title: Macrophage-based delivery of interleukin-10 alleviates atherosclerosis

first: MingYi

last: Wang

address: No.28 Fuxing Road, Haidian District,

institute: The First Medical Center of Chinese PLA General Hospital

summary: Background: Arteriosclerosis (AS) involves arterial inflammation. Using macrophage-based  drug delivery system, we aim to enhance local drug concentration, especially for short-lived anti-inflammatory molecules like interleukin-10. Our study intervenes in plaque progression by boosting IL-10 expression in macrophages lentiviral transfection and introducing these anti-inflammatory cells into Apoe-/- mice. Methods: We engineered RAW264.7 cells to overexpress IL-10 (referred to as IL-10M) using lentivirus vectors. Subsequent in vitro experiments were conducted to validate the effects and cellular functions of IL-10M. Fluorescence imaging allowed us to track the localization of IL-10M at atherosclerotic plaque sites after intravenous (IV) injection in Apoe-/- mice. We administered periodic injections of IL-10M at different stages of plaque progression in AS mice to assess its therapeutic impact on plaque advancement. Following the intervention, we collected samples from major organs and serum to evaluate the safety of IL-10M treatment. Results:  Our engineered IL-10M exhibits robust IL-10 secretion, maintaining macrophage phagocytic function, and showing a tendency toward an M2 phenotype when exposed to inflammatory stimuli. Upon intravenous IL-10M administration, fluorescence imaging highlights precise plaque localization in both global and cross-sectional aortic regions. Regardless of whether intervention is initiated early or late in plaque progression, we observe significant reductions in plaque area and necrotic core. Importantly, IL-10M intervention does not impact the histological characteristics of the heart, liver, spleen, lungs, and kidneys, nor does it influence systemic inflammation levels. Conclusion: Our team has devised a novel anti-inflammatory protein delivery system utilizing modified macrophages, which exhibit a remarkable ability to target atherosclerotic plaques, resulting in the reduction of both plaque area and necrotic core. This innovative approach demonstrates favorable safety profiles and holds significant potential as a therapeutic strategy for managing atherosclerosis.

overall_design: To investigate the effect of lentiviral transfection of Il-10 RNA into macrophages,we performed comparative gene expression profiling analysis using data obtained from RNA-seq of macrophages treated differently(IL-10M vs ConM; IL-10M with LPS stimulation vs ConM with LPS stimulation; IL-10M with oxLDL stimulation vs ConM with oxLDL stimulation).

first: Ming-Yi

first: Shan-Shan

last: Zhou

first: Ying-Yun

last: Hu

first: Wei

last: Tong

first: Hao

first: Xing-Xuan

last: Cai

first: Ming-Rui

last: MA

first: Zheng-Bin

last: Zhang

first: Luo

first: Yun-Dai

last: Chen


title: Transcriptomics of LoVo cells exposed to DCC-2036.

status: Public on Jan 15 2025

city: Hengyang

first: Xiguang

state: Hunan

address: #28 Changsheng Road

country: China

institute: University of South China

type: Expression profiling by high throughput sequencing

summary: To investigate the mechanisms mediating the inhibitory effects of DCC-2036 on LoVo,  gene expression profiling analysis using data obtained from RNA-seq of LoVo cells treated with/without DCC-2036.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LoVo cells treated with/without DCC-2036.

first: Xuyu

last: Zu

first: Jianghua

last: Liu

first: Yingying

last: Shen


title: mTOR pathway inhibition attenuates hypercapnia-induced autophagy arrest and dysfunctional myogenesis

city: Albany

first: Ariel

last: Jaitovich

email: balnisj@amc.edu, jaitova@amc.edu

state: NY

address: 47 New Scotland Ave.

department: MCP

country: USA

institute: Albany Medical College

summary: Hypercapnia exposure in mice leads to reduced skeletal muscle repair capacity and myogenic potential. Autophagy is also reduced in this context. Satellite cells from mice treated with hypercapnia were isolated and compared to satellite cells from normocapnia control mice. Cells were isolated by FACS using Pax7-GFP tamoxifen inducible reporter to ensure enrichment of Pax7 cells.

overall_design: Differential expression of genes (mRNA) isolated from muscle satellite cells between normocapnia (NC) and hypercapnia (HC) mice.

first: Joseph

last: Balnis


title: Human helicase RECQL5-Flag ChIP DNA from Saccharomyces cerevisiae strain W303-1AR5, asynchronous culture

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

type: Genome binding/occupancy profiling by genome tiling array

summary: We expressed human RECQL5 in the yeast model Sacharomyces cerevisiae. Being RECQL5 the only member of the family shown to interact with the RNA polymerase II we explored the recruitment of RECQL5 to chromatin. Data reveal a genome wide recruitment of RECQL5 at actively transcribed regions that increases toward the 3’ end of the gene.

overall_design: ChIP-chip studies were performed with antibodies against Flag-tagged RECQL5 protein in yeast wild-type cells expressing human RECQL5

first: Juan

last: Lafuente-Barquero

first: Jesper

middle: Q

last: Svejstrup

first: Rosa

last: Luna

first: Andres


title: scRNAseq Data Analysis Code Muscle Inflammation is Regulated by NF-kB From Multiple Cells to Control Distinct States of Wasting in Cancer Cachexia

