title: DNase-seq from caudate nucleus (ENCSR816UJX)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR842BYR)


title: DNase-seq from substantia nigra (ENCSR834HPX)


title: DNase-seq from anterior cingulate cortex (ENCSR811HRV)


title: DNase-seq from caudate nucleus (ENCSR812OQB)


title: DNase-seq from nucleus accumbens (ENCSR833RZM)


title: DNase-seq from caudate nucleus (ENCSR817GTB)


title: DNase-seq from cerebellum (ENCSR857IYQ)


title: DNase-seq from amygdala (ENCSR809VUP)


title: DNase-seq from putamen (ENCSR806EIL)


title: DNase-seq from cerebellum (ENCSR802XPH)


title: DNase-seq from nucleus accumbens (ENCSR806GVM)


title: DNase-seq from nucleus accumbens (ENCSR817EUV)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR809SER)


title: DNase-seq from hypothalamus (ENCSR797UUC)


title: DNase-seq from hypothalamus (ENCSR872HRU)


title: DNase-seq from nucleus accumbens (ENCSR794LDL)


title: DNase-seq from cerebellum (ENCSR789TWI)


title: DNase-seq from cerebellum (ENCSR800ZMK)


title: DNase-seq from putamen (ENCSR805MYY)


title: DNase-seq from caudate nucleus (ENCSR804WSV)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR794ZBF)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR794KHT)


title: DNase-seq from putamen (ENCSR789MCM)


title: DNase-seq from cerebellum (ENCSR788HVV)


title: DNase-seq from caudate nucleus (ENCSR785YUC)


title: DNase-seq from hypothalamus (ENCSR779MNG)


title: DNase-seq from substantia nigra (ENCSR785IDX)


title: DNase-seq from cerebellum (ENCSR772IVY)


title: DNase-seq from putamen (ENCSR801KMJ)


title: DNase-seq from anterior cingulate cortex (ENCSR770JXK)


title: DNase-seq from amygdala (ENCSR784ONO)


title: DNase-seq from nucleus accumbens (ENCSR772CNQ)


title: DNase-seq from cerebellum (ENCSR773YKD)


title: DNase-seq from cerebellum (ENCSR789QJY)


title: DNase-seq from cerebellum (ENCSR787VSW)


title: DNase-seq from cerebellum (ENCSR769IWY)


title: DNase-seq from caudate nucleus (ENCSR766HHX)


title: DNase-seq from nucleus accumbens (ENCSR767XFW)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR764HAG)


title: DNase-seq from Ammon's horn (ENCSR799FDC)


title: DNase-seq from Ammon's horn (ENCSR761JIJ)


title: DNase-seq from amygdala (ENCSR758FVN)


title: DNase-seq from putamen (ENCSR756MTS)


title: DNase-seq from Ammon's horn (ENCSR754BDW)


title: DNase-seq from nucleus accumbens (ENCSR752PPX)


title: DNase-seq from caudate nucleus (ENCSR747KLO)


title: DNase-seq from nucleus accumbens (ENCSR743YEP)


title: DNase-seq from caudate nucleus (ENCSR738AGR)


title: DNase-seq from amygdala (ENCSR742ZLS)


title: DNase-seq from amygdala (ENCSR739UIY)


title: DNase-seq from Ammon's horn (ENCSR764ELW)


title: DNase-seq from cerebellum (ENCSR720GHF)


title: DNase-seq from putamen (ENCSR733NLD)


title: DNase-seq from hypothalamus (ENCSR721CYZ)


title: DNase-seq from hypothalamus (ENCSR726FJJ)


title: DNase-seq from amygdala (ENCSR712NQU)


title: DNase-seq from putamen (ENCSR755TFJ)


title: DNase-seq from caudate nucleus (ENCSR715VWX)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR748RZI)


title: DNase-seq from amygdala (ENCSR701IOE)


title: DNase-seq from substantia nigra (ENCSR702ZLX)


title: DNase-seq from substantia nigra (ENCSR694YEJ)


title: DNase-seq from anterior cingulate cortex (ENCSR711ZCQ)


title: DNase-seq from caudate nucleus (ENCSR694QES)


title: DNase-seq from anterior cingulate cortex (ENCSR706XMF)


title: DNase-seq from substantia nigra (ENCSR732ANC)


title: DNase-seq from anterior cingulate cortex (ENCSR691SIC)


title: DNase-seq from nucleus accumbens (ENCSR698SGQ)


title: DNase-seq from nucleus accumbens (ENCSR747NFC)


title: DNase-seq from anterior cingulate cortex (ENCSR691TRJ)


title: DNase-seq from putamen (ENCSR689AYP)


