title: Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean. [RNA-seq]

first: Hao

last: Tian

address: 105 West Third Ring Road North, Haidian District, Beijing,

institute: Capital normal university

summary: The circadian clock is a universal intrinsic mechanism that rhythmically regulates most molecular, metabolic, and physiological events rhythmically across the living kingdom. Although master transcription factors composed of circadian oscillators have been identified to maintain conserved transcription-translational feedback loops (TTFL), the correlation between epigenetic and chromatin states and rhythmic transcription remains unclear. In this study, we established large-scale chromatin landscapes in soybean using a diurnal time series of ATAC-seq and ChIP-seq, alongside RNA-seq assays A common oscillating pattern that chromatin accessibility synchronizes with gene expression is characterized across the whole genome of soybean. This study enhances our understanding of the epigenetic regulation of the circadian clock and rhythmic physiology

overall_design:
The Ws82's leaf were collected after free-running treatment. All the plants were grown in Middle-day(12h Light and 12h Dark,24℃) for 14 days, and treat with constant light for 1 day. After free-running treatment, 3 individuals with consitstent growth rate and phenotype were used for an independent experiment.
The notations L, M, R represent three indepentent biological replicates.

first: Qichao

last: Lian

first: Hequan

last: Sun

first: Shuo

first: Liangyu


title: Macrophage-Mediated IL1beta/IL23 Signaling Regulates gamma delta (gammadelta) T Cell Immunity Against Non-Tuberculous Mycobacteria [RNA-seq]

status: Public on Mar 01 2026

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: Mechanistic Insights. Our study reveals the crucial role of gammadelta T cells in non-tuberculous mycobacteria (NTM) infection. We observed a significant increase and activation of gammadelta T cells in mice infected with MAB or with MAB infection combined with pulmonary fibrosis. Depletion of gammadelta T cells worsened the infection, while transfer of gammadelta T cells reversed this effect. Mechanistically, we found that MAB infection stimulates macrophages to produce IL-1beta and IL-23, which promotes the expansion of gammadelta T17 cells. MAB can also directly activate gammadelta T cells, leading to the clearance of MAB through an IL-17A-dependent pathway. Our findings suggest that gammadelta T cells represent a potential therapeutic target for NTM infections.

overall_design: γδT cells were isolated from WT or Il17a−/− mice by MACS and then infected with M.abscessus for 12h. Unstimulated γδT cells served as a control group.


title: Synergism between plant beneficial microbes enhances salinity tolerance in Arabidopsis

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

summary: The objective of the study was to understand the transcriptional regulation of genes involved in salt-stress response upon colonization with plant beneficial microbes SA187 and S. indica

overall_design: Col0 plants colonized with mock, SA187 and S. indica alone or together as a Synccom. were treated with or without 100mM NaCl

first: Anamika

last: Rawat

first: Baoda

last: Han

first: Niketan

last: Patel

first: Hanaa

last: Allehaibi

first: Alexandre

last: Rosado

first: Heribert

last: Hirt


title: AUF1 mRNA binding protein therapy in severe muscle injury blocks atrophy, accelerates regeneration and neuromuscular junction formation

city: NY

first: Robert

last: Schneider

address: 550 1ST AVE

country: USA

institute: NYU Langone Health

summary: There are currently no approved therapeutic interventions to promote skeletal muscle regeneration following traumatic muscle injury, among the most common debilitating injuries. Here we developed a new therapeutic approach for severe muscle injury that significantly prevents muscle atrophy, while promoting rapid muscle repair, regeneration and regeneration of neuro-muscular junctions (NMJs), orchestrated by gene delivery of the mRNA binding protein AUF1. Key regulators of myogenesis and NMJs are encoded by mRNAs that are regulated in their stability and translation by AUF1. Using preclinical mouse models of severe muscle injury, we show that delivery of the AUF1 gene to muscle cells systemically or intramuscularly by AAV8 or lentivirus vectors, prophylactically, during or 24 hours after injury, is highly effective in reducing muscle atrophy, rapidly expanding muscle stem cells, promoting accelerated muscle repair, regeneration and maturation, while restoring NMJs. Animals receiving AUF1 therapy following severe tibialis anterior muscle injury, rapidly regained near-normal muscle strength and function by two weeks, whereas control animals showed continued significant deficit four months later. Histologic and ultrastructure electron micrographic analysis shows that AUF1 gene therapy restores normal muscle architecture and muscle mass. AUF1 therapy is a potential new approach for treating severe muscle injury.

overall_design: To investigate the role of AUF1 overexpression in controllong the stability and translation of key mRNAs involved in muscle regeneration. We used C2C12 cells o/e AUF1 and collected total and cytoplasmic actively translating mRNA loaded on heavy polysome fractions 48hrs upon myoblast differentiation.  Comparative gene expression analysis using  Polysome Seq.

first: Dounia

last: Abbadi

first: Olga

last: Katsara


title: Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean. [ATAC-seq]

city: Beijing

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
The Ws82's leaf were collected after free-running treatment. All the plants were grown in Short-day(8h Light and 16h Dark,24℃) for 14 days, and treat with constant light for 1 day. After free-running treatment, 3 individuals with consistent growth rate and phenotype were used for an independent experiment.
The notations L, M, R represent three indepentent biological replicates.

last: Liu


title: IRE1α limits Golgi expansion during early stages of β-cell compensation [WD]

city: Iowa City

first: Samuel

last: Stephens

state: Iowa

address: 169 Newton Rd, 3400 PBDB

institute: University of Iowa

summary: Examine expression changes in mouse pancreatic islets following 4 week western diet

overall_design: Male C57BL/6J mice 8-10 weeks of age were fed western diet or standard chow diet for 4 weeks. Pancreatic islets were isolated and immediately processed

middle: B


title: Role of monocytes and meningeal macrophages in bacterial meningoencephalitis

city: Freiburg

first: Vitka

last: Gres

address: Breisacherstraße 115b

department: Institute for Infection Prevention and Control

country: Germany

institute: University of Freiburg

summary: Macrophages in the dura mater  are substantial contributors to the immune defense of the brain, however, their site-specific origin and function in bacterial infections of the central nervous system are incompletely understood. In a natural model of streptococcal meningoencephalitis, where bacteria systemically spread via the bloodstream to the brain , we found streptococci to be largely restricted in the meninges . Further sporadic spread of bacteria to the underlying brain parenchyma caused a region-restricted microglia activation. Invasion of monocytes, but not granulocytes into brain  and leptomeninges correlated to the disease severity. Inflammation in the dura was accompanied by activation and loss of dural macrophages, and by the rapid engraftment of highly activated monocytes. In addition, monocyte progenitors in the skull marrow underwent drastic changes and acquired a more immature phenotype likely due to infection-induced emergency myelopoiesis.  Notably, while dural monocytes were derived from adjacent skull marrow in a CCR2-independent fashion, the high demand for dural monocytes in streptococcal meningoencephalitis required intact CCR2 signalling and involved the long bone marrow, indicating heterogeneity in monocyte recruitment. Furthermore, meningoencephalitis increased monocyte progeny from monocyte-dendritic cell progenitors compared to the homeostatic, granulocyte-monocyte progenitor-dominated origin. Accordingly, monocytes in the dura, recruited from distinct reservoirs depending on disease-inherent needs, are intertwined with the disease course and may thus offer opportunities for therapeutic interventions.  Macrophages in the dura mater  are substantial contributors to the immune defense of the brain, however, their site-specific origin and function in bacterial infections of the central nervous system are incompletely understood. In a natural model of streptococcal meningoencephalitis, where bacteria systemically spread via the bloodstream to the brain , we found streptococci to be largely restricted in the meninges . Further sporadic spread of bacteria to the underlying brain parenchyma caused a region-restricted microglia activation. Invasion of monocytes, but not granulocytes into brain  and leptomeninges correlated to the disease severity. Inflammation in the dura was accompanied by activation and loss of dural macrophages, and by the rapid engraftment of highly activated monocytes. In addition, monocyte progenitors in the skull marrow underwent drastic changes and acquired a more immature phenotype likely due to infection-induced emergency myelopoiesis.  Notably, while dural monocytes were derived from adjacent skull marrow in a CCR2-independent fashion, the high demand for dural monocytes in streptococcal meningoencephalitis required intact CCR2 signalling and involved the long bone marrow, indicating heterogeneity in monocyte recruitment. Furthermore, meningoencephalitis increased monocyte progeny from monocyte-dendritic cell progenitors compared to the homeostatic, granulocyte-monocyte progenitor-dominated origin. Accordingly, monocytes in the dura, recruited from distinct reservoirs depending on disease-inherent needs, are intertwined with the disease course and may thus offer opportunities for therapeutic interventions.

overall_design: We investigated the transcriptional differences between dural macrophages (DM) and microglia (MG) in control or infected mice 2 days post group B streptococcal (GBS) infection. We used three control and three infected Mrc1CreER;R26Tomato mice that were induced with tamoxifen 8 weeks prior.