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: Although cancer cachexia is classically characterized as a systemic inflammatory disorder, emerging evidence indicates that weight loss also associates with local tissue inflammation. We queried the regulation of this inflammation and its causality to cachexia by exploring skeletal muscle, whose atrophy strongly associates with poor outcome. Using multiple mouse models and patient samples, we show that cachectic muscle is marked by enhanced innate immunity. NF-kB activity in multiple cells, including satellite cells, myofibers, and fibro-adipogenic progenitors, promotes macrophage expansion derived equally from infiltrating monocytes and resident tissue. Moreover, NF-kB activated cells and macrophages undergo crosstalk: whereas NF-kB+ cells recruit macrophages to inhibit regeneration and promote atrophy, while interestingly also protecting myofibers, macrophages stimulate NF-kB+ cells in a feed forward loop to sustain inflammation. Together, we propose that NF-kB functions in multiple cells in the muscle microenvironment to stimulate macrophage inflammation that both promotes and protects against muscle wasting in cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scRNA sequencing was done for 3 datasets, one from Human Pancreatic ductal adenocarcinoma (PDAC) and other two from cachexia in mice induced by C26 colon cancer cells and cachexia in KPP mice(KrasLSL-G12D/+, Ptenf/f, Ptf1aER-Cre/+).For the human  dataset Muscles from human samples were taken at time of pancreatic tumor resection, or time of other abdominal surgery for control patients. Muscle were digested in an enzymatic buffer and CD45 negative and positive cells were separated by MACs beads. Both fractions were sent for single cell RNA sequencing. Samples include CD45-/CD45+ Weight Stable PDAC(Neg_WS_PDAC,Pos_WS_PDAC),CD45-/CD45+ Control(Neg_Control,Pos_Control) and CD45-/CD45+ Cachetic PDAC(Neg_C_PDAC, Pos_C_PDAC). For cachexia in mice we induced  cancer by injecting the C-26 colon cancer cells subcutaneously in CD2F1 mice. At endpoint, hindlimb muscle was extracted and enzymatically digested. MACs beads were used to sort CD45 positive and negative fractions for single cell sequencing.Samples include CD45-/+ Control and CD45-/+ C26 cachexia from two batches(S1 and S2). For cachexia in KPP mice tamoxifen was injected for 5 days to induce pancreatic tumor formation. Mice were euthanized after tumor formation and cachexia development.MACs beads were used to sort CD45 positive and negative fractions for single cell sequencing. Samples include CD45-/+ Control and CD45-/+ Kpp cachexia.

first: Suganya

last: Subramanian

first: Benjamin

last: Pryce

first: Denis

last: Guttridge


title: Extrinsic induction of apoptosis and tumor suppression via the p53-Reprimo-Hippo-YAP/TAZ-p73 pathway

status: Public on Jan 14 2025

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: Tumor progression is suppressed by inherent cellular mechanisms such as apoptosis.  The p53 tumor suppressor gene is the most commonly mutated gene in human cancer and plays a pivotal role in tumor suppression.  RPRM is a target gene of p53 known to be involved in tumor suppression, but its molecular function has remained elusive.  Here we report that Reprimo (the protein product of RPRM) is secreted and extrinsically induces apoptosis in recipient cells.  We identified FAT1, FAT4, CELSR1, CELSR2, and CELSR3, members of the protocadherin family, as receptors for Reprimo.  Subsequent analyses revealed that Reprimo acts upstream of the Hippo-YAP/TAZ-p73 axis and induces apoptosis by transactivating various pro-apoptotic genes.  In vivo analyses further support the tumor suppressive effects of secreted Reprimo.  These findings identify the p53-Reprimo-Hippo-YAP/TAZ-p73 axis as a novel extrinsic apoptosis pathway that plays a crucial role in tumor suppression.  Our discovery of the innate tumor eliminator Reprimo and the downstream pathway offers a new promising avenue for the pharmacological treatment of cancer.

overall_design: RNA-seq profiling of HeLa or H1299 cells treated with or without recombinant Reprimo protein at 0.5 ug/ml for 8 or 32 hours.

first: Masahiro

last: Takikawa

first: Atsushi

last: Okabe


title: Accurate Identification of Sites of Origin in Carcinoma of Unknown Primary (CUP) Tumors Using DNA Methylation I

city: Chicago

first: Drew

last: Duckett

state: IL

address: 541 N Fairbanks Ct, 8th Floor

department: Pathology

institute: Northwestern Medicine

summary: 53 tumors used in the clinical training and validation of a CUP machine learning classifier using methylation profiling

overall_design: methylation by array

first: Erica

middle: R

last: Vormittag-Nocito

first: Pouya

last: Jamshidi

first: Madina

last: Sukhanova

first: Stephanie

last: Parker

first: Daniel

middle: J

last: Brat

first: Lawrence

last: Jennings

first: Lucas

last: Santana-Santos


title: The effect of different concentrations of ruminal VFAs on the circadian rhythm of gene expression in ovine ruminal epithelial cells using RNA-seq

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

summary: This experiment aimed to investigate the effect of different concentrations of ruminal VFAs on the circadian rhythm of gene expression in ORECs of Grain-diet and Hay-diet groups. The ORECs treated with  Grain-VFAs and Hay-VFAs were collected at six different timepoints (T0, T4, T8, T12, T16, and T20) for the circadian rhythm analysis using RNA sequencing.

overall_design: In Grain-diet group, 71.1 mM acetate (AA, prepared with sodium acetate, 241245, Sigma-Aldrich, St. Louis, MO), 20.1 mM propionate (PA, prepared with sodium propionate, P1880, Sigma-Aldrich), 16.0 mM butyrate (BA, prepared with sodium butyrate, 303410, Sigma-Aldrich), 1.7 mM valerate (VA, 75054, Sigma-Aldrich), 1.1 mM isobutyrate (IBA, I1754, Sigma-Aldrich), and 5.3 mM isovalerate (IVA, 129542, Sigma-Aldrich) were added into the culture medium (Grain-VFAs culture medium, GVCM); in Hay-diet group, 60.8 mM AA, 14.6 mM PA, 9.2 mM BA, 1.2 mM VA, 1.0 mM IBA, and 3.0 mM IVA were added into the culture medium (Hay-VFAs culture medium, HVCM) . The total VFAs concentration in the GVCM was 115.78 mM, while the total VFAs concentration in the HCM was 89.79 mM. After preparation, the pH value of the culture medium was adjusted to 7.2 using 7.5% NaHCO₃ solution (C0220, Beyotime). Cells were cultured in 6-well plates, when the cells were reached at 70% density, the culture medium was changed to DMEM/F12 containing 100 nM dexamethasone (DEX) and 1% penicillin-streptomycin solution without FBS (Synchronous culture medium, SCM) . The cells were synchronized to the initial circadian rhythm state after incubation with SCM for 2 hours, and then the cells were treatment with GVCM and HVCM for 24 hours. Cells in the Grain-diet and Hay-diet groups were then harvest at 4-hour interval at 24h (T0), 28h (T4), 32h (T8), 36h (T12), 40h (T16), and 44h (T20), each timepoint had 3 replicates per treatment.