title: DNase-seq from cerebellum (ENCSR689LJP)


title: DNase-seq from hypothalamus (ENCSR689AKJ)


title: DNase-seq from caudate nucleus (ENCSR688LIZ)


title: DNase-seq from caudate nucleus (ENCSR687QUX)


title: DNase-seq from caudate nucleus (ENCSR679RZN)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR679OSG)


title: DNase-seq from nucleus accumbens (ENCSR674QAG)


title: DNase-seq from nucleus accumbens (ENCSR678LTS)


title: DNase-seq from amygdala (ENCSR661CZE)


title: DNase-seq from substantia nigra (ENCSR673DPE)


title: DNase-seq from putamen (ENCSR656QJP)


title: DNase-seq from anterior cingulate cortex (ENCSR674VIK)


title: DNase-seq from hypothalamus (ENCSR666GIK)


title: DNase-seq from anterior cingulate cortex (ENCSR657SFP)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR651FQS)


title: DNase-seq from cerebellum (ENCSR654CUJ)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR680JGE)


title: DNase-seq from cerebellum (ENCSR672VOY)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR688HDU)


title: DNase-seq from cerebellum (ENCSR674AVG)


title: DNase-seq from Ammon's horn (ENCSR661CHK)


title: DNase-seq from substantia nigra (ENCSR660HSO)


title: DNase-seq from hypothalamus (ENCSR681JWS)


title: DNase-seq from anterior cingulate cortex (ENCSR648HYQ)


title: DNase-seq from anterior cingulate cortex (ENCSR646KWH)


title: DNase-seq from amygdala (ENCSR668XRU)


title: DNase-seq from substantia nigra (ENCSR650URF)


title: DNase-seq from caudate nucleus (ENCSR644PBL)


title: DNase-seq from nucleus accumbens (ENCSR648AAH)


title: DNase-seq from hypothalamus (ENCSR650FAV)


title: DNase-seq from substantia nigra (ENCSR640MXT)


title: DNase-seq from substantia nigra (ENCSR644KXH)


title: DNase-seq from anterior cingulate cortex (ENCSR639BIZ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR660GZY)


title: DNase-seq from substantia nigra (ENCSR639NAH)


title: DNase-seq from caudate nucleus (ENCSR754ZSF)


title: DNase-seq from amygdala (ENCSR658EUG)


title: DNase-seq from caudate nucleus (ENCSR637IXV)


title: DNase-seq from anterior cingulate cortex (ENCSR646CJG)


title: DNase-seq from putamen (ENCSR629ZDJ)


title: DNase-seq from substantia nigra (ENCSR626NGB)


title: DNase-seq from nucleus accumbens (ENCSR622YET)


title: DNase-seq from caudate nucleus (ENCSR616UDW)


title: DNase-seq from amygdala (ENCSR631VBB)


title: DNase-seq from hypothalamus (ENCSR619OGY)


title: DNase-seq from Ammon's horn (ENCSR625XKF)


title: DNase-seq from hypothalamus (ENCSR612KFD)


title: DNase-seq from anterior cingulate cortex (ENCSR616PKU)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR610IKS)


title: DNase-seq from nucleus accumbens (ENCSR628ICO)


title: DNase-seq from Ammon's horn (ENCSR607MRE)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR603VXZ)


title: DNase-seq from caudate nucleus (ENCSR591VFR)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR596OSX)


title: DNase-seq from putamen (ENCSR605PMD)


title: DNase-seq from Ammon's horn (ENCSR604DFY)


title: DNase-seq from amygdala (ENCSR611NHP)


title: DNase-seq from anterior cingulate cortex (ENCSR614IPP)


title: DNase-seq from anterior cingulate cortex (ENCSR586WGL)


title: DNase-seq from caudate nucleus (ENCSR577BCI)


title: DNase-seq from Ammon's horn (ENCSR586NBV)


title: DNase-seq from hypothalamus (ENCSR585NVI)


title: DNase-seq from amygdala (ENCSR571XNF)


title: DNase-seq from nucleus accumbens (ENCSR582LVC)


title: DNase-seq from Ammon's horn (ENCSR565QNJ)


title: DNase-seq from nucleus accumbens (ENCSR571EDT)


title: DNase-seq from cerebellum (ENCSR564YDM)


title: DNase-seq from hypothalamus (ENCSR568ZVZ)


title: DNase-seq from anterior cingulate cortex (ENCSR558JMZ)


title: DNase-seq from caudate nucleus (ENCSR561DSZ)


title: DNase-seq from amygdala (ENCSR590CBB)


title: DNase-seq from Ammon's horn (ENCSR556AOQ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR575UNV)