first: Florens

last: Lohrmann

first: Vidmante

last: Fuchs

first: Lance

middle: F

last: Pahutan Bosch

first: Anne

last: Lösslein

first: Jana

last: Neuber

first: Zohreh

last: Mansoori Moghadam

first: Tiago

last: Martins

first: Sebastian

last: Baasch

first: Julia

last: Henschel

first: Mirjam

last: Freudenhammer

first: Marco

last: Prinz

first: Katrin

last: Kierdorf

last: Kolter

first: Daniel

last: Erny

first: Philipp

last: Henneke


title: Synergistic degradation of circRNAs by RNase K and lysosomes

city: Hefei

first: Ruikun

last: Wu

state: Anhui

address: No.443 Huangshan Road

institute: University of Science and Technology of China

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) are vital in many physiological and pathological events. Compared to the other processes of circRNA metabolism, circRNA degradation is less understood. Through screening and further characterization, RNAseK and lysosome are identified as circRNA degradation modules in metazoan, and RNase 1 as a lysosomal circRNA endoribonuclease in mammal. RNAseK and lysosome function synergistically with RNAseK degrading circRNAs outside and lysosome degrading those inside of the organelle. Mutations of RNAseK- or lysosome-sensitive sites in in vitro synthesized circRNA reporters lead to higher expression levels, and simultaneous mutations of both sensitive sites result in further increase. Under stress stimuli such as heat shock and ER stress, significantly decreased global circRNA levels are observed in C. elegans. RNAseK deficiency or lysosome inhibition diminishes the decreases in circRNA levels, and impedes the induction of stress response, suggesting that circRNA degradation by RNAseK and lysosome plays protective roles in C. elegans stress response.

sample_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus

overall_design: To investigate circRNA degradation factors, we set out to establish a circReporter system with genome-wide CRIPSR-Cas9 knockout screen. Then, we performed circRNA and mRNA profiles in HEK293T cells, HeLa cells, 3T3-L1 cells, N2a cells and C. elegans upon RNase K knockdown or lysosomal inhibition by CQ or BafA1 treatment. We also performed circRNA and/or mRNA profiles in HEK293T cells by manipulating lysosomal RNases levels. We futher performed RNAseq for C. elegans upon stress stimuli.

first: Yuqi

last: Deng

first: Yuyao

last: Luo


title: The function and mechanism of aldh3b1 in diabetic retinopathy

city: Mannheim

first: Xin

last: Qian

state: Baden-Wuerttemberg

address: Ludolf-Krehl-Str. 13-17

department: Vascular Biology&Tumor Angiogenesis

institute: Medical Faculty Mannheim, Heidelberg University

summary: Sphingosine-1-phosphate (S1P), a crucial sphingolipid mediator, plays a pivotal role in the pathogenesis of diabetic retinopathy (DR) by influencing angiogenesis, inflammation, photoreceptor apoptosis, neurodegeneration, and fibrosis through interaction with its five specific receptors (S1PRs). These receptors have been recognized as promising targets for therapeutic intervention in various diseases and several S1PR-targeted drugs are already in clinical use or trials. Despite extensive research into the role of S1P, the impact of its primary metabolic product, 2-hexadecenal (2-HD), remains unexplored. Recent studies have suggested ALDH3B1 as an enzyme in the detoxification of 2-HD. In this study, we established a CRISPR-mediated aldh3b1 knockout zebrafish to examine the in vivo effects of 2-HD accumulation. The absence of aldh3b1 led to elevated 2-HD levels, causing abnormal retinal vasculature in larval and adult zebrafish. Using transcriptomic and metabolomic analyses, we discovered that 2-HD accumulation and aldh3b1 deficiency triggered iron dysregulation and subsequent ferroptosis in both larval and adult zebrafish. Further examination revealed that 2-HD modulates ferroptosis by directly interacting with S1PR5. This finding is supported by integrative analyses of single-cell RNA sequencing and RNA sequencing from human retinal DR samples  , highlighting the therapeutic potential of targeting S1PR5. In summary, our findings not only elucidate a novel pathway involving 2-HD detoxification and its critical role in the retinal vasculature, but also propose targeting S1PR5 as an innovative therapeutic strategy in the treatment of DR.

overall_design: A CRISPR based knockout aldh3b1 was created in zebrafish. The development of the fish was analyzed, as well as organ specific glucose metabolism. Imaging studies of Retina, and trunk vasculature were conducted. RNA sequencing was performed on the larvae of aldh3b1+/+, aldh3b1-/- and 2-HD treated aldh3b1+/+  by BGI .


title: Identification of chromatin at the nuclear periphery in EMS lineage of early C. elegans embryos

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

summary: We performed DNA Adenine Methyltransferase Identification (DamID) to map the contacts between the genome and the nuclear lamina in the EMS lineage of early embryos. Dam::EMR-1 and GFP::Dam fusion proteins were expressed from single-copy transgenes inserted into an intergenic region on chromosome II. To induce a short burst of transcription of the transgenes, we used the med-1 promoter, which is active in the EMS cell of 4 cell-stage embryos and repressed in the descendants of EMS.

overall_design: Cell type-specific DamID in early C. elegans embryos to determine chromatin binding profiles of the nuclear envelope protein EMR-1.

first: Adrián

last: Fragoso-Luna

first: Fei

last: Xu

first: Susan

middle: E

last: Mango


title: IRE1α limits Golgi expansion during early stages of β-cell compensation [HG]

first: Samuel

last: Stephens

summary: Examine expression changes in mouse pancreatic islets in response to chronic exposure to elevated glucose

overall_design: Mouse pancreatic islets were cultured in RPMI media containing either 20 mM glucose (HG) or 7.5 mM glucose (LG) for 72 h (4 samples per condition). Samples were processed for bulk RNAseq


title: Analyze the transcriptional signature of kidney glomerular cells in male, female wild-type mice and in female mouse models of estrogen knockout

city: Firenze

first: Giulia

last: Carangelo

address: Viale Pieraccini 6

country: Italy

institute: University of Florence

summary: We found that RPC contributed to the sexual dimorphism of kidney disorders in an ERα-dependent manner. To study the mechanisms controlling these differences we characterized the transcriptional signature of glomeruli isolated from male, female wild type and female RPC ERα-knockout mice.

overall_design: Transcriptional signature of glomeruli isolated from male, female wild type and female RPC ERα-knockout mice.

first: Carolina

last: Conte

first: Benedetta

last: Mazzinghi

first: Paola

last: Romagnani


title: Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean. [ChIP-seq]

first: Hao

last: Tian

overall_design: The Ws82's leaf were collected after free-running treatment. All the plants were grown in Middle-day(12h Light and 12h Dark,24℃) for 14 days, and treat with constant light for 1 day. After free-running treatment, 3 individuals with consitstent growth rate and phenotype were used for an independent experiment.

first: Qichao

last: Lian

first: Hequan

last: Sun

first: Shuo

last: Liu

first: Liangyu


title: Effect of  Rimegepant treatment on gene expression  in the trigeminal ganglion of mice on the tumor-transplanted side.

first: mingtao

last: Chen

address: 180 Fenglin Road, Xuhui District, Shanghai

institute: Zhongshan Hospital, Fudan University

summary: The trigeminal nerve is primarily responsible for facial sensation and exhibits the highest expression of CGRP.  Here, we explored the impact of Rimegepant on the transcriptome of the trigeminal ganglion in mice and found that the transcription profiles changed significantly following treatment compared to the control group.  Following Rimegepant administration, we observed a significant downregulation of innate immune-related items within the trigeminal ganglia, as well as functional items directly associated with pain perception and calcium signaling pathways.The activation of  innated immune within the trigeminal ganglia is known to enhance nociceptive responses, which were also directly linked to the activation of calcium signaling pathways.  These results suggest that Rimegepant alleviates OSCC-related pain by mitigating the inflammatory condition within the trigeminal ganglion. We then categorized the genes enriched in these functional groups.  Genes that promote the proliferation and differentiation of innate immune cells, and those related to the expression of proinflammatory mediators, were significantly downregulated, while those associated with anti-inflammatory functions were significantly upregulated.  Additionally, genes from various chemokine receptor families and ion channel genes linked to neuronal activity were significantly downregulated.  Collectively, these results suggest that CGRP influences OSCC-related pain by modulating the innate immune status of the trigeminal nerve.

overall_design: To investigate the mechanism of Rimegepant on OSCC-related pain,  we established unilateral tongue orthotopic transplantation modelson BALB/c nude mice which were randomly divided into an experimental group and a control group (n=3 in each group). In the experimental group, Rimegepant was intraperitoneally injected every 24 h for 4 consecutive days, starting from the 5th day after tumor inoculation. The control group received an equal volume of physiological saline. After the final drug treatment, both groups of mice were euthanized, with the trigeminal ganglia on the side of the transplantation tumor carefully isolated.

first: Mingtao

first: Yibo

last: Guo

first: Yu

last: Zhang


title: MiRNA sequencing on plasma samples from pregnant women with different outcomes

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

summary: To explore differentially expressed miRNAs in maternal peripheral blood between term labor, term not in labor and preterm labor women

overall_design: The peripheral blood samples were stored in EDTA tubes, then were centrifuged in 1,600g for 10 minutes to remove blood cells. The supernatant was transferred to a new EP tube and was centrifuged at 16,000g for another 10 minutes to obtain the purified plasma, which was stored at -80 °C until analysis.

first: Yuanyuan

first: Lu

last: Gao


title: Cancer-associated synonymous mutations selectively target the p53 DNA damage response [ChIP-seq]

city: Umeå

first: Lixiao

state: Sverige

address: Medicinsk biovetenskap, M21, Försörjningsvägen 1

department: Department of Medical Biosciences

country: Sweden

institute: Umeå University

summary: Recent technical advances have facilitated studies on changes in mRNA structures in response to signaling pathways, but how mRNA structures relate to the function of the encoded protein remains poorly understood. Synonymous mutations (SMs) possess comparable oncogenic potential to missense mutations. Here we have taken advantage of two Cancer Associated SMs at codon 34 (CASM34) in the p53 mRNA to demonstrate the impact of the RNA structure on protein activity in response to DNA damage. In-cell RNA structural probing illustrates how CASM34s prevent DNA damage-induced p53 mRNA folding. Genome-wide transcriptomics show that CASM34 alters the expression of genes in the p53 DNA-damage response pathway. DNA ChIP-seq analysis reveals that p53 expressed from CASM34 has reduced promoter binding and reduced induction of p53 downstream target genes PUMA and 14-3-3-σ but not p21CDKN1A. These results demonstrate that CASM34s selectively target p53 activity towards downstream targets in the DNA damage response pathway by interfering with p53 mRNA folding.