title: Type I interferon limits ILC2 effector functions through suppression of the CCR8-CCL1/CCL8 axis

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

summary: Group 2 innate lymphoid cells (ILC2s) exert critical roles in anti-helminth immunity and  the pathogenesis of allergic diseases by rapidly secreting vast amounts of type 2  signature cytokines. Type 1 interferons (IFN-I) are critical negative regulators of ILC2  effector functions and associated innate and adaptive type 2 immunopathologies.  Exposure to IFN-I inhibits ILC2 proliferation as well as type 2 cytokine production,  however, the mechanistic underpinnings of IFN-I-mediated ILC2 regulation remain largely  elusive. Using RNA-sequencing analysis, we demonstrate that IFN-I treatment inhibits  the production of the chemokine CCL1 by ILC2s. Moreover, expression of CCR8, the  cognate chemokine receptor for CCL1, is downregulated upon IFN-I-stimulation ex vivo  as well as in vivo upon sublethal influenza A virus infection (IAV) or upon IFN-I administration following pulmonary IL-33 challenge. In addition, expression of CCL8, the chemotactic ligand of CCR8, was suppressed in an IFN-I dependent manner in the lungs of IAV-infected mice. IFN-b potently restrained pulmonary CCL1/CCL8 expression as well as CCR8 expression by ILC2 and CD4+ T cells in a model of IL-33-driven allergic airway inflammation. Thus, this study sheds new light on the underlying mechanisms of ILC2 regulation by identifying the CCR8-CCL1/CCL8 axis as a target for IFN-I-driven ILC2 inhibition.

overall_design: Murine lun ILC2 were isolated and stimulated or not for 4h or 24h with rmIL33 and/or IFNb. The transcriptional response was analyzed by RNA sequencing.

first: Jorg

middle: H

last: Fritz

first: Barbara

middle: C

last: Mindt

first: Claudia

middle: U

last: Duerr


title: snATAC-seq from transverse colon (ENCSR997YNO)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
snATAC-seq of human colon transverse

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


title: snATAC-seq from forebrain (ENCSR997YJI)

summary:
snATAC-seq of mouse forebrain

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


title: snRNA-seq from layer of hippocampus (ENCSR995ZKH)

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: snRNA-seq from heart left ventricle (ENCSR991LHO)


title: snRNA-seq from heart left ventricle (ENCSR994VEG)


title: snRNA-seq from adrenal gland (ENCSR988AMY)


title: snRNA-seq from heart left ventricle (ENCSR980OCK)


title: snRNA-seq from layer of hippocampus (ENCSR987SOK)


title: DNA affinity purification sequencing of ClNAC56 and genomic DNA

city: Beijing

first: Jinfang

last: Wang

address: No.50 Zhanghua Road, Haidian District

institute: Beijing Academy of Agricultural and Forestry Sciences

summary: DAPseq was performed to confirm the target genes of ClNAC56. DAP-seq results showed that there were 3646 peaks (p<0.05) identified and among these peaks, 45.4% peaks identified in 5’UTR region, 12% peaks identified in genomic DNA region, 39.2% peaks in distal intergenic and 3.4% in downstream. The top motifs for ClNAC56 binding was confirmed as ‘(A/G)(G/A)(T/A)(T/G)(A/G/C)CGT(G/A)(T/C/A)’ which showed high similarity to ANACs in Arabidopisis.

overall_design: Examination of the binding motif and the target genes of ClNAC56

first: Wang

last: Jinfang

first: Yu

last: Yongtao

first: Xu

last: Yong


title: snRNA-seq from left lung (ENCSR966DDY)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR816NWE).

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


title: snRNA-seq from layer of hippocampus (ENCSR968RPR)


title: snRNA-seq from heart left ventricle (ENCSR962JKS)


title: snRNA-seq from layer of hippocampus (ENCSR944XPC)


title: snRNA-seq from ureter (ENCSR964JZN)


title: Expression data from Saccharomyces cerevisiae strains expressing human RECQL5 helicase

first: Andrés

last: Aguilera

summary: We expressed human RECQL5 in the model organism Sacharomyces cerevisiae. We found that RECQL5 overexpression in yeast leads to cell growth inhibition and increased genotoxic sensitivity.  We carried-out transcriptome analysis of yeast strains overexpressing human RECQL5 helicase to explore its impact on gene expression.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: S. cerevisiae strains transformed with a plasmid carrying a tetp-RECQL5 construct were grown in selective minimal medium. Total RNA was isolated from exponential cultures and hybridized on Affymetrix microarrays.

first: Juan

last: Lafuente-Barquero

first: Jesper

last: Svejstrup

first: Rosa

last: Luna


title: snATAC-seq from upper lobe of left lung (ENCSR952HMV)

summary:
snATAC-seq of human 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: snRNA-seq from right cardiac atrium (ENCSR943HBF)


title: Transcriptomes of WT and clnor mutant lines during watermelon fruit development and ripening

summary: Analysis of gene expression level. The hypothesis tested in the present study is that ClNOR positively regulates watermelon fruit development and ripening.

overall_design: mRNA profiles of  wild type (WT) and clnor mutant fruits at 10 DAP,18 DAP,26 DAP, 34 DAP and 42 DAP were generated by deep sequencing, in triplicate, using Illumina Novaseq 6000 (Citrullus lanalus).

first: Yong

last: Xu


title: snRNA-seq from ovary (ENCSR938CZJ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR197GLE).