title: DNase-seq from Ammon's horn (ENCSR547QPY)


title: DNase-seq from amygdala (ENCSR551KJH)


title: DNase-seq from Ammon's horn (ENCSR543GPI)


title: DNase-seq from putamen (ENCSR542LBV)


title: DNase-seq from substantia nigra (ENCSR536OWC)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR523WWM)


title: DNase-seq from hypothalamus (ENCSR529OUT)


title: DNase-seq from caudate nucleus (ENCSR523IBJ)


title: DNase-seq from anterior cingulate cortex (ENCSR530AUB)


title: DNase-seq from cerebellum (ENCSR523PNS)


title: DNase-seq from caudate nucleus (ENCSR518OUF)


title: DNase-seq from Ammon's horn (ENCSR515QIF)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR554EZP)


title: DNase-seq from substantia nigra (ENCSR510DSI)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR537KZC)


title: DNase-seq from anterior cingulate cortex (ENCSR514WFN)


title: DNase-seq from cerebellum (ENCSR513GQE)


title: DNase-seq from amygdala (ENCSR507HVU)


title: DNase-seq from Ammon's horn (ENCSR508MTS)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR504BVS)


title: DNase-seq from anterior cingulate cortex (ENCSR507RDH)


title: DNase-seq from putamen (ENCSR503IRE)


title: DNase-seq from amygdala (ENCSR502XLP)


title: DNase-seq from Ammon's horn (ENCSR498IFE)


title: DNase-seq from nucleus accumbens (ENCSR499FBT)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR497GVB)


title: DNase-seq from caudate nucleus (ENCSR502ZRV)


title: DNase-seq from hypothalamus (ENCSR508UEW)


title: DNase-seq from cerebellum (ENCSR494WPH)


title: DNase-seq from cerebellum (ENCSR529ECX)


title: DNase-seq from putamen (ENCSR522VCX)


title: DNase-seq from Ammon's horn (ENCSR497WDC)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR485PFX)


title: DNase-seq from putamen (ENCSR493EKM)


title: DNase-seq from anterior cingulate cortex (ENCSR512GOI)


title: DNase-seq from caudate nucleus (ENCSR485IIT)


title: DNase-seq from hypothalamus (ENCSR487OSU)


title: DNase-seq from substantia nigra (ENCSR492XAM)


title: DNase-seq from putamen (ENCSR477VYA)


title: DNase-seq from Ammon's horn (ENCSR479AHN)


title: DNase-seq from anterior cingulate cortex (ENCSR479HTJ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR494YNX)


title: DNase-seq from cerebellum (ENCSR483LYC)


title: DNase-seq from cerebellum (ENCSR474DCY)


title: DNase-seq from amygdala (ENCSR491HOK)


title: DNase-seq from cerebellum (ENCSR477LTA)


title: DNase-seq from putamen (ENCSR494EIL)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR465RJI)


title: DNase-seq from anterior cingulate cortex (ENCSR466LWQ)


title: DNase-seq from hypothalamus (ENCSR472JUH)


title: DNase-seq from amygdala (ENCSR458UNC)


title: DNase-seq from hypothalamus (ENCSR473PBZ)


title: DNase-seq from nucleus accumbens (ENCSR467ZWA)


title: DNase-seq from Ammon's horn (ENCSR468VXW)


title: DNase-seq from anterior cingulate cortex (ENCSR459HEA)


title: DNase-seq from nucleus accumbens (ENCSR453MLG)


title: DNase-seq from putamen (ENCSR458KJY)


title: DNase-seq from caudate nucleus (ENCSR454INE)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR453BZU)


title: DNase-seq from cerebellum (ENCSR451ECU)


title: DNase-seq from anterior cingulate cortex (ENCSR450EGX)


title: DNase-seq from Ammon's horn (ENCSR444OFO)


title: DNase-seq from substantia nigra (ENCSR451SQM)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR447ZCY)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR441NLO)


title: DNase-seq from Ammon's horn (ENCSR439NVW)


title: DNase-seq from hypothalamus (ENCSR442UYJ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR441FBD)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR437SJV)


title: DNase-seq from putamen (ENCSR434CMW)


title: DNase-seq from substantia nigra (ENCSR429BZH)


title: DNase-seq from caudate nucleus (ENCSR433MMU)


title: DNase-seq from cerebellum (ENCSR429DNW)


title: DNase-seq from nucleus accumbens (ENCSR426LAJ)


title: DNase-seq from substantia nigra (ENCSR426CDK)


title: DNase-seq from nucleus accumbens (ENCSR440YHV)


title: DNase-seq from Ammon's horn (ENCSR422LOI)


title: DNase-seq from Ammon's horn (ENCSR423RVG)