overall_design: p53 ChIP-seq profiling between p53-WT and CASM34 mutant expressed in H1299 p53 null cells

first: Sivakumar

last: Vadivel Gnanasundram


title: Gene expression profile on a single-cell level of myeloid cells isolated from dura mater, from control mice, and mice infected with group B streptococci

first: Vitka

last: Gres

summary: Macrophages and monocytes in dura play a central role in CNS defence against bacteria. Here, we wanted to examine heterogeneity and expression profiles of different myeloid populations in control and streptocicci infected dura.

overall_design: Prior FACS, cells from individual control or infected mice were labelled using the 10X 3' CellPlex Kit Set A (PN-1000261) following manufacturer’s recommendations. CD45+CD11b+ cell population was sorted. In total, 5-6 individual animals per group were pooled after FACS. For controls, around 10 750 cells were sorted per mouse (64 500 cells in total), and for infected mice, in average 11 600 cells were sorted per mouse (46 400 cells in total).

first: Florens

last: Lohrman

first: Vidmante

last: Fuchs

first: Philipp

last: Henneke


title: Cabozantinib inhibits the growth of lenvatinib-resistant hepatoma cells restoring FTCD expression

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: The present study aims to determine whether cabozantinib can suppress tumor growth of lenvatinib-resistant HCC cell lines in vitro and in vivo. We established a lenvatinib-resistant Hep3B cell line (Hep3B-LR) and evaluated the inhibitory effect of cabozantinib on the growth of Hep3B-LR cells. Hep3B-LR exhibited approximately 20 times greater IC50 for lenvatinib than the wild type.Cabozantinib suppressed tumor growth of Hep3B-LR in vitro and in vivo.

first: Koji

last: Fujita

first: Mari

last: Yamada


title: Examination of the Functions and Mechanism of KCP in Mediating Paclitaxel Resistance in Cervical Squamous Carcinoma Cells

city: 北京

first: 何玥

middle: 玥

last: 何

address: 东城区骑河楼街17号

institute: 首都医科大学附属北京妇产医院

summary: To evaluate the mechanism of Kielin/chordin-like protein (KCP) in the resistance of cervical cancer cells to paclitaxel to provide a new target for the precise treatment of patients with cervical cancer resistant to paclitaxel.

overall_design: Using a whole human genome microarray, a total of 491 differentially expressed genes were identified in KCP knockout versus the NC SiHa cells. IPA-based bioinformatics analysis of upstream regulators showed that SPI1 was strongly activated and that SPI1 inhibited CCND1 and activated PML and CEBPA.

first: Yue

last: He

first: Jian-Qing

last: Xu

first: Jing-Jing

first: Zhen-You

first: Chen

last: Ji

first: Yang

first: Yun-Fan

first: Ming

first: Yu-Mei

last: Wu

first: Yan


title: Cytokine supplementation influences bovine embryo transcriptome during the preimplantation period

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

summary: The central goal of the following studies was to understand how FGF2, LIF, and IGF1, a cocktail called “FLI,” modulates embryo development and pregnancy outcomes in cattle. All embryos were produced in vitro with or without FLI supplementation at the beginning of culture. For each treatment, embryos were collected at the 4-6 cell, 9-16 cell, morula, or blastocyst stages and RNA was isolated and sequenced at a depth of 50 million reads per sample. In the FLI group, at the 9-16 cell stage, there were 7 upregulated and 6 downregulated differentially expressed genes (DEGs). Of those gene messages, ISG15 and USP18, mediators of interferon signaling were downregulated while message for MGLL, a gene involved in lipid regulation and the PI3K-ATK pathway was upregulated. At the morula stage, 1856 DEGs (580 upregulated in FLI) increased MAPK signaling, TGF-beta signaling, and Hippo signaling which all help regulate cell adhesion, lineage commitment, and growth regulation in the developing embryo. In FLI blastocyst stage embryo, 199 upregulated and 545 downregulated DEGs revealed an increase in processes associated with interferon gamma production and cell differentiation. Many of the downregulated DEGs are involved in MAPK signaling and WNT signaling pathways warranting further research of the fine regulation and interplay of these mechanisms. The addition of FLI at the beginning of culture initiates changes in the early embryo that are reflected during the entire preimplantation period. FLI modulates many of the regulatory pathways in the developing embryo to drive increased cell survival, cell integrity, and overall embryo development.

overall_design: Evaluation of FGF2, LIF, and IGF1 supplementation during bovine embryo culture on embryo development by transcriptomic analyses of in vitro produced bovine embryos treated with FGF2, LIF, and IGF1 and control

first: M

middle: S

first: Katy

last: McDonald

first: Randall

last: Prather


title: RNA-seq of ER+ PDX models treated with GDC-9545

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: We measured gene expression using RNA-sequencing for HCI-011 and HCI-003 PDX models with or without treatment of giredestrant (GDC-9545).

overall_design: Expression profiling by high throughput sequencing

first: Ciara

last: Metcalfe

first: Musa

last: Ahmed

first: Natalie

last: Fox


title: Transcriptome analysis of Rv0043c, Rv0165c, and Rv3060c deletion in Mycobacterium tuberculosis

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

summary: Using Total RNA sequencing, We report the effects of deleting either Rv0043c, Rv0165c, and Rv3060c on the transcriptome of M. tuberculosis. For RNA-seq experiments, mid-log phase cultures (OD600nm ~ 0.8) of H37Rv, ΔRv0043c, ΔRv0165c, and ΔRv3060c M. tuberculosis strains were harvested by centrifugation, washed twice with 1x PBS and lysed by bead beating in Trizol. Total RNA was extracted using Qiagen RNA isolation kit as per manufacturer’s instructions. The samples were shipped to AgriGenome Labs Private Limited for RNA-seq analysis.

overall_design: Mid-log phase cultures of H37Rv, and its mutants harbouring deletions in either Rv0043c, Rv0165c, or Rv3060c were used for RNA-Seq analysis. Experiment was performed with two biological replicates of each strain.

first: Saurabh

last: Chugh

first: Bhupinder

last: Singh

first: Raghavan

last: Varadarajan

first: Ramandeep


title: Arabidopsis thaliana accumulates DHEA after infection with phytopathogenic fungi - effects on plants and fungi

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

institute: Friedrich Schiller University Jena

summary: Progestogens and androgens have been found in many plants, but their physiological functions remain unclear. We here show that the dehydroepiandrosterone, a C19-steroid, accumulates during infection of A. thaliana with the pathogenic fungus A. brassicicola. Moreover, dehydroepiandrosterone inhibits growth of the A. brassicicola in an ergosterol-independent way. We hypothesize that this is caused by an infection-adapted metabolism of A. thaliana as part of stress-response.

overall_design:
Dehydroepiandrosterone was applied exogenously to analyze the effects of this androgen on development and gene expression of Arabidopsis thaliana. Moreover, we analyzed growth, sterol pattern and membrane-integrity of Alternaria brassicicola confronted with dehydroepiandrosterone.
Comparative gene expression profiling analysis using data obtained from RNA-seq of A. thaliana leaves under three different conditions.

first: Ceren

last: Oktay

first: Glendis

last: Shiko

first: Maximilian

last: Liebl

first: Felix

last: Feiste

first: Sarah

last: Mußbach

first: Karl

middle: L

last: Körber

first: Michael

last: Reichelt

first: Kilian

last: Ossetek

first: Christoph

last: Müller

first: Alexandra

middle: C

last: Furch

first: Jan

last: Klein


title: A generic drug combination synergizes as exercise enhancers to ameliorate various metabolically-related diseases

first: Shilin

last: Ma

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To confirm if the combination of A and B therapy is beneficial for metabolic disease, we fed genetically obese Lepob/Lepob mice with a high fat, high fructose, high cholesterol diet ad libitum, to establish liver steatosis and moderate fibrosis in a way that faithfully recapitulates key features of human metabolic disease. And we performed gene expression analysis on muscle and liver from metabolic disease mice after treatment. 24 hours after drug treatment, the quadriceps muscle significantly upregulating gene signatures for innervation (NGF signaling), mitochondrial fatty acid oxidation (FAO) and vascularization (VEGF signaling). In the liver there was an increase in liver development genes and an increase in mitochondrial genes 24 hours after drug treatment. After 40 days of treatment, the drug treatment increased insulin-PI3K-mTOR signaling and neuromuscular Slit-Robo signaling, while decreasing extracellular matrix collagen production and fatty acid metabolism in muscles. The drug treatment increased anti-inflammatory signatures while decreasing lipogenesis signaling in the live. Taken together, our data showed that the liver is reversing steatosis and inflammation, and the muscle increased muscle insulin signaling sensitivity and function in metabolic disease after the drug treatment.

overall_design: To explore whether the combination of A and B therapy improve metabolic disease, we injected metabolic disease mice with the drug continuously and analyzed gene expression in the muscle and liver of the mice after 24 hours of treatment and 40 days of treatment.