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


title: dsDAP: an efficient method for high-abundance DNA-encoded library construction in mammalian cells

city: Tianjin

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

summary: DNA-encoded libraries are invaluable tools for high-throughput screening and functional genomics studies. However, constructing high-abundance libraries in mammalian cells remains challenging. Here, we present dsDNA-assembly-PCR (dsDAP), a novel Gibson-assembly-PCR strategy for creating DNA-encoded libraries, offering improved flexibility and efficiency over previous methods. We demonstrated this approach by investigating the impact of translation initiation sequences (TIS) on protein expression in HEK293T cells. Both CRISPR-Cas9 and piggyBac systems were employed for genomic integration, allowing comparison of different integration methods. Our results confirmed the importance of specific nucleotides in the TIS region, particularly the preference for adenine at the -3 position in high-expression sequences. We also explored the effects of library dilution on genotype-phenotype correlations. This Gibson-assembly-PCR strategy overcomes limitations of existing methods, such as restriction enzyme dependencies, and provides a versatile tool for constructing high-abundance libraries in mammalian cells. Our approach has broad applications in functional genomics, drug discovery, and the study of gene regulation.

overall_design: We developed a novel DNA-encoded library construction strategy named dsDNA-assembly-PCR (dsDAP). This dsDNA-based method utilizes Gibson assembly for library construction, eliminating the need for restriction endonucleases. As a result, the library preparation process becomes more straightforward and feasible compared to the in-vitro-ligation-PCR strategy. By stably integrating the dsDAP library into the HEK293T cell genome through the CRISPR-Cas9 and piggyBac systems, we investigated the impact of translation initiation sequences (TISs) on translation efficiency.


title: snATAC-seq from thyroid gland (ENCSR909OXO)

summary:
snATAC-seq of human thyroid

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


title: snRNA-seq from adrenal gland (ENCSR908CQZ)


title: snRNA-seq from heart left ventricle (ENCSR919ENI)


title: snATAC-seq from body of pancreas (ENCSR893WOE)

summary:
snATAC-seq of human body of pancreas

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


title: snRNA-seq from heart left ventricle (ENCSR899GYX)


title: snATAC-seq from body of pancreas (ENCSR979ZOG)


title: snATAC-seq from forebrain (ENCSR978IKJ)


title: scRNA-seq from forelimb (ENCSR874BOF)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 10.5 day embryonic mouse forelimb

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


title: snRNA-seq from heart left ventricle (ENCSR851JBE)


title: snATAC-seq from esophagus muscularis mucosa (ENCSR871CTA)

summary:
snATAC-seq of human esophagus muscularis mucosa

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


title: snATAC-seq from stomach (ENCSR940QRM)

summary:
snATAC-seq of human stomach

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


title: snATAC-seq from breast epithelium (ENCSR845QFX)

summary:
snATAC-seq of human breast epithelium

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


title: snRNA-seq from gastrocnemius (ENCSR835ZXV)


title: snRNA-seq from liver (ENCSR955TRT)


title: snATAC-seq from thyroid gland (ENCSR817VFO)


title: snATAC-seq from thoracic aorta (ENCSR822GXQ)

summary:
snATAC-seq of human thoracic 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: snATAC-seq from forebrain (ENCSR937PSF)


title: snRNA-seq from heart left ventricle (ENCSR906MRL)


title: snATAC-seq from ascending aorta (ENCSR808WCV)

summary:
snATAC-seq of human 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: snRNA-seq from liver (ENCSR807BYQ)


title: snRNA-seq from heart left ventricle (ENCSR801DHT)


title: scRNA-seq from forelimb (ENCSR792LNZ)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 14.0 day embryonic mouse forelimb

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


title: snRNA-seq from placenta (ENCSR789PLK)

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: snRNA-seq from ovary (ENCSR876EUH)


title: snATAC-seq from gastroesophageal sphincter (ENCSR868ZEI)

summary:
snATAC-seq of human gastroesophageal sphincter

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


title: snRNA-seq from heart left ventricle (ENCSR788SNY)


title: snATAC-seq from stomach (ENCSR848EID)


title: snRNA-seq from heart left ventricle (ENCSR777RUZ)


title: scRNA-seq from forelimb stylopod (ENCSR847RRR)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 15.0 day embryonic mouse proximal forelimb

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


title: snATAC-seq from forebrain (ENCSR836VNN)

summary:
snATAC-seq of mouse forebrain

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


title: snRNA-seq from layer of hippocampus (ENCSR835JFN)


title: snATAC-seq from gastrocnemius medialis (ENCSR819EGE)

summary:
snATAC-seq of human gastrocnemius medialis

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


title: snRNA-seq from bile duct (ENCSR769KWM)


title: snATAC-seq from right atrium auricular region (ENCSR776EOI)

summary:
snATAC-seq of human right atrium auricular region

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


title: snRNA-seq from uterus (ENCSR762LZV)


title: snRNA-seq from heart left ventricle (ENCSR762LML)


title: snRNA-seq from Right ventricle myocardium superior (ENCSR813PWQ)

summary:
snRNA on human right ventricle myocardium superior. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR548IRG)

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


title: snRNA-seq from lower lobe of left lung (ENCSR753YPW)


title: snRNA-seq from heart left ventricle (ENCSR755CIF)

summary:
snRNA on left heart ventricle. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR918VTH).

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


title: snRNA-seq from heart left ventricle (ENCSR814LMX)


title: snRNA-seq from heart left ventricle (ENCSR751BHQ)


title: snRNA-seq from adrenal gland (ENCSR749GDE)


title: snATAC-seq from forebrain (ENCSR750EXW)


title: snATAC-seq from thyroid gland (ENCSR796RXX)

summary:
snATAC-seq of human thyroid

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


title: snRNA-seq from layer of hippocampus (ENCSR742NWO)


title: scRNA-seq from forelimb (ENCSR787QXE)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (version 2 kit) that was sequenced in PE151 format. They are from monocellular suspensions of 8,000 dispersed embryonic limb buds.

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


title: snATAC-seq from lower leg skin (ENCSR733SZL)

summary:
snATAC-seq of human lower leg skin

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


title: snRNA-seq from heart left ventricle (ENCSR727OYO)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR785BSP).

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


title: snATAC-seq from tibial nerve (ENCSR726QTF)

summary:
snATAC-seq of human tibial nerve

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


title: snRNA-seq from left cerebral cortex (ENCSR720TUP)


title: snATAC-seq from upper lobe of left lung (ENCSR718WGE)

summary:
snATAC-seq of human 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: snRNA-seq from adrenal gland (ENCSR726IPC)

summary:
snRNA on human adrenal gland. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR194KHA).

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


title: snRNA-seq from heart left ventricle (ENCSR763BII)


title: snATAC-seq from right atrium auricular region (ENCSR717FVA)


title: snRNA-seq from posterior vena cava (ENCSR716VLR)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR352RMS).