title: DNase-seq from putamen (ENCSR422TKP)


title: DNase-seq from amygdala (ENCSR421CNQ)


title: DNase-seq from hypothalamus (ENCSR419TLP)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR421GCN)


title: DNase-seq from anterior cingulate cortex (ENCSR412XNT)


title: DNase-seq from Ammon's horn (ENCSR414DVM)


title: DNase-seq from caudate nucleus (ENCSR417NHZ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR405CSK)


title: DNase-seq from putamen (ENCSR413XPN)


title: DNase-seq from Ammon's horn (ENCSR404CEY)


title: DNase-seq from caudate nucleus (ENCSR397CSB)


title: DNase-seq from Ammon's horn (ENCSR404CHS)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR397DUU)


title: DNase-seq from cerebellum (ENCSR401GHH)


title: DNase-seq from anterior cingulate cortex (ENCSR395CLE)


title: DNase-seq from cerebellum (ENCSR393SRR)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR389ZCR)


title: DNase-seq from anterior cingulate cortex (ENCSR389MRF)


title: DNase-seq from putamen (ENCSR386SSR)


title: DNase-seq from caudate nucleus (ENCSR375VVY)


title: DNase-seq from cerebellum (ENCSR383VQO)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR383PEK)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR384VQA)


title: DNase-seq from substantia nigra (ENCSR369HYM)


title: DNase-seq from hypothalamus (ENCSR375RLN)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR362LXQ)


title: DNase-seq from cerebellum (ENCSR358VXC)


title: DNase-seq from nucleus accumbens (ENCSR359SKY)


title: DNase-seq from cerebellum (ENCSR353FCV)


title: DNase-seq from substantia nigra (ENCSR355WIW)


title: DNase-seq from caudate nucleus (ENCSR356CVQ)


title: DNase-seq from hypothalamus (ENCSR366PXI)


title: DNase-seq from cerebellum (ENCSR350KKE)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR341WDJ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR344AUJ)


title: DNase-seq from putamen (ENCSR341AEE)


title: DNase-seq from amygdala (ENCSR348BRS)


title: DNase-seq from amygdala (ENCSR338TYX)


title: DNase-seq from Ammon's horn (ENCSR332ZVT)


title: DNase-seq from cerebellum (ENCSR370NOI)


title: DNase-seq from substantia nigra (ENCSR341XLE)


title: DNase-seq from nucleus accumbens (ENCSR351TVZ)


title: DNase-seq from Ammon's horn (ENCSR338TTD)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR328YIC)


title: DNase-seq from cerebellum (ENCSR332JNP)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR320ELE)


title: DNase-seq from nucleus accumbens (ENCSR331JWC)


title: DNase-seq from anterior cingulate cortex (ENCSR316TRV)


title: DNase-seq from amygdala (ENCSR318ULV)


title: DNase-seq from substantia nigra (ENCSR314ZUG)


title: DNase-seq from amygdala (ENCSR315RKJ)


title: DNase-seq from substantia nigra (ENCSR312IVR)


title: DNase-seq from hypothalamus (ENCSR314QWD)


title: DNase-seq from caudate nucleus (ENCSR314CFL)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR310GCP)


title: DNase-seq from substantia nigra (ENCSR307ARR)


title: DNase-seq from cerebellum (ENCSR330JXZ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR306TVF)


title: DNase-seq from nucleus accumbens (ENCSR306UAJ)


title: DNase-seq from amygdala (ENCSR309ISJ)


title: DNase-seq from amygdala (ENCSR306EVC)


title: DNase-seq from hypothalamus (ENCSR304GAB)


title: DNase-seq from amygdala (ENCSR306OZD)


title: DNase-seq from substantia nigra (ENCSR301QGF)


title: DNase-seq from anterior cingulate cortex (ENCSR304EJF)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR300AQA)


title: DNase-seq from caudate nucleus (ENCSR298CUB)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR293ISO)


title: DNase-seq from substantia nigra (ENCSR298WTS)


title: DNase-seq from amygdala (ENCSR293IQG)


title: DNase-seq from putamen (ENCSR297KYW)


title: DNase-seq from Ammon's horn (ENCSR292WDL)


title: DNase-seq from hypothalamus (ENCSR308KZF)


title: DNase-seq from putamen (ENCSR298CAP)


title: DNase-seq from nucleus accumbens (ENCSR290PWH)


title: DNase-seq from Ammon's horn (ENCSR291TYM)


title: DNase-seq from putamen (ENCSR287KKC)


title: DNase-seq from substantia nigra (ENCSR285WND)


title: DNase-seq from anterior cingulate cortex (ENCSR285MPF)