first: Shyh-Chang

last: Ng


title: RNA-seq of MCF-7 cells with ER or FOXA1 knockout and/or GDC-9545 treatment

first: Marc

last: Hafner

summary: We measured gene expression using RNA-sequencing for MCF-7 cells with and without CRISPR-Cas9-mediated knockout of ER or FOXA1, and in the presence of vehicle or giredestrant (GDC-9545) treatment. RNP is ribonucleoprotein. NTC is non-targeting control.

first: Ciara

last: Metcalfe

first: Musa

last: Ahmed

first: Jane

last: Guan

first: Natalie

last: Fox


title: MCF-7 RPMI ERa and FOXA1 ChIP-seq in GDC-9545 and GNE-858

summary: We performed ChIPseq for ER, FOXA1 and H3K27ac on MCF-7 cells treated with vehicle (DMSO), GDC-9545 or GNE-858. GNE-858 is a non-ER degrader (SERM) from the same chemical series as GDC-9545.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ERa, FOXA1 or histone modification H3K27ac in MCF-7 cells.


title: Autosomal dominant gain-of-function mutations in LCP1 cause syndromiceneutropenia and immunodeficiency-

city: Chongqing

first: Yunfei

last: An

address: No. 136, Zhongshan 2nd Road, Yuzhong District

institute: Children's Hospital of Chongqing Medical University

summary: To further evaluate the impact of LCP1 dysfunction on hematopoiesis, we performed single-cell RNA sequencing (scRNA-seq) for bone marrow cells from patients and two matched healthy controls. Total 39, 028 cells were included in the sequential analysis after quality control.

overall_design: Bone marrow cells were collected for 10X Chromium scRNA-seq.

first: Lang

last: Yu

first: Bo

last: Zhou

first: Xiaodong

last: Zhao


title: ChIP-seq of GATA3 in MCF-7 cells treated with GDC-9545 and GNE-858

summary: We performed ChIPseq for GATA3 on MCF-7 cells treated with vehicle (DMSO), GDC-9545 or GNE-858. GNE-858 is a non-ER degrader (SERM) from the same chemical series as GDC-9545.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for GATA3 in MCF-7 cells.


title: Performance of a Logistic Regression Model Using Paired miRNAs to Stratify Abnormal Mammograms for Benign Breast Lesions

first: Satoshi

last: Kondo

summary: We have generated EarlyGuard™, a novel logistic regression model using five paired miRNAs, to stratify subjects with abnormal mammograms who are proven benign, i.e., neither a breast cancer nor a pre-cancerous diagnosis, on a subsequent diagnostic biopsy at NPV of 96.9%. The classifier could be used as a “rule-out” test in the management of subjects with suspicious breast imaging findings who undergo subsequent biopsy of the breast and would have a diagnosis of neither breast cancer nor a pre-cancerous condition (e.g., ductal carcinoma in situ (DCIS)).

overall_design: We performed miRNA profiling on a prospectively collected serum specimen obtained from subjects who received abnormal mammograms or imaging results. The miRNA classifier, named EarlyGuard™, was developed using a subset of 174 subjects as a Training Set” comprising 34 subjects with a malignant biopsy result and 140 subjects with one or more benign breast lesions. The performance of the classifier was evaluated using a “Test Set” of the remaining 91 subjects comprising 24 subjects with a malignant biopsy result and 67 subjects with benign lesions.

first: Hideo

last: Akiyama

first: Lora

last: Barke

first: Therese

last: Bevers

first: Thomas

last: Soriano


title: RNA-seq of MCF-7 cells treated with GDC-9545 and GNE-858

summary: We measured gene expression using RNA-sequencing for MCF-7 cells treated with vehicle (DMSO), GDC-9545 or GNE-858. GNE-858 is a non-ER degrader (SERM) from the same chemical series as GDC-9545.


title: ATAC-seq of ER+ PDX model treated with GDC-9545

summary: We measured chromatin accessibility using ATAC-sequencing for HCI-011 PDX model and HCI-003 PDX model with or without treatment of giredestrant.

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) in HCI-011 and HCI-003 PDX model.

first: Xiaosai

last: Yao


title: MCF-7 cells and ER+ PDX model treated with GDC-9545

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

overall_design: Refer to individual Series


title: Ribosome profiling of dorsal root ganglia tissues from mice with metabolic neuropathy

first: Zachary

middle: T

last: Campbell

state: WI

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

summary: The reactive metabolite methylgloxal sensitizes nociceptive neurons through activation of the integrated stress response. To define how it alters the landscape of nascent protein synthesis, we applied riobosome profiling to the DRG in parallel with RNA-seq.

overall_design: Comparative gene expression analysis of RNA-seq and ribosome profiling data on mouse DRG tissues.

first: June

last: de La Peña

first: Rebecca

last: Chase


title: RNA-seq data for MCF-7 cells with ER knockdown or GDC-9545 treatment

first: Marc

last: Hafner

summary: We measured gene expression using RNA-sequencing for MCF-7 cells with and without knockdown of ER using siRNA, compared with giredestrant (GDC-9545) treatment. NTC refers to non-targeting control.

first: Ciara

last: Metcalfe


title: RNA sequencing of dorsal root ganglia tissues from mice with metabolic neuropathy


title: Tumour-associated high endothelial venules drive portal-specific immune evasion in lymph nodes via ALOX12 [III]

city: Guangzhou

first: Qidong

last: Xia

state: Guangdong

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: High-endothelial-venules (HEVs) offer another entry point for tumor metastasis in mice. To investigate whether HEVs and non-specialized blood vessels exert different effects on disseminating tumor cells, we enriched EO771 derivatives HEVM3 (preferentially metastasize through HEVs) cells and BVM3 (preferentially metastasize through blood vessels) cells. To explore how HEVs regulate immunogenicity of tumor cells, we compared the transcriptomes of BECs isolated from mammary blood vessels and HECs isolated from lymph nodes of mice inoculated with or without EO771-HEVM3 tumors. We demonstrated that ALOX12 specifically expressed in HEVs in LNs induces immune evasion of neighboring tumor cells by 12-HETE. To identify the factor(s) that upregulate ALOX12, we compared the mRNA transcriptomes between EO771-HEVM3 cells and EO771-BVM3 cells. To explore how 12-HETE promotes immune evasion of tumor cells, we performed total RNA-seq analysis in EO771 cells after 12-HETE treatment.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for EO771 with ADAR1 p150 overexpression or empty vector (appended data).
Comparative gene expression profiling analysis of total RNA-seq data for EO771 cells with vehicle or 12-HETE treatment (appended data for avoiding batch effects).

first: Xia

last: Qidong

first: Su

last: Shicheng


title: Uncovering the cellular heterogeneity and origin of neutrophils at the onset of acute graft-versus-host disease (GVHD) by single-cell RNA-seq

first: Guoju

last: You

state: Beijing

address: Shuangqing Road

institute: Tsinghua University

summary: Acute graft-versus-host disease (GVHD) is the main cause of morbidity and mortality after allo-HSCT, which is determined by interactions between innate and adaptive immune system. We used single cell RNA sequencing (scRNA-seq) to construct transcriptional profile of immune cells in peripheral blood from patients with or without acute GVHD.

overall_design: All patients enrolled were adult recipients who underwent haploidentical HSCT for acute leukemia and achieved stable engraftment. Peripheral blood was sampled from 4 patients at the time of the first flare-up episode of acute GVHD (Glucksberg grade II) without initiation of any treatment for GVHD (range: 20-31 days after transplantation). The non-GVHD controls (n = 2) were sampled at similar time point (28 days) after HSCT.The collected CD45+ pertpheral blood cells were ananlyzed using scRNA-seq.

first: Yandong

last: Gong

last: Peng


title: Cooperativity between H3-K27M and PDGFRA poses multiple therapeutic vulnerabilities in human iPSC-derived diffuse midline glioma avatars (RNA-Seq)

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

summary: PDGFRA and H3.3 mutations cooperate in an iPSC-based model of diffuse midline glioma to alter tumor biology.

overall_design: Cleavage Under Targets & Release Using Nuclease of iDMG tumor cells

first: Kasey

middle: R

last: Skinner

first: Tomoyuki

last: Koga

first: Shunichiro

last: Miki

first: Robert

last: Gruener

first: Florina-Nicoleta

last: Grigore

first: Emma

middle: H

last: Torii

first: Davis

middle: M

last: Seelig

first: Yuta

last: Suzuki

first: Daisuke

last: Kawauchi

first: Benjamin

last: Lin

first: Sriram

last: Venneti

first: Denise

last: Malicki

first: Clark

last: Chen

first: Etty

middle: N

last: Benveniste

first: Rakesh

middle: P

last: Patel

first: Braden

last: McFarland

first: R

last: Huang

first: Chris

last: Jones

first: Alan

last: Mackay

first: C

first: Frank

last: Furnari


title: Expression data changes induced by long-term 3D conditions in T-ALL cells

city: Madrid

first: Javier

last: Redondo-Muñoz

address: C/ Ramiro de Maeztu 9

institute: Centro de Investigaciones Biológicas Margarita Salas - CSIC

summary: Long-term 3D constrained conditions promoted changes in the biophysical properties of the nucleus and transcriptional changes related to cell cycle, apoptosis, DNA repair and cell migration.