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


title: snATAC-seq from esophagus squamous epithelium (ENCSR757EGB)

summary:
snATAC-seq of human esophagus squamous epithelium

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


title: snRNA-seq from mucosa of descending colon (ENCSR707LLI)

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: snRNA-seq from heart left ventricle (ENCSR753YOZ)


title: snATAC-seq from heart left ventricle (ENCSR704SKG)

summary:
snATAC-seq of human heart left ventricle

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


title: snRNA-seq from colonic mucosa (ENCSR707ECV)


title: scRNA-seq from forelimb zygopod (ENCSR698TMC)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 15.0 day embryonic mouse mid forelimb

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


title: snATAC-seq from gastrocnemius medialis (ENCSR696YOC)


title: snRNA-seq from pancreas (ENCSR684KYI)

summary:
snRNA on human 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: snRNA-seq from lower lobe of left lung (ENCSR683ONV)


title: snRNA-seq from left cardiac atrium (ENCSR700UVN)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR777GVP).

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


title: snRNA-seq from heart left ventricle (ENCSR681GPY)


title: snRNA-seq from heart (ENCSR665HPR)


title: snRNA-seq from lower lobe of right lung (ENCSR671FDY)


title: scRNA-seq from forelimb (ENCSR745DNK)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 12.0 day embryonic mouse forelimb

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


title: snRNA-seq from upper lobe of left lung (ENCSR662VTU)


title: snRNA-seq from adrenal gland (ENCSR724KET)

summary:
snRNA on human adrenal gland. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR693GAD)

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


title: snATAC-seq from esophagus muscularis mucosa (ENCSR660NEE)

summary:
snATAC-seq of human esophagus muscularis mucosa

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


title: snRNA-seq from heart left ventricle (ENCSR654MFX)


title: snATAC-seq from Peyer's patch (ENCSR652WJE)

summary:
snATAC-seq of human Peyer's patch

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


title: snRNA-seq from colonic mucosa (ENCSR656VWP)


title: snRNA-seq from heart (ENCSR644VVE)


title: scRNA-seq from forelimb (ENCSR642XVO)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 11.0 day embryonic mouse forelimb

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


title: snRNA-seq from fallopian tube (ENCSR642GFM)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR690KGJ).

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


title: snRNA-seq from left cerebral cortex (ENCSR632EIK)


title: snRNA-seq from heart left ventricle (ENCSR630LZS)


title: snATAC-seq from omental fat pad (ENCSR644SCP)

summary:
snATAC-seq of human omental fat pad

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


title: snRNA-seq from heart (ENCSR627MEA)


title: snRNA-seq from left cerebral cortex (ENCSR624WDN)


title: snRNA-seq from psoas muscle (ENCSR641MWO)


title: snRNA-seq from adrenal gland (ENCSR620AJZ)

summary:
snRNA on human adrenal gland

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


title: snRNA-seq from heart (ENCSR607AZP)


title: snRNA-seq from right lobe of liver (ENCSR602SGU)

summary:
snRNA on human right lobe of liver

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


title: snRNA-seq from left colon (ENCSR587SPO)


title: snATAC-seq from ovary (ENCSR582VOF)

summary:
snATAC-seq of human 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: snATAC-seq from esophagus muscularis mucosa (ENCSR577BWJ)


title: snRNA-seq from heart (ENCSR571FEW)


title: snRNA-seq from gastrocnemius (ENCSR771MOE)


title: snRNA-seq from heart (ENCSR568GGW)


title: snATAC-seq from forebrain (ENCSR580SVE)

summary:
snATAC-seq of mouse forebrain

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


title: snATAC-seq from right lobe of liver (ENCSR559MJT)

summary:
snATAC-seq of human right lobe of liver

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


title: snRNA-seq from layer of hippocampus (ENCSR539XHZ)

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: snRNA-seq from kidney (ENCSR548HED)


title: snRNA-seq from heart left ventricle (ENCSR540DHJ)


title: snATAC-seq from stomach (ENCSR549JEQ)

summary:
snATAC-seq of human stomach

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


title: snRNA-seq from heart (ENCSR533IGQ)


title: snRNA-seq from liver (ENCSR523HMC)


title: snATAC-seq from heart left ventricle (ENCSR538FPK)

summary:
snATAC-seq of human heart left ventricle

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


title: snRNA-seq from left cardiac atrium (ENCSR527MGL)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR299NEP).

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


title: snRNA-seq from right cardiac atrium (ENCSR522HNR)


title: snATAC-seq from lower leg skin (ENCSR513HZN)

summary:
snATAC-seq of human lower leg skin

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


title: snATAC-seq from transverse colon (ENCSR506YMX)

summary:
snATAC-seq of human transverse colon

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


title: snRNA-seq from heart (ENCSR497FRI)


title: snRNA-seq from heart left ventricle (ENCSR489URW)


title: snRNA-seq from heart left ventricle (ENCSR488UUT)


title: snRNA-seq from heart left ventricle (ENCSR485GOL)


title: snRNA-seq from right lobe of liver (ENCSR484YSK)


title: scRNA-seq from forelimb (ENCSR476JWN)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 13.0 day embryonic mouse forelimb

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


title: snRNA-seq from heart left ventricle (ENCSR481QQR)

summary:
snRNA on human heart left ventricle. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR131DKN)

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


title: snRNA-seq from pancreas (ENCSR478FQR)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snATAC experiment (ENCSR690NZI).

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


title: snRNA-seq from liver (ENCSR474DKO)


title: snATAC-seq from lower leg skin (ENCSR474TGL)


title: snRNA-seq from pancreas (ENCSR472RRP)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR229VVY).

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


title: snRNA-seq from psoas muscle (ENCSR471YTA)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR000XQD).

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


title: snRNA-seq from left cardiac atrium (ENCSR463EEP)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR491LSZ).

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


title: snRNA-seq from heart (ENCSR462HCD)


title: snRNA-seq from mucosa of descending colon (ENCSR460MGC)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR922FEK).