title: DNase-seq from substantia nigra (ENCSR286RDE)


title: DNase-seq from nucleus accumbens (ENCSR289IBE)


title: DNase-seq from amygdala (ENCSR272JSI)


title: DNase-seq from caudate nucleus (ENCSR284PSE)


title: DNase-seq from nucleus accumbens (ENCSR271UQD)


title: DNase-seq from hypothalamus (ENCSR272YHH)


title: DNase-seq from caudate nucleus (ENCSR267WZK)


title: DNase-seq from caudate nucleus (ENCSR269PMA)


title: DNase-seq from cerebellum (ENCSR283EEG)


title: DNase-seq from nucleus accumbens (ENCSR265MSR)


title: DNase-seq from Ammon's horn (ENCSR267RKG)


title: DNase-seq from cerebellum (ENCSR259SVX)


title: DNase-seq from substantia nigra (ENCSR257KSS)


title: DNase-seq from substantia nigra (ENCSR255IVN)


title: DNase-seq from amygdala (ENCSR257SMO)


title: DNase-seq from substantia nigra (ENCSR241TSG)


title: DNase-seq from caudate nucleus (ENCSR240BUK)


title: DNase-seq from amygdala (ENCSR253RHN)


title: DNase-seq from putamen (ENCSR249FCV)


title: DNase-seq from Ammon's horn (ENCSR237HPK)


title: DNase-seq from substantia nigra (ENCSR222XKC)


title: DNase-seq from amygdala (ENCSR235WIJ)


title: DNase-seq from nucleus accumbens (ENCSR229JFT)


title: DNase-seq from substantia nigra (ENCSR237AHR)


title: DNase-seq from Ammon's horn (ENCSR222VDZ)


title: DNase-seq from Ammon's horn (ENCSR214BAJ)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR210NNR)


title: DNase-seq from anterior cingulate cortex (ENCSR251WRE)


title: DNase-seq from putamen (ENCSR207KAZ)


title: DNase-seq from putamen (ENCSR221TJZ)


title: DNase-seq from amygdala (ENCSR207NON)


title: DNase-seq from Ammon's horn (ENCSR234YGD)


title: DNase-seq from caudate nucleus (ENCSR205ZJO)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR238LSQ)


title: DNase-seq from substantia nigra (ENCSR200VJW)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR222LOP)


title: DNase-seq from putamen (ENCSR197HFX)


title: DNase-seq from caudate nucleus (ENCSR194HVD)


title: DNase-seq from caudate nucleus (ENCSR197HHU)


title: DNase-seq from anterior cingulate cortex (ENCSR199DJG)


title: DNase-seq from amygdala (ENCSR185IID)


title: DNase-seq from hypothalamus (ENCSR182MRI)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR193LCA)


title: DNase-seq from putamen (ENCSR249PKR)


title: DNase-seq from anterior cingulate cortex (ENCSR220ETD)


title: DNase-seq from nucleus accumbens (ENCSR181MYF)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR178XHL)


title: DNase-seq from nucleus accumbens (ENCSR178IUD)


title: DNase-seq from Ammon's horn (ENCSR181BYP)


title: DNase-seq from substantia nigra (ENCSR175QDE)


title: DNase-seq from amygdala (ENCSR169VIC)


title: DNase-seq from caudate nucleus (ENCSR163CXS)


title: DNase-seq from cerebellum (ENCSR167NWY)


title: DNase-seq from amygdala (ENCSR165TAZ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR160PPK)


title: DNase-seq from anterior cingulate cortex (ENCSR157UQY)


title: DNase-seq from putamen (ENCSR147XZQ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR159GVI)


title: DNase-seq from cerebellum (ENCSR159GHL)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR141HQJ)


title: DNase-seq from cerebellum (ENCSR156BWT)


title: DNase-seq from cerebellum (ENCSR137NDN)


title: DNase-seq from hypothalamus (ENCSR144RDG)


title: DNase-seq from amygdala (ENCSR136FJS)


title: DNase-seq from hypothalamus (ENCSR143CJJ)


title: DNase-seq from substantia nigra (ENCSR143VEP)


title: DNase-seq from hypothalamus (ENCSR171JAP)


title: DNase-seq from anterior cingulate cortex (ENCSR135EKC)


title: DNase-seq from cerebellum (ENCSR136ECA)


title: DNase-seq from amygdala (ENCSR141UWM)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR134TVI)


title: DNase-seq from hypothalamus (ENCSR148TWM)


title: DNase-seq from nucleus accumbens (ENCSR132UYU)


title: DNase-seq from nucleus accumbens (ENCSR125FPU)


title: DNase-seq from cerebellum (ENCSR132DSW)