overall_design: Control cells are Jurkat cells cultured in normal conditions in suspension in RPMI supplememented with 10% FBS at 37ºC 5% CO2. TR cells were obtained upon long-term 3D confinement. For this, Jurkat cells were embedded in a solution of 3.3 mg/mL of collagen type I from bovine in complete medium and neutralized with 7.5% NaHCO3 and 25 mM Hepes. After 1 hour polymerization at 37ºC, additional complete medium was added at the top of the 3D collagen matrix. Jurkat cells were maintained in the 3D matrix for 10 days and complete medium was changed every 3-4 days. Then, cells were collected from the collagen gel mechanically, the collagen fragments were filtered, and cells were cultured, expanded, and kept in culture conditions as TR. Cells were lysed and mRNA was isolated and hybridized on Affymetrix microarrays to compare expression profiles. We used 2 replicates of each sample.

first: Raquel

last: González-Novo

first: Héctor

last: Zamora-Carreras

first: Ana

last: de Lope-Planelles

first: Horacio

last: López-Menéndez

first: Pedro

last: Roda-Navarro

first: Francisco

last: Monroy

first: Lin

last: Wang

first: Christopher

last: Toseland


title: YlaN is an iron binding protein that is required to relieve Fur-mediated gene expression

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Iron (Fe) is an essential nutrient required by nearly all organisms. Due to the toxic nature of free-Fe, and the high demand forFe for metabolic processes, protein-based systems have evolved to tightly regulate the uptake of Fe and the usage of Fe. Fur is the master regular of Fe ion homeostasis in Staphylococcus aureus. We have discovered that YlaN works with Fur to regulate Fe uptake and central metabolism.

overall_design: 12 data sets in total. Three biological replicates for each strain (WT, fur) with and without 2,2-dipyridyl (WT, fur, WT + DIP, fur + DIP).

first: Jeffrey

last: Boyd

first: Karla

last: Esquilín-Lebrón

first: Courtney

last: Campbell

first: Javiera

last: Norambuena

first: Mary

last: Foley

first: Jisun

last: Kim

first: Timothy

last: Stephens

first: Gustavo

last: Rios

first: Vincent

last: Zheng

first: William

last: Beavers

first: Valerie

middle: J

last: Carabetta

first: Debashish

last: Bhattacharya

first: Eric

last: Skaar

first: Dane

last: Parker

middle: K

last: Stemmler


title: Targeting TRIM24 promotes neuroblastoma differentiation and decreases tumorigenicity via LSD1/CoREST complex

city: Shanghai

first: Haizhong

last: Feng

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

summary: High-risk neuroblastoma (NB) still has an unfavorable prognosis and inducing NB differentiation is a potential strategy for clinical treatment, yet underlying mechanisms are still elusive. Here we identify TRIM24 as an important regulator of NB differentiation. Trim24 was highly expressed in spontaneous NB in TH-MYCN transgenic mice and clinical NB specimens. And it was associated with poor NB differentiation and functioned as an unfavorable prognostic factor. Knockout of TRIM24 in MYCN-amplified neuroblastoma cells promoted cell differentiation and reduced cell stemness, cell colony formation in soft agar and subcutaneous xenograft tumor growth in nude mice. Mechanistic investigations demonstrated that TRIM24 knockout activated retinoic acid pathway and suppressed LSD1/CoREST complex formation and inhibited the transcription of genes involved in NB differentiation such as ZIC4. Targeting TRIM24 in combination with retinoic acid (RA) synergistically promoted NB cell differentiation and inhibited cell viability. Taken together, Our findings demonstrate that TRIM24 is critical for NB differentiation and suggest that TRIM24 is a promising therapeutic target in combination with RA in NB differentiation therapy.

overall_design: Gene expression profiling of in vitro control and TRIM24 knockout CHP-134 cells (in biological replicates).


title: Tumour-associated high endothelial venules drive portal-specific immune evasion in lymph nodes via ALOX12 [I]

first: Qidong

last: Xia

summary: High-endothelial-venules (HEVs) offer another entry point for tumor metastasis in mice. To investigate whether HEVs and non-specialized blood vessels exert different effects on disseminating tumor cells, we enriched EO771 derivatives HEVM3 (preferentially metastasize through HEVs) cells and BVM3 (preferentially metastasize through blood vessels) cells. To further explore the lymph node metastasis of breast tumor cells, we selected the primary tumors and paired lymph nodes from six C57BL/6J mice were analyzed with single-cell RNA sequencing.

overall_design: The primary tumors (EO771-HEVM3) and paired lymph nodes from six C57BL/6J mice were analysed with single-cell RNA sequencing.

first: Shicheng

last: Su


title: ATAC-seq of MCF-7 cells treated with GDC-9545 and GNE-858

first: Marc

last: Hafner

summary: We measured chromatin accessibility using ATAC-sequencing for MCF-7 cells treated with vehicle (DMSO), GDC-9545 or GNE-858. GNE-858 is a non-ER degrader (SERM) from the same chemical series as GDC-9545.

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) in MCF-7 cells

first: Ciara

last: Metcalfe

first: Musa

last: Ahmed

first: Jane

last: Guan

first: Natalie

last: Fox


title: Gene Regulation through the downregulation of H3K9ac induced by heat shock

first: Fang

last: Guo

address: 800 Dongchuan RD. Minhang District

summary: We investigated the effect of downregulation of H3K9ac induced by heat shock on gene expression in AGS cells, using RNA-seq analysis. We found that heat shock at 43°C resulted in the upregulation of 792 genes and the downregulation of 292 genes in AGS cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AGS cells treated with or without heat shock at 43°C for 1 h and subsequently upregulated by SAHA treatment

first: Huiyun

last: Lin

first: Yinrui

last: Lei


title: Critical role of Cathepsin L/V in regulating endothelial cell senescence

city: changsha

first: Chan

last: Li

state: Hunan

address: No 87 Xiangya road, Changsha, Hunan, China.

institute: Xiangya Hospital, Central South University

summary: To explore the role of Cathepsin L/V in regulating endothelial endothelial cell senescence.

overall_design: 400μM H2O2 was used to induce cellular senescence and adenovirus was applied to enhance the expression of CTSV in HUVECs.RNA-sequencng analysis was conducted to compare gene expressons in different groups

first: Zhaoya

last: Liu

first: Ruizheng

last: Shi

first: Hua

last: Zhong


title: Effects of disease risk on spleen and liver transcriptomic responses in domestic canaries - pilot study

city: Orange

first: Patricia

last: Lopes

address: 450 N Center St

institute: Chapman University

summary: The aim of this experiment was to gain knowledge on tissue-specific transcriptomic changes experienced by animals exposed to high disease risk

overall_design: Canaries either observed infected canaries (Mycoplasma gallisepticum conjunctiva infection) (MG_OBS) or control canaries (CONT) for 5-6 days and then tissue (liver = liver; spleen = spl) was collected. Tissue was also collected from MG-infected animals (MG) for comparison. Tissue was preserved in RNAlater.


title: Tumour-associated high endothelial venules drive portal-specific immune evasion in lymph nodes via ALOX12


title: Tumour-associated high endothelial venules drive portal-specific immune evasion in lymph nodes via ALOX12 [II]

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for blood vessel endothelial cells (BECs) isolated from mammary blood vessels and HECs isolated from lymph nodes of mice inoculated with or without tumors.
Comparative gene expression profiling analysis of total RNA-seq data for EO771 cells with vehicle or 12-HETE treatment.


title: Single cell transcriptome landscape of human hematopoietic stem and progenitor cells during postnatal development

city: Tianjin

first: xiaowei

last: xie

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

summary: We have constructed a transcriptional atlas of HSPCs during the temporal span of human postnatal development. Our work demonstrated the transcriptional changes in HSPCs from birth to the aging stage, part of which was further validated by in vitro functional assays.

overall_design:
Single cell RNAseq for BM-derived HSPCs from 8 healthy donors.
It could be combined with the samples from 3 healthy adults in GSE137864.


title: Candidate master microRNA regulator of arsenic-induced pancreatic beta cell impairment revealed by multi-omics analysis

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Arsenic is a pervasive environmental toxin that is ranked as the number one investigative priority by the Agency for Toxic Substance and Disease Registry. Chronic exposure to arsenic has been associated with type 2 diabetes (T2D). However, the underlying mechanisms remain largely unknown. We have recently demonstrated that arsenic treatment of INS-1 832/13 pancreatic beta-cells impairs glucose stimulated insulin secretion (GSIS), a hallmark of T2D. We have also shown that arsenic alters the microRNA (miRNA) profile in beta-cells more dramatically than other metals. miRNAs have a well-established regulatory role in both normal beta-cell function and T2D pathogenesis. We hypothesized that there are miRNA master regulators that mediate arsenic-associated GSIS defects. To test this hypothesis, we first treated INS-1 832/13 beta-cells with either 1 μM of inorganic arsenic (iAsIII) or 0.5 μM of monomethylarsenite (MAsIII) and confirmed that GSIS is significantly reduced.  We then performed multi-omic analysis using chromatin run-on sequencing (ChRO-seq), RNA-sequencing (RNA-seq), and small RNA-seq in order to define arsenic-associated chromatin and transcriptional activity, gene expression, and miRNA profiles, respectively. Integrating across these data sets we first showed that genes downregulated by iAsIII treatment are enriched in insulin secretion, T2D, and maturity onset diabetes of the young (MODY) pathways, whereas genes downregulated by MAsIII treatment are enriched in cell cycle and include genes that encode the critical beta cell maintenance factors Neurod1 and Rfx6. Secondly, we also identified those genes that are subject primarily to post-transcriptional regulation in response to arsenicals. Finally, we demonstrated that miR-29a is the top candidate master regulator of these genes. Our study is the first multi-omic analysis of beta cells after exposure to arsenicals, and the results strongly suggest that arsenicals lead to aberrant miR-29 expression and activity in beta-cells, which in turn leads to the repression of critical genes for beta-cell function, ultimately predisposing to diabetes.