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


title: snRNA-seq from heart left ventricle (ENCSR455MGH)


title: snATAC-seq from uterus (ENCSR455CVZ)

summary:
snATAC-seq of human 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: snATAC-seq from omental fat pad (ENCSR492GGN)

summary:
snATAC-seq of human omental fat pad

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


title: snRNA-seq from gastrocnemius (ENCSR478PUL)


title: snRNA-seq from pancreas (ENCSR445LCA)


title: snATAC-seq from vagina (ENCSR441ZWO)

summary:
snATAC-seq of human vagina

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


title: snATAC-seq from esophagus squamous epithelium (ENCSR453TVZ)

summary:
snATAC-seq of human esophagus squamous epithelium

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


title: snRNA-seq from heart left ventricle (ENCSR439ZVQ)

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: snATAC-seq from tibial nerve (ENCSR453BVR)

summary:
snATAC-seq of human tibial nerve

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


title: snATAC-seq from breast epithelium (ENCSR438ETW)

summary:
snATAC-seq of human breast epithelium

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


title: snRNA-seq from gastrocnemius (ENCSR438FRT)


title: snATAC-seq from transverse colon (ENCSR434SXE)

summary:
snATAC of human colon transverse

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


title: snRNA-seq from heart right ventricle (ENCSR426PDU)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR169BCG).

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


title: snRNA-seq from left cerebral cortex (ENCSR421YXX)


title: snRNA-seq from left cerebral cortex (ENCSR467GGT)


title: snRNA-seq from heart (ENCSR417FCM)


title: snRNA-seq from heart (ENCSR415HEP)


title: scRNA-seq from autopod region (ENCSR416FHN)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 15.0 day embryonic mouse distal forelimb

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


title: snATAC-seq from ascending aorta (ENCSR411MLR)

summary:
snATAC-seq of human 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: snRNA-seq from heart (ENCSR409CQM)


title: snRNA-seq from adrenal gland (ENCSR402PHR)


title: snRNA-seq from heart left ventricle (ENCSR398YBK)


title: snATAC-seq from thoracic aorta (ENCSR402SNA)

summary:
snATAC-seq of human thoracic 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: snRNA-seq from right lobe of liver (ENCSR398PIW)


title: snRNA-seq from heart left ventricle (ENCSR405YKM)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR318ERF).

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


title: snATAC-seq from lower leg skin (ENCSR397ODX)

summary:
snATAC-seq of human lower leg skin

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


title: snATAC-seq from suprapubic skin (ENCSR397LYX)

summary:
snATAC-seq of human suprapubic skin

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


title: snATAC-seq from sigmoid colon (ENCSR388NCA)

summary:
snATAC-seq of human colon sigmoid

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


title: snRNA-seq from left lobe of liver (ENCSR369UFT)

summary:
snRNA on left lobe of liver. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR139ATR).

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


title: snRNA-seq from right lobe of liver (ENCSR367YUX)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR630YEA).

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


title: snATAC-seq from sigmoid colon (ENCSR367GKP)


title: snATAC-seq from suprapubic skin (ENCSR364GEA)


title: snATAC-seq from forebrain (ENCSR374QZJ)

summary:
snATAC-seq of mouse forebrain

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


title: snRNA-seq from adrenal gland (ENCSR362YDM)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR420EWQ).

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


title: snATAC-seq from transverse colon (ENCSR349XKD)

summary:
snATAC-seq of human transverse colon

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


title: snRNA-seq from heart left ventricle (ENCSR349AHE)

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: snRNA-seq from ovary (ENCSR362HUP)


title: scRNA-seq from forelimb (ENCSR337QTQ)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 15.0 day embryonic mouse forelimb

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


title: snRNA-seq from heart left ventricle (ENCSR345CVL)


title: snRNA-seq from adrenal gland (ENCSR356VJZ)


title: snRNA-seq from heart left ventricle (ENCSR352DXB)


title: snRNA-seq from natural killer cell (ENCSR337HKS)


title: snRNA-seq from heart (ENCSR333SLJ)


title: snATAC-seq from adrenal gland (ENCSR302LEY)

summary:
snATAC-seq of human adrenal gland

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


title: snRNA-seq from heart left ventricle (ENCSR328GTN)


title: snRNA-seq from ovary (ENCSR297ZTQ)


title: scRNA-seq from forelimb (ENCSR306UHC)


title: snRNA-seq from liver (ENCSR292BJF)


title: snRNA-seq from liver (ENCSR291IHH)


title: snRNA-seq from left colon (ENCSR289ANH)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR830FPR).

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


title: snATAC-seq from tibial artery (ENCSR302CMX)

summary:
snATAC-seq of human tibial 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: snRNA-seq from pancreas (ENCSR281NBH)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR868CRK).

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


title: snATAC-seq from omental fat pad (ENCSR274HQD)

summary:
snATAC-seq of human omental fat pad

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


title: snRNA-seq from heart (ENCSR288WET)


title: snRNA-seq from heart (ENCSR268GBA)


title: snRNA-seq from heart left ventricle (ENCSR273JWD)


title: snATAC-seq from stomach (ENCSR266ZPZ)

summary:
snATAC-seq of human stomach

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


title: snRNA-seq from right lobe of liver (ENCSR261LPM)


title: snRNA-seq from psoas muscle (ENCSR281RIH)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR869LEV).

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


title: snATAC-seq from body of pancreas (ENCSR261TQO)

summary:
snATAC-seq of human body of pancreas

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


title: snRNA-seq from pancreas (ENCSR261BXB)

summary:
snRNA on human pancreas. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR496XXB).

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


title: snRNA-seq from heart left ventricle (ENCSR237HWJ)


title: snRNA-seq from heart right ventricle (ENCSR258SZI)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR681OLJ).

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


title: snRNA-seq from heart (ENCSR252RYC)


title: snATAC-seq from gastrocnemius medialis (ENCSR244GZL)

summary:
snATAC-seq of human gastrocnemius medialis

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


title: snRNA-seq from heart left ventricle (ENCSR231FNL)


title: snRNA-seq from lung (ENCSR225OII)

summary:
snRNA on human lung. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR083HFN)

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


title: snRNA-seq from adrenal gland (ENCSR224OUG)


title: snRNA-seq from heart left ventricle (ENCSR259VOY)


title: snATAC-seq from gastroesophageal sphincter (ENCSR215BTH)

summary:
snATAC-seq of human gastroesophageal sphincter

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


title: snATAC-seq from tibial nerve (ENCSR205TUH)

summary:
snATAC-seq of human tibial nerve

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


title: snRNA-seq from left cerebral cortex (ENCSR224RWH)


title: snATAC-seq from forebrain (ENCSR205OEF)

summary:
snATAC-seq of mouse forebrain

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


title: snRNA-seq from heart left ventricle (ENCSR203YOV)

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: snRNA-seq from psoas muscle (ENCSR203THX)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR916EDP).