title: DNase-seq from nucleus accumbens (ENCSR127BQL)


title: DNase-seq from nucleus accumbens (ENCSR128PGE)


title: DNase-seq from substantia nigra (ENCSR135UCR)


title: DNase-seq from Ammon's horn (ENCSR117RUZ)


title: DNase-seq from Ammon's horn (ENCSR110MYS)


title: DNase-seq from nucleus accumbens (ENCSR113ZKW)


title: DNase-seq from cerebellum (ENCSR109OTE)


title: DNase-seq from nucleus accumbens (ENCSR129UPE)


title: DNase-seq from amygdala (ENCSR115LHB)


title: DNase-seq from hypothalamus (ENCSR101JUF)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR106LXV)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR108KVV)


title: DNase-seq from amygdala (ENCSR126ZZQ)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR100JVV)


title: DNase-seq from cerebellum (ENCSR106CAP)


title: DNase-seq from cerebellum (ENCSR100EVG)


title: DNase-seq from Ammon's horn (ENCSR093HBV)


title: DNase-seq from caudate nucleus (ENCSR101FLG)


title: DNase-seq from putamen (ENCSR120MHH)


title: DNase-seq from anterior cingulate cortex (ENCSR102ZXS)


title: DNase-seq from C1 segment of cervical spinal cord (ENCSR092LHI)


title: DNase-seq from nucleus accumbens (ENCSR087VYL)


title: DNase-seq from Ammon's horn (ENCSR087WQF)


title: DNase-seq from nucleus accumbens (ENCSR085FYV)


title: DNase-seq from hypothalamus (ENCSR092PYP)


title: DNase-seq from nucleus accumbens (ENCSR087ASG)


title: DNase-seq from hypothalamus (ENCSR077DYH)


title: DNase-seq from caudate nucleus (ENCSR103JDI)


title: DNase-seq from anterior cingulate cortex (ENCSR079IAM)


title: DNase-seq from cerebellum (ENCSR075VZR)


title: DNase-seq from putamen (ENCSR081PVE)


title: DNase-seq from putamen (ENCSR075FRQ)


title: DNase-seq from putamen (ENCSR072HSD)


title: DNase-seq from hypothalamus (ENCSR073CUH)


title: DNase-seq from putamen (ENCSR069WFA)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR069LMC)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR060QMW)


title: DNase-seq from nucleus accumbens (ENCSR060WFE)


title: DNase-seq from nucleus accumbens (ENCSR063SNR)


title: DNase-seq from putamen (ENCSR080XGJ)


title: DNase-seq from anterior cingulate cortex (ENCSR065USE)


title: DNase-seq from substantia nigra (ENCSR070SVO)


title: DNase-seq from amygdala (ENCSR053GLL)


title: DNase-seq from nucleus accumbens (ENCSR057MAC)


title: DNase-seq from putamen (ENCSR048QZY)


title: DNase-seq from substantia nigra (ENCSR051TPB)


title: DNase-seq from Ammon's horn (ENCSR050IGM)


title: DNase-seq from cerebellum (ENCSR048PMY)


title: DNase-seq from anterior cingulate cortex (ENCSR047WUB)


title: DNase-seq from dorsolateral prefrontal cortex (ENCSR048KUD)


title: DNase-seq from Ammon's horn (ENCSR046VFU)


title: DNase-seq from hypothalamus (ENCSR046VKG)


title: DNase-seq from substantia nigra (ENCSR039BAA)


title: DNase-seq from anterior cingulate cortex (ENCSR034ILY)


title: DNase-seq from amygdala (ENCSR034PUJ)


title: DNase-seq from nucleus accumbens (ENCSR034HPF)


title: DNase-seq from anterior cingulate cortex (ENCSR038VQB)


title: DNase-seq from putamen (ENCSR024URI)


title: DNase-seq from putamen (ENCSR031KAI)


title: DNase-seq from putamen (ENCSR046FVG)


title: DNase-seq from amygdala (ENCSR023UNS)


title: DNase-seq from anterior cingulate cortex (ENCSR047HME)


title: DNase-seq from caudate nucleus (ENCSR025TQQ)


title: DNase-seq from putamen (ENCSR018YAL)


title: DNase-seq from substantia nigra (ENCSR043OJZ)


title: DNase-seq from amygdala (ENCSR023AEW)


title: DNase-seq from caudate nucleus (ENCSR015WAR)


title: DNase-seq from nucleus accumbens (ENCSR010VHC)


title: DNase-seq from Ammon's horn (ENCSR022NUX)


title: DNase-seq from substantia nigra (ENCSR047BGB)


title: DNase-seq from substantia nigra (ENCSR014GCS)