overall_design: Multi-omic comparison of small RNAseq, RNAseq, and ChROseq data from Rattus norvegicus INS-1 832/13 cells following arsenic challege.

first: Matt

last: Kanke


title: Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_RNA-seq 2]

status: Public on Feb 28 2026

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: High aerobic glycolysis in retinal photoreceptors, as in cancer cells, is implicated in mitigating energy and metabolic demands. Lactate, a key product of glycolysis, is implicated in epigenetic regulation through histone lactylation in cancer. Here, we demonstrate that increased ATP production during retinal development is achieved primarily through augmented glycolysis. Histone lactylation, especially H3K18La, parallels enhanced glycolysis and its product, lactate, in developing retina and in retinal explants. Multi-omics analyses, combined with confocal imaging, reveal the localization of H3K18La near H3K27Ac in euchromatin at promoters of active retinal, especially photoreceptor, genes. H3K18La and gene expression also correspond to glucose metabolism in retinal explants. Evaluation of accessible chromatin at H3K18La promoters uncovers an enrichment of GC-rich motifs for transcription factors of SP, KMT and KLF families, among others, indicating specificity of H3K18La-mediated gene regulation. Our results highlight glycolysis/lactate/H3K18La as a regulatory axis in fine-tuning gene expression in developing and mature retina.

overall_design: Biologically replicated RNA-seq was performed on retinal explant cultures. The dissected retinas were incubated in Neurobasal-A media supplemented with 5 mM glucose with and without 20 mM 2-DG. Gene-level differential expression analysis was performed using RNA-seq data.

first: Mohita

last: Gaur

first: Xulong

last: Liang

first: Milton

last: English

first: Laura

last: Campello

first: Claire

last: Marchal

first: Anand

last: Swaroop


title: proliferation CRISPR screen from K562 (ENCSR398UPE)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Functional characterization experiment for CRISPRi/dCas9-RYBP sparse-tiling proliferation screens at ~7500 cCREs around ~450 essential genes in K562

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


title: PRO-cap from uterus (ENCSR399LAD)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Uterus.

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: Nanopore Direct RNA sequencing of mice hippocampal brain tissues

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

summary: Oxford Nanopore enables direct RNA sequencing allowing for base calling of RNA modifications. However, current direct RNA sequencing protocols may not be detecting some classes of non-coding RNAs such as SINE RNAs produced by Short Interspersed Nuclear Elements (SINEs). Using mouse hippocampi RNA samples, we have established a novel Nanopore direct RNA-seq protocol that in addition to long poly A selected RNAs allows sequencing also of non-poly A RNAs as well as short RNAs < 200nt (including SINE RNAs and other non poly A non coding RNAs). We provide here as a resource the first direct RNA-sequencing performed in mouse brain tissues that includes both mRNAs and non poly A or short non-coding RNAs such as SINEs.

overall_design: In this study, we employed a transgenic mouse model of amyloid pathology, APP NL−G−F (APP) (Saito et al., 2014) and the respective wild type control C57BL/6J (WT). We have tested mice at the stage of symptom manifestation (that coincides with the active neurodegeneration phase and appearance of amyloid plaques (6 months - 6m/ APP: 3x mice, WT:3x mice), The mice were then sequenced by Nanopore sequencing direct RNA SQK-RNA_002 protocol using the PromethION platform.

first: Luke

last: Saville

first: Yubo

last: Cheng

first: Liam

last: Mitchell

first: Travis

last: Haight


title: long read scRNA-seq from adrenal gland (ENCSR399GDY)

summary:
PacBio long-read B6/Cast F1 adrenal 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: CRISPR screen from K562 (ENCSR395WAX)

summary:
Control for CRISPR screen targeting candidate CREs

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: PRO-cap from breast epithelium (ENCSR393PGX)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Breast epithelium.

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


title: DNase-seq from HUDEP-2 (ENCSR391LFS)

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR387WVY)


title: DNase-seq from suppressor macrophage (ENCSR389MPM)


title: long read scRNA-seq from layer of hippocampus (ENCSR398ZEK)

summary:
ONT long-read B6/Cast F1 hippocampus P14 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: Flow-FISH CRISPR screen from K562 (ENCSR389DPQ)


title: Control CRISPR screen from HCT116 (ENCSR393DOW)

summary:
Growth-based CRISPR screen targeting genomic regions near MYC and MYB 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: proliferation CRISPR screen from K562 (ENCSR397CXJ)

summary:
Tiling, dCas9-VPR/CRISPRa proliferation screen at the GATA1, MYB, and ZMYND8 loci

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: Flow-FISH CRISPR screen from Jurkat (ENCSR390VJM)


title: Flow-FISH CRISPR screen from K562 (ENCSR394QIN)


title: PRO-cap from peripheral blood mononuclear cell (ENCSR386UFU)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PBMCs.

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 K562 (ENCSR398UMD)


title: DNase-seq from activated T-cell (ENCSR386VAP)


title: Flow-FISH CRISPR screen from K562 (ENCSR386RWO)


title: Flow-FISH CRISPR screen from K562 (ENCSR387DZX)


title: DNase-seq from stimulated activated naive CD4-positive, alpha-beta T cell (ENCSR384YHO)


title: DNase-seq from T-cell (ENCSR385UWL)


title: PRO-cap from subcutaneous adipose tissue (ENCSR386RDW)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Subcutaneous adipose tissue.

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR384XZK)


title: long read scRNA-seq from adrenal gland (ENCSR382FLX)

summary:
ONT long-read B6/Cast F1 adrenal P18-20mo 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: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR382DPL)


title: Flow-FISH CRISPR screen from K562 (ENCSR381LLB)


title: DNase-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR389VFA)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR381PYB)


title: Flow-FISH CRISPR screen from THP-1 (ENCSR381IXT)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR380XNG)


title: CRISPR screen from WTC11 (ENCSR380RDA)


title: PRO-cap from heart right ventricle (ENCSR380VKC)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Right ventricle of heart.

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


title: PRO-cap from peripheral blood mononuclear cell (ENCSR382HFH)


title: DNase-seq from Kasumi-1 (ENCSR599KVP)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR379LON)


title: DNase-seq from MCF-7 (ENCSR378FRD)


title: DNase-seq from globus pallidus (ENCSR599MFU)


title: DNase-seq from T47D (ENCSR378PVK)


title: DNase-seq from T47D (ENCSR377MBS)


title: PRO-cap from ascending aorta (ENCSR384HWB)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Ascending aorta.

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: long read scRNA-seq from layer of hippocampus (ENCSR596GDP)

summary:
ONT long-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: long read scRNA-seq from adrenal gland (ENCSR598DOS)

summary:
PacBio long-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: DNase-seq from suppressor macrophage (ENCSR377SES)


title: DNase-seq from liver (ENCSR597WUD)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR595VTN)


title: proliferation CRISPR screen from K562 (ENCSR377LWO)

summary:
Functional characterization experiment for CRISPRi/dCas9-KRAB-WSR7EEE sparse-tiling proliferation screens at ~7500 cCREs around ~450 essential genes in K562

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


title: DNase-seq from activated T-cell (ENCSR593TQV)


title: DNase-seq from immature natural killer cell (ENCSR375TBE)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR595BVP)


title: DNase-seq from suppressor macrophage (ENCSR593ZPX)


title: Flow-FISH CRISPR screen from K562 (ENCSR592ONV)


title: DNase-seq from CD14-positive monocyte (ENCSR376UDG)


title: DNase-seq from MCF-7 (ENCSR376GDE)


title: PRO-cap from cytotoxic T cell (ENCSR594WJV)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Cytotoxic T cells.

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 HCT116 (ENCSR374TMP)


title: Flow-FISH CRISPR screen from K562 (ENCSR592PMY)

summary:
MEF2C

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: PRO-cap from breast (ENCSR374RDU)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Breast mammary.

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: PRO-cap from pancreas (ENCSR374OGG)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Pancreas.

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


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR591ZIA)


title: DNase-seq from inflammatory macrophage (ENCSR372AMW)


title: DNase-seq from immature natural killer cell (ENCSR376VHG)


title: DNase-seq from suprapubic skin (ENCSR598JCD)


title: DNase-seq from A673 (ENCSR598EYT)


title: proliferation CRISPR screen from K562 (ENCSR371TIR)

summary:
Functional characterization experiment for tiling, dCas9-KRAB/CRISPRi proliferation screens at CTCF motifs in loop anchors

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 T47D (ENCSR589FJB)

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR375GZY)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR370SDS)


title: Control CRISPR screen from K562 (ENCSR591JER)


title: DNase-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR588SBG)


title: DNase-seq from OCI-M1 (ENCSR370KGA)


title: total RNA-seq from regulatory T cell (ENCSR586TYE)


title: Flow-FISH CRISPR screen from K562 (ENCSR368YJH)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR368MTT)


title: DNase-seq from HUDEP-2 (ENCSR586LND)


title: DNase-seq from HUDEP-2 (ENCSR583WHC)


title: STARR-seq from K562 (ENCSR585AGE)

summary:
Single human gDNA fragments and concatenated pairs of such fragments were tested for their enhancer activity with eSTARR-seq. The RNAs derived from the transfected plasmids were sequenced and reported here.

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 immature natural killer cell (ENCSR582EPN)


title: PRO-cap from pulmonary artery (ENCSR368ARY)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Pulmonary artery.