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


title: snRNA-seq from mucosa of gallbladder (ENCSR201WJO)


title: snRNA-seq from heart left ventricle (ENCSR204RHR)


title: snRNA-seq from ovary (ENCSR298MPV)


title: snRNA-seq from liver (ENCSR192UEL)


title: snRNA-seq from heart left ventricle (ENCSR190TRK)


title: snRNA-seq from gastrocnemius (ENCSR188GDL)


title: snATAC-seq from upper lobe of left lung (ENCSR182PJN)

summary:
snATAC-seq of human 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: snATAC-seq from body of pancreas (ENCSR234CRD)


title: snATAC-seq from esophagus squamous epithelium (ENCSR164GSH)

summary:
snATAC-seq of human esophagus squamous epithelium

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


title: snATAC-seq from esophagus muscularis mucosa (ENCSR168TFI)

summary:
snATAC-seq of human esophagus muscularis mucosa

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


title: snATAC-seq from omental fat pad (ENCSR181XXQ)


title: snRNA-seq from gastrocnemius (ENCSR163GJZ)


title: snRNA-seq from heart left ventricle (ENCSR175TRJ)


title: snRNA-seq from heart left ventricle (ENCSR176WWW)


title: snRNA-seq from heart (ENCSR170SFR)


title: snRNA-seq from adrenal gland (ENCSR157YJO)


title: snRNA-seq from upper lobe of right lung (ENCSR142RRV)


title: scRNA-seq from forelimb (ENCSR156HHE)

summary:
10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 13.0 day embryonic mouse forelimb

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


title: snRNA-seq from Right ventricle myocardium inferior (ENCSR151ONW)

summary:
snRNA on human right ventricle myocardium inferior. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR628POB)

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


title: snRNA-seq from heart left ventricle (ENCSR138JCM)


title: snRNA-seq from left cerebral cortex (ENCSR133XJX)


title: snRNA-seq from heart left ventricle (ENCSR157FDD)


title: snRNA-seq from liver (ENCSR133IBO)


title: snATAC-seq from gastrocnemius medialis (ENCSR139TIQ)


title: snRNA-seq from left cerebral cortex (ENCSR132MEW)


title: snRNA-seq from gastrocnemius (ENCSR125XUV)


title: snATAC-seq from Peyer's patch (ENCSR101JHK)

summary:
snATAC-seq of human Peyer's patch

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


title: snATAC-seq from upper lobe of left lung (ENCSR089CGX)


title: snRNA-seq from right cardiac atrium (ENCSR087YKG)


title: snRNA-seq from heart left ventricle (ENCSR084XKX)


title: snRNA-seq from heart left ventricle (ENCSR085XEW)


title: snRNA-seq from heart left ventricle (ENCSR093GXF)


title: snRNA-seq from heart left ventricle (ENCSR076ZLE)


title: snRNA-seq from heart left ventricle (ENCSR067BOK)


title: snRNA-seq from left ventricle myocardium superior (ENCSR079LVG)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR425CZQ).

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


title: snRNA-seq from bile duct (ENCSR060SEA)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR833BMK).

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


title: snRNA-seq from heart right ventricle (ENCSR060ZXZ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR588PEE).

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


title: snATAC-seq from tibial artery (ENCSR058XJK)

summary:
snATAC-seq of human tibial 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: snATAC-seq from uterus (ENCSR028RFK)

summary:
snATAC-seq of human 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: snRNA-seq from adrenal gland (ENCSR035BDI)


title: snATAC-seq from gastrocnemius medialis (ENCSR023FME)

summary:
snATAC-seq of human gastrocnemius medialis

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


title: snRNA-seq from adrenal gland (ENCSR021YYL)


title: snRNA-seq from heart left ventricle (ENCSR056QLB)


title: snATAC-seq from Peyer's patch (ENCSR052DKH)


title: snRNA-seq from gastrocnemius (ENCSR021MHR)


title: snRNA-seq from mucosa of descending colon (ENCSR028MBY)


title: snRNA-seq from placenta (ENCSR021QIA)


title: snRNA-seq from heart left ventricle (ENCSR008CVR)


title: snRNA-seq from psoas muscle (ENCSR005TCL)

summary:
snRNA on human psoas muscle. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR332XEW).

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


title: snRNA-seq from heart left ventricle (ENCSR012APQ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR668XPI).

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


title: snATAC-seq from transverse colon (ENCSR007QIO)

summary:
snATAC-seq of human transverse colon

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


title: snRNA-seq from fallopian tube (ENCSR011EDH)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR815FGT).

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


title: snRNA-seq from heart left ventricle (ENCSR002SMQ)

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: Chronic stress-induced cholesterol metabolism abnormalities promote ESCC tumorigenesis and predict neoadjuvant therapy response [RNA-Seq]

city: Zhengzhou

first: Ting

address: No. 100 Keke Avenue, Zhengzhou City, Henan Province

institute: Zhengzhou University

summary: This project reported that chronic stress activates the GCR-HMGB2-LDLR axis via cortisol release, leading to abnormal cholesterol metabolism and ultimately promoting esophageal carcinogenesis. Chronic stress is associated with increased ESCC risk, and further exacerbates ESCC progression through HMGB2. Cortisol, by activating GCR, stimulates ESCC cell proliferation. Moreover, GCR activation enhances HMGB2 transcription, which in turn binds to SREBF1, thereby upregulating LDLR transcription and disrupting cholesterol metabolism. Clinical parameters in stressed ESCC patients underscore the relevance of stress management as a pivotal strategy for both the prevention and treatment of this malignancy.

overall_design: Use RNA-seq to find the important gene significantly regulate cholesterol metabolism pathway


title: single cell RNA-seq analysis of lung cancer cell lines treated with JTE-607

city: shanghai

first: Xiaolan

middle: Phenome

last: Zhou

state: State

address: Songhu road

institute: fudan

summary: To assess the impact of CPA inhibition by JTE-607 on intra-cell-line transcriptomic heterogeneity, we  profiled two lung cancer cell lines treated with DMSO or JTE-607 by 3' tag-based single-cell RNA-seq with 10x Chromium. For data analysis, we performed transcriptome quantification at the PAS-based transcript level to generate a PAS-by-cell count matrix, and then investigate the effect of JTE-607 treatment on PAS usage pattern and cellular states.

overall_design: Two different lung cancer cell lines were treated with DMSO or JTE-607. scRNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ kit version 2. To perform PAS-based transcript expression analysis, all samples were profiled using 3' sequencing.

first: Zhaozhao

last: Zhao

first: Yue

last: Chu

last: Ni


title: FosB/ΔFosB are induced in mast cells and regulate gene expression to modulate inflammatory responses to allergens and immune stimuli in male mice

city: East Lansing

first: Dimitri

last: Joseph

state: MI

address: 8254 Life Science Bldg

department: Pharmacology and Toxicology

institute: Michigan State University

summary: Mast cells are innate immune cells that play a crucial role in numerous physiological processes across tissues by releasing pre-stored and newly synthesized mediators in response to stimuli, an activity largely driven by changes in gene expression. Given their widespread influence, dysfunction in mast cells can contribute to a variety of pathologies including allergies, long COVID, and autoimmune and neuroinflammatory disorders. Despite this, the specific transcriptional mechanisms that control mast cell mediator release remain poorly understood, significantly hindering the development of effective therapeutic strategies. We found that the two proteins encoded by the transcription factor FosB, FOSB and the highly stable variant ΔFOSB, are robustly expressed upon stimulation in both murine and human mast cell progenitors. Motivated by these findings, we generated a novel mouse model with targeted ablation of FosB gene expression specifically in mast cells (MC FosB- ) by crossing a mast cell-specific Cre reporter line (Mcpt5-Cre) with a Cre-dependent floxed FosB mouse lines. We found that mast cell progenitors derived from MC FosB- mice, compared to wild types (WT), exhibit baseline increased histamine content and vesicle numbers. Additionally, they show enhanced calcium mobilization, degranulation, and histamine release following allergy-related IgE-mediated stimulation, along with heightened IL-6 release in response to infection-like LPS stimulation. In vivo experiments with IgE- mediated and LPS challenges revealed that MC FosB- mice experience greater drops in body temperature, heightened activation of tissue-resident mast cells, and increased release of pro-inflammatory mediators compared to their WT counterparts. These findings suggest that FosB products play a crucial regulatory role in moderating stimulus-induced mast cell activation in response to both IgE and LPS stimuli. Lastly, by integrating CUT&RUN and RNAseq data, we identified several genes targeted by ΔFOSB that could mediate these observed effects, including Mir155hg, CLCF1, DUSP4, and Trib1. Together, this study provides the first evidence that FOSB/ΔFOSB modulate mast cell functions and provides a new possible target for therapeutic interventions aimed at ameliorating mast cell-related diseases.

overall_design: Bone marrow progenitor cells were isolated from the femurs of 6-8-week-old male WT  mice.For FcεRI crosslinking, bone marrow-derived mast cells (BMMCs) were sensitized overnight with 0.5 µg/mL anti-DNP IgE. Cells were either left unstimulated or stimulated with 15 ng/mL DNP-HSA for one hour. Cell pellets (2 × 10⁶ cells per well) were collected and flash-frozen for CUT&RUN analysis. The experimental conditions included FosBWT and FosBNull genotypes under stimulated (DNP) and unstimulated (vehicle) conditions. n= 3 unstimulated/stimulated BMMC samples from 3 different C57 WT 8 week old male n=2 unstimulated/stimulated BMMC samples from 2 different MCFosB- (from a cross between MCPT5-Cre/+ mice (kindly provided by Dr. Soman Abraham, Duke University, developed by Dr. Axel Roers) and floxed FosB mice generated by Eric Nestler’s lab) CUT&RUN was performed using antibodies targeting FosB and IgG as a negative control. Libraries were prepared and sequenced to assess genome-wide chromatin accessibility and FosB-DNA interactions across the experimental conditions

first: Natalia

last: Duque-Wilckens

first: Meesum

last: Syed

first: Brianna

last: Smith

first: Vidhula

last: Srinavasan

first: Yeh

last: Szu-Ying

first: Nidia

last: Maradiaga

first: Kyan

last: Thelen

first: Fabiola

last: Sotomayor

first: Kait

last: Durga

first: Eric

last: Nestler

first: Adam

last: Moeser

first: A

last: Robison


title: mRNA sequencing of RPE1-TP53KO and RPE1-TP53KO-EIF2AKO cells

city: Groningen

first: Maurits

last: Roorda

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

summary: The alternative translation initiation factor EIF2A encoded by the EIF2A gene (not to be confused with EIF2alpha, encoded by the EIF2S1 gene) plays a role in translation initiation from both conventional methionine codons, but also leucine and others upon activation of the integrated stress response. We sought to investigate the effects on global transcription of genes upon loss of EIF2A.

overall_design: In this experiment, EIF2A was knocked out using CRISPR-Cas9 based gene editing and confirmed using sanger sequencing and western blot in RPE1-TP53KO cells. Cells were grown to ~70% confluency and RNA was harvested using standard protocols.

first: Steven

last: de Jong

first: Marcel

last: van Vugt


title: RmpA as a Global Regulator Modulates Switching Between Hypermucoviscosity and Biofilm in Hypervirulent Klebsiella pneumoniae [ChIP-seq]

first: Jiangqing

last: Huang

address: No 3, 1st Beichen West Road, Chaoyang District

institute: Chinese Academy of Sciences

summary: Hypervirulent Klebsiella pneumoniae (hvKp) is a significant pathogen causing severe community-acquired infections, characterized by the presence of a virulence plasmid. The plasmid-encoded regulator of mucoid phenotype A (RmpA) activates the expression of capsule genes, resulting in a hypermucoviscosity phenotype strongly associated with increased virulence. RmpA features a LuxR DNA