title: DNase-seq from caudate nucleus (ENCSR034SGT)


title: DNase-seq from anterior cingulate cortex (ENCSR016KLL)


title: DNase-seq from amygdala (ENCSR018LPY)


title: DNase-seq from nucleus accumbens (ENCSR033QXT)


title: DNase-seq from caudate nucleus (ENCSR010BRB)


title: DNase-seq from Ammon's horn (ENCSR014QBR)


title: DNase-seq from Ammon's horn (ENCSR007GLQ)


title: DNase-seq from anterior cingulate cortex (ENCSR008EPU)


title: DNase-seq from nucleus accumbens (ENCSR006NRS)


title: DNase-seq from cerebellum (ENCSR010CKD)


title: DNase-seq from putamen (ENCSR005ZWB)


title: DNase-seq from amygdala (ENCSR014SNN)


title: DNase-seq from caudate nucleus (ENCSR004WWN)


title: DNase-seq from cerebellum (ENCSR005HBB)


title: DNase-seq from putamen (ENCSR004BCA)


title: snATAC-seq from heart (ENCSR805DID)


title: snATAC-seq from liver (ENCSR825WYQ)


title: snATAC-seq from heart (ENCSR715JSZ)


title: snATAC-seq from liver (ENCSR659ANG)


title: snATAC-seq from liver (ENCSR650BBI)


title: snATAC-seq from liver (ENCSR552QVU)


title: snATAC-seq from liver (ENCSR497ZST)


title: snATAC-seq from heart (ENCSR306FRQ)


title: snATAC-seq from liver (ENCSR074DOR)


title: snATAC-seq from liver (ENCSR594BJF)


title: STARR-seq from K562 (ENCSR312UQM)


title: snATAC-seq from heart (ENCSR282FAK)


title: snATAC-seq from heart (ENCSR024TGD)


title: snATAC-seq from activated CD8-positive, alpha-beta T cell (ENCSR472HFJ)


title: snATAC-seq from liver (ENCSR118PUH)


title: snATAC-seq from heart (ENCSR890TGR)


title: snATAC-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR600UDB)


title: snRNA-seq from adrenal gland (ENCSR998YMP)

summary:
Illumina short-read B6/Cast F1 adrenal P14 female normal 12k

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: snRNA-seq from layer of hippocampus (ENCSR983TAK)

summary:
Illumina short-read B6/Cast F1 hippocampus P25 male normal 2k

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: snATAC-seq from heart (ENCSR004IAY)


title: snRNA-seq from layer of hippocampus (ENCSR979MRY)

summary:
Illumina short-read B6/Cast F1 hippocampus P10 male ont_match 2k

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: snATAC-seq from activated naive CD8-positive, alpha-beta T cell (ENCSR110IID)


title: snATAC-seq from heart (ENCSR515SNH)


title: snATAC-seq from activated CD4-positive, alpha-beta T cell (ENCSR569ZMI)


title: snRNA-seq from gastrocnemius (ENCSR974ODT)

summary:
Illumina short-read B6/Cast F1 gastrocnemius P18-20mo female normal 1k

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: snRNA-seq from heart (ENCSR975YAQ)

summary:
Illumina short-read B6/Cast F1 heart P10 male normal 2k

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: snATAC-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR196EOO)


title: snRNA-seq from layer of hippocampus (ENCSR973WCI)

summary:
Illumina short-read B6/Cast F1 hippocampus P14 female ont_match 2k

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: snRNA-seq from adrenal gland (ENCSR982GYD)

summary:
Illumina short-read B6/Cast F1 adrenal P18-20mo male normal 2k

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: snATAC-seq from activated CD4-positive, alpha-beta memory T cell (ENCSR810IIV)


title: Control MPRA from HepG2 (ENCSR990ZAU)

summary:
Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.

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: snRNA-seq from left cerebral cortex (ENCSR964OQW)

summary:
Illumina short-read B6/Cast F1 cortex P25 female normal 2k

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: snRNA-seq from gastrocnemius (ENCSR961HBK)

summary:
Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 1k

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: MPRA from K562 (ENCSR987WTK)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.

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: MPRA from glial cell (ENCSR976YTH)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.

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: snRNA-seq from layer of hippocampus (ENCSR967YET)

summary:
Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k

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: MPRA from MIN6 (ENCSR981ILP)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TCF7L2 enhancer.

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: MPRA from HEK293T (ENCSR934HHR)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.

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: snRNA-seq from adrenal gland (ENCSR950SIX)

summary:
Illumina short-read B6/Cast F1 adrenal P2mo female normal 2k

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


title: Control MPRA from HEK293T (ENCSR916DHS)


title: Control MPRA from HepG2 (ENCSR902NRZ)

summary:
Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.