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


title: DNase-seq from K562 (ENCSR581WTK)


title: DNase-seq from GM12878 (ENCSR581CCT)


title: Flow-FISH CRISPR screen from K562 (ENCSR580OSP)


title: DNase-seq from T47D (ENCSR581GVV)


title: DNase-seq from T47D (ENCSR366ULU)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR581EVP)


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR580MXV)


title: Control CRISPR screen from glutamatergic neuron (ENCSR364KFC)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR579VQJ)


title: DNase-seq from CD14-positive monocyte (ENCSR364YDG)


title: Flow-FISH CRISPR screen from K562 (ENCSR580ZYW)

summary:
MYC

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 adrenal gland (ENCSR598YQI)


title: DNase-seq from HCT116 (ENCSR364TYN)


title: DNase-seq from NCI-H187 (ENCSR367TKT)


title: Flow-FISH CRISPR screen from K562 (ENCSR363OEF)


title: Flow-FISH CRISPR screen from K562 (ENCSR366AJP)


title: DNase-seq from activated T-cell (ENCSR364KAX)


title: Flow-FISH CRISPR screen from K562 (ENCSR579FRW)


title: DNase-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR578YFZ)


title: Flow-FISH CRISPR screen from K562 (ENCSR579DCX)


title: Control CRISPR screen from HepG2 (ENCSR362QSD)

summary:
Growth-based CRISPR screen targeting genomic regions near MYC and MYB 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: Flow-FISH CRISPR screen from K562 (ENCSR361FSA)


title: Flow-FISH CRISPR screen from K562 (ENCSR578WTE)


title: DNase-seq from K562 (ENCSR578GHZ)


title: long read scRNA-seq from adrenal gland (ENCSR578XKS)

summary:
ONT long-read B6/Cast F1 adrenal P2mo 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: DNase-seq from MCF-7 (ENCSR361BGH)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR360STF)


title: total RNA-seq from T-helper 2 cell (ENCSR578RIQ)


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR577OFX)


title: DNase-seq from heart left ventricle (ENCSR576PKO)


title: STARR-seq from activated T-helper 17 cell (ENCSR576KQE)


title: DNase-seq from K562 (ENCSR359UQN)


title: PRO-cap from H9 (ENCSR359PWL)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 ESCs.

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 K562 (ENCSR577KGS)


title: PRO-cap from ovary (ENCSR357VUN)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Ovary.

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 TF-1.CN5a.1 (ENCSR355NOR)


title: DNase-seq from T-cell (ENCSR359MGP)


title: Flow-FISH CRISPR screen from K562 (ENCSR575CFM)


title: long read scRNA-seq from layer of hippocampus (ENCSR355VSY)

summary:
PacBio long-read B6/Cast F1 hippocampus P14 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: PRO-cap from right lobe of liver (ENCSR575NNF)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Right lobe of liver.

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


title: DNase-seq from HUDEP-2 (ENCSR354TAL)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR574WTK)


title: DNase-seq from K562 (ENCSR574BOG)


title: PRO-cap from ovary (ENCSR574ZMF)


title: DNase-seq from COR-L47 (ENCSR574JNS)


title: proliferation CRISPR screen from K562 (ENCSR356RUW)

summary:
Tiling, dCas9-KRAB/CRISPRi proliferation screen at the GATA1, MYB, and ZMYND8 loci

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: PRO-cap from SP-49 (ENCSR353ZXW)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SP49.

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: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCSR575EOB)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Metastatic breast cancer to brain.

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 spleen (ENCSR573XQQ)


title: DNase-seq from astrocyte (ENCSR573XFU)


title: Flow-FISH CRISPR screen from K562 (ENCSR351NHK)


title: Flow-FISH CRISPR screen from K562 (ENCSR353ICQ)


title: total RNA-seq from T-cell (ENCSR351WPZ)


title: DNase-seq from MCF-7 (ENCSR349HVV)


title: DNase-seq from suppressor macrophage (ENCSR354GEV)


title: PRO-cap from spinal cord (ENCSR353JON)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Spinal cord.

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: Flow-FISH CRISPR screen from BJAB (ENCSR350ZIZ)


title: DNase-seq from MCF-7 (ENCSR348RBN)


title: DNase-seq from skin of body (ENCSR573VBJ)


title: DNase-seq from immature natural killer cell (ENCSR348QXB)


title: Control CRISPR screen from F123 (ENCSR572QYM)


title: Flow-FISH CRISPR screen from K562 (ENCSR571UMQ)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR348EZO)


title: DNase-seq from inflammatory macrophage (ENCSR570VVF)


title: DNase-seq from suppressor macrophage (ENCSR348JIL)


title: DNase-seq from NCI-H510A (ENCSR573PUI)


title: DNase-seq from DND-41 (ENCSR571RJW)


title: PRO-cap from mesothelial cell of epicardium (ENCSR571OAW)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived epicardium (mesothelium).

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: PRO-cap from upper lobe of left lung (ENCSR347PQY)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Upper lobe of left lung.

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


title: DNase-seq from MCF-7 (ENCSR567BOA)


title: Flow-FISH CRISPR screen from K562 (ENCSR346PHE)


title: Flow-FISH CRISPR screen from THP-1 (ENCSR568BYM)


title: DNase-seq from kidney (ENCSR346RPY)


title: DNase-seq from globus pallidus (ENCSR347RHJ)


title: DNase-seq from pancreas (ENCSR570RRZ)


title: DNase-seq from HUDEP-2 (ENCSR563VJZ)


title: DNase-seq from CD14-positive monocyte (ENCSR343TXL)


title: DNase-seq from inflammatory macrophage (ENCSR571EXD)


title: DNase-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCSR346KOV)


title: DNase-seq from SHP77 (ENCSR563NIX)


title: DNase-seq from activated T-cell (ENCSR345ZWI)


title: FACS CRISPR screen from glutamatergic neuron (ENCSR562YXE)


title: DNase-seq from MOLM-13 (ENCSR562UWH)


title: Flow-FISH CRISPR screen from THP-1 (ENCSR343INU)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR564RTW)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR346UXU)


title: DNase-seq from activated T-cell (ENCSR341ORA)


title: DNase-seq from ovary (ENCSR342NAG)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR344RFB)


title: PRO-cap from neuron (ENCSR342WAR)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PGP-1 derived excitatory cortical neurons.

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: Flow-FISH CRISPR screen from K562 (ENCSR340BXS)

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 liver (ENCSR339EMU)


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR562TLN)


title: PRO-cap from pancreas (ENCSR338WJS)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Pancreas.

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


title: DNase-seq from MCF-7 (ENCSR335KNZ)


title: Flow-FISH CRISPR screen from K562 (ENCSR338VCJ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR336MXG)


title: DNase-seq from activated T-helper 1 cell (ENCSR338QHF)


title: DNase-seq from SKNO-1 (ENCSR334ZQD)


title: Flow-FISH CRISPR screen from K562 (ENCSR558KQP)

summary:
FADS1

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: PRO-cap from OCI-LY7 (ENCSR335ZMZ)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in OCI-LY7.

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 stimulated activated CD4-positive, alpha-beta T cell (ENCSR561QYI)


title: DNase-seq from HUDEP-2 (ENCSR558CHH)


title: DNase-seq from HUDEP-2 (ENCSR336PZI)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR333NUA)


title: DNase-seq from K562 (ENCSR558GSX)


title: DNase-seq from NCI-H2029 (ENCSR556KKU)


title: PRO-cap from Colon Carcinoma Metastatic in the Lung (ENCSR331QXJ)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Metastatic colon cancer to lung.

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


title: proliferation CRISPR screen from HCT116 (ENCSR553VAO)


title: DNase-seq from DMS153 (ENCSR557WQO)


title: DNase-seq from NCI-H2141 (ENCSR329BVR)


title: PRO-cap from liver (ENCSR331UGM)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Liver.

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


title: total RNA-seq from T-helper 2 cell (ENCSR552NZO)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR327TKJ)


title: DNase-seq from T47D (ENCSR553FMA)


title: DNase-seq from brain (ENCSR328XHS)


title: FACS CRISPR screen from F123 (ENCSR552KGE)


title: proliferation CRISPR screen from MCF-7 (ENCSR325WCA)

summary:
Growth-based CRISPR screen targeting genomic regions near MYC and MYB 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: Control CRISPR screen from A549 (ENCSR330GSS)


title: Flow-FISH CRISPR screen from Jurkat (ENCSR556AXL)


title: DNase-seq from HUDEP-2 (ENCSR332OXB)


title: proliferation CRISPR screen from K562 (ENCSR325SMP)

summary:
Control for CRISPR screen targeting candidate CREs

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 HUDEP-2 (ENCSR325HYO)


title: DNase-seq from HUDEP-2 (ENCSR332BXV)


title: ATAC-seq from T-helper 2 cell (ENCSR550NOH)


title: DNase-seq from immature natural killer cell (ENCSR329BRN)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR556EKY)


title: DNase-seq from NCI-H524 (ENCSR549RDB)


title: DNase-seq from suppressor macrophage (ENCSR550BBN)


title: DNase-seq from MCF-7 (ENCSR324KKN)


title: PRO-cap from neural crest cell (ENCSR321WCE)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived neural crest cells.

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: Flow-FISH CRISPR screen from K562 (ENCSR323QFP)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR548GMZ)


title: Control CRISPR screen from K562 (ENCSR327XSO)


title: DNase-seq from activated B cell (ENCSR320ICS)


title: DNase-seq from suppressor macrophage (ENCSR551PUD)


title: Flow-FISH CRISPR screen from K562 (ENCSR551PUZ)


title: DNase-seq from DMS 273 (ENCSR319ZGQ)


title: DNase-seq from dendritic cell (ENCSR546QFM)


title: DNase-seq from stimulated activated naive CD4-positive, alpha-beta T cell (ENCSR326UAU)


title: DNase-seq from T-cell (ENCSR326GZS)


title: Flow-FISH CRISPR screen from K562 (ENCSR550ZDC)


title: Control CRISPR screen from PC-3 (ENCSR325SWE)


title: long read scRNA-seq from layer of hippocampus (ENCSR325RRB)

summary:
ONT long-read B6/Cast F1 hippocampus P14 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: DNase-seq from immature natural killer cell (ENCSR318IYF)


title: FACS CRISPR screen from WTC11 (ENCSR542MMN)


title: proliferation CRISPR screen from K562 (ENCSR546ILA)

summary:
Functional characterization experiment for CRISPRi/dCas9-RYBP sparse-tiling proliferation screens at ~7500 cCREs around ~450 essential genes in K562

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


title: Flow-FISH CRISPR screen from K562 (ENCSR550MSE)


title: PRO-cap from testis (ENCSR542IVL)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Testis.

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


title: proliferation CRISPR screen from K562 (ENCSR322MGX)

summary:
Functional characterization experiment for Cas9/CRISPR fine-mapping proliferation screens at hit and non-hit CTCF motifs in loop anchors (and their partner anchors) from the CTCF growth screen

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 MV-4-11 (ENCSR320VYP)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR541SYG)


title: Flow-FISH CRISPR screen from K562 (ENCSR317NSN)


title: DNase-seq from smooth muscle cell (ENCSR547XDW)


title: PRO-cap from stomach (ENCSR548GOG)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Stomach.

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


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR325CHP)


title: total RNA-seq from T-helper 1 cell (ENCSR314LMX)


title: DNase-seq from stimulated activated naive CD4-positive, alpha-beta T cell (ENCSR537SRE)


title: proliferation CRISPR screen from K562 (ENCSR546TAV)


title: DNase-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR316DUO)


title: STARR-seq from MCF-7 (ENCSR547SBZ)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR547RAS)


title: STARR-seq from A549 (ENCSR319VAS)


title: DNase-seq from SHP77 (ENCSR319KKN)


title: DNase-seq from MCF-7 (ENCSR545JUV)


title: DNase-seq from HUDEP-2 (ENCSR545JJM)


title: proliferation CRISPR screen from WTC11 (ENCSR536LLM)


title: DNase-seq from T47D (ENCSR312KEH)


title: Flow-FISH CRISPR screen from K562 (ENCSR545ODU)


title: Flow-FISH CRISPR screen from K562 (ENCSR538TGD)

summary:
ERP29

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: proliferation CRISPR screen from K562 (ENCSR536ZNM)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR535XEZ)


title: DNase-seq from CD14-positive monocyte (ENCSR539ZYY)


title: Control CRISPR screen from K562 (ENCSR311XHA)


title: DNase-seq from MCF-7 (ENCSR541KYJ)


title: DNase-seq from NCI-H1048 (ENCSR314EOY)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR315ASD)


title: STARR-seq from A549 (ENCSR543JLA)


title: DNase-seq from K562 (ENCSR308IDW)


title: DNase-seq from cortex of kidney (ENCSR534XJP)


title: Flow-FISH CRISPR screen from GM12878 (ENCSR307GDA)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR536XRT)


title: DNase-seq from NCI-H2227 (ENCSR307PHD)


title: DNase-seq from T-helper 17 cell (ENCSR306VGY)


title: DNase-seq from NCI-H187 (ENCSR534BJZ)


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR306NPY)


title: Flow-FISH CRISPR screen from K562 (ENCSR308OSK)


title: Flow-FISH CRISPR screen from THP-1 (ENCSR309IHO)


title: STARR-seq from A549 (ENCSR534WIF)


title: DNase-seq from NCI-H2081 (ENCSR528ZIM)


title: Control STARR-seq from K562 (ENCSR306NNT)

summary:
Human gDNA fragments were selected based on DHS data, GRO-cap data, and/or histone marks in K562 cells and tested for their enhancer activity with eSTARR-seq. The transfected plasmids (post-transfection DNA sample) were sequenced and reported here.

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: FACS CRISPR screen from F123 (ENCSR312ISP)


title: Flow-FISH CRISPR screen from K562 (ENCSR304WRC)


title: Flow-FISH CRISPR screen from K562 (ENCSR532DXP)


title: PRO-cap from testis (ENCSR305RPP)


title: DNase-seq from stimulated activated naive CD4-positive, alpha-beta T cell (ENCSR301LKN)


title: DNase-seq from NCI-H2171 (ENCSR301HWX)


title: Flow-FISH CRISPR screen from K562 (ENCSR529OEG)


title: DNase-seq from HUDEP-2 (ENCSR301NNN)


title: DNase-seq from activated B cell (ENCSR527ZIM)


title: Flow-FISH CRISPR screen from K562 (ENCSR306HNR)

summary:
LMO2

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: STARR-seq from activated T-helper 2 cell (ENCSR300TTB)

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: Flow-FISH CRISPR screen from K562 (ENCSR531LPK)

summary:
GATA1

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 heart left ventricle (ENCSR527TRA)


title: DNase-seq from lower lobe of right lung (ENCSR299WPC)


title: proliferation CRISPR screen from K562 (ENCSR303GYT)

summary:
Tiling, Cas9/CRISPRk proliferation screen at the GATA1, MYB, and ZMYND8 loci

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 hippocampal formation (ENCSR302MJR)


title: DNase-seq from T47D (ENCSR299EKI)


title: DNase-seq from globus pallidus (ENCSR527SDF)


title: DNase-seq from HUDEP-2 (ENCSR301INY)


title: Control CRISPR screen from F123 (ENCSR299NFV)


title: Flow-FISH CRISPR screen from K562 (ENCSR298NSD)


title: PRO-cap from helper T cell (ENCSR528FMA)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Helper T cells.

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 HUDEP-2 (ENCSR298FNY)


title: DNase-seq from MCF-7 (ENCSR300HSK)


title: PRO-cap from Metastatic Liver Carcinoma in the Adrenal Gland (ENCSR300AAD)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Metastatic liver cancer to adrenal gland.

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


title: DNase-seq from HUDEP-2 (ENCSR527GLS)


title: Flow-FISH CRISPR screen from K562 (ENCSR298MDI)


title: Flow-FISH CRISPR screen from K562 (ENCSR297DDV)


title: long read scRNA-seq from layer of hippocampus (ENCSR299OFL)

summary:
ONT long-read B6/Cast F1 hippocampus P36 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: Flow-FISH CRISPR screen from K562 (ENCSR527GMG)


title: PRO-cap from ureter (ENCSR526QVD)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Ureter.

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: PRO-cap from NALM6 (ENCSR526XOQ)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in NALM-6.

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR297CAE)


title: DNase-seq from activated T-cell (ENCSR524XMS)


title: DNase-seq from MCF-7 (ENCSR295EGN)


title: Flow-FISH CRISPR screen from K562 (ENCSR296ANQ)


title: PRO-cap from T-cell (ENCSR296XBI)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Pan T cells.

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 HUDEP-2 (ENCSR526ANP)


title: DNase-seq from K562 (ENCSR295RGD)


title: PRO-cap from left ventricle myocardium (ENCSR294JPW)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left ventricle myocardium inferior of heart.

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


title: long read scRNA-seq from layer of hippocampus (ENCSR297ZAZ)

summary:
ONT long-read B6/Cast F1 hippocampus 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: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR293UHG)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR521EVK)


title: DNase-seq from NCI-H1105 (ENCSR292COP)


title: PRO-cap from psoas muscle (ENCSR521BLL)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Psoas muscle.

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: PRO-cap from left common carotid artery plus branches (ENCSR296MTV)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left carotid artery.

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


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR518ZID)


title: DNase-seq from T47D (ENCSR523WVG)


title: proliferation CRISPR screen from K562 (ENCSR294JZL)

summary:
Functional characterization experiment for dCas9 tiling proliferation screens at a subset of cCREs around essential 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: DNase-seq from brain (ENCSR291STT)


title: DNase-seq from U-87 MG (ENCSR296NTM)


title: PRO-cap from HEK293 (ENCSR520PUD)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Embryonic kidney cell line.

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: Flow-FISH CRISPR screen from Jurkat (ENCSR524HYW)


title: DNase-seq from T47D (ENCSR518PDW)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR292ZPF)


title: Flow-FISH CRISPR screen from Jurkat (ENCSR290PZQ)


title: PRO-cap from heart left ventricle (ENCSR290MPW)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left ventricle of heart.

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


title: DNase-seq from DMS53 (ENCSR291OJV)


title: DNase-seq from inflammatory macrophage (ENCSR291PNO)


title: DNase-seq from MCF-7 (ENCSR289STI)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR290TTN)


title: DNase-seq from activated T-cell (ENCSR518DRJ)


title: DNase-seq from MCF-7 (ENCSR521YSA)


title: proliferation CRISPR screen from NCI-H460 (ENCSR515OUJ)

summary:
Growth-based CRISPR screen targeting genomic regions near MYC and MYB 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: DNase-seq from spleen (ENCSR517YHO)

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: Flow-FISH CRISPR screen from BJAB (ENCSR516ZEM)


title: DNase-seq from cerebellum (ENCSR288OXC)


title: total RNA-seq from T-cell (ENCSR515KJR)


title: Flow-FISH CRISPR screen from K562 (ENCSR516MPE)