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


title: Control MPRA from LNCAP (ENCSR905UEC)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs11986220.

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


title: Control MPRA from HepG2 (ENCSR974CHK)

summary:
Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.

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: MPRA from MIN6 (ENCSR909OSG)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ZFAND3 enhancer.

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


title: Control MPRA from HepG2 (ENCSR932ZCL)

summary:
Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.

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: snRNA-seq from gastrocnemius (ENCSR966QJD)

summary:
Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 15k

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


title: Control MPRA from K562 (ENCSR897BXT)

summary:
Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential WTC11 enhancers and promoters of all protein-coding genes.

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: MPRA from HEK293T (ENCSR883DOL)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs6983267.

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


title: Control MPRA from HepG2 (ENCSR849IXM)

summary:
Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.

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


title: Control MPRA from HaCaT (ENCSR849FAC)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF6 enhancer.

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: MPRA from HepG2 (ENCSR912KDN)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.

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: MPRA from HepG2 (ENCSR839LDC)


title: Control MPRA from glial cell (ENCSR958QFH)


title: snRNA-seq from adrenal gland (ENCSR943REW)

summary:
Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k

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


title: Control MPRA from HepG2 (ENCSR837DCD)

summary:
Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential enhancers from HepG2, K562, and WTC11 cells, and promoters of protein-coding genes.

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: MPRA from HEK293T (ENCSR821FQH)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.

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


title: Control MPRA from SK-MEL-28 (ENCSR814CZJ)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF4 enhancer.

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: MPRA from K562 (ENCSR845WND)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.

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: snRNA-seq from layer of hippocampus (ENCSR944KUB)

summary:
Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k

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: MPRA from HepG2 (ENCSR881ERG)

summary:
Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.

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


title: Control MPRA from HEL (ENCSR901KLZ)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the GP1BB promoter.

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: snRNA-seq from layer of hippocampus (ENCSR940VCU)

summary:
Illumina short-read B6/Cast F1 hippocampus P36 male normal 12k

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


title: Control MPRA from glial cell (ENCSR799YAF)


title: MPRA from LNCAP (ENCSR812ICI)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs11986220.

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: MPRA from HepG2 (ENCSR787MOJ)

summary:
Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as ORI, and serves as an internal control to ORI_full.

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: MPRA from glial cell (ENCSR782GCT)


title: Control MPRA from glial cell (ENCSR772XSY)


title: Control MPRA from HEL (ENCSR769LVZ)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the HBB promoter.

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 amygdala (ENCSR050QPI)

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: MPRA from HepG2 (ENCSR760GMX)

summary:
Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.

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: snRNA-seq from heart (ENCSR938YKJ)

summary:
Illumina short-read B6/Cast F1 heart P14 female normal 12k

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


title: Control MPRA from HepG2 (ENCSR742NIM)

summary:
Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.

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


title: Control MPRA from HepG2 (ENCSR752EIG)

summary:
Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of a mix of short, medium, and long elements in parallel.

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: MPRA from glial cell (ENCSR759LCV)


title: Control MPRA from HepG2 (ENCSR730SAC)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT enhancer, using 3' to 5' direction.

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: MPRA from HepG2 (ENCSR739VGY)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.

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


title: Control MPRA from HepG2 (ENCSR721BJI)

summary:
Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.

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: MPRA from HEK293T (ENCSR701WDZ)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the HNF4A promoter.

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


title: Control MPRA from HepG2 (ENCSR642ECM)


title: Control MPRA from WTC11 (ENCSR653CPO)

summary:
Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential WTC11 enhancers and promoters of protein-coding genes.

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: MPRA from HepG2 (ENCSR632EPR)


title: Control MPRA from HEL (ENCSR651OGV)

summary:
Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the HBG1 promoter.

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: snRNA-seq from gastrocnemius (ENCSR930FUM)

summary:
Illumina short-read B6/Cast F1 gastrocnemius P4 male normal 12k

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


title: Control MPRA from HEK293T (ENCSR672AWI)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs6983267.

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: MPRA from HEL (ENCSR686LKF)


title: MPRA from HepG2 (ENCSR661ZUO)

summary:
Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.

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


title: Control MPRA from HEL (ENCSR549UBJ)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the BCL11A enhancer.

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


title: Control MPRA from HepG2 (ENCSR579XDB)

summary:
Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.

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: MPRA from Neuro-2a (ENCSR642DFC)

summary:
Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the ultra conserved element UC88.

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


title: Control MPRA from HEK293T (ENCSR629KNC)


title: Control MPRA from WTC11 (ENCSR517VUU)

summary:
Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test neuronal enhancers and promoters.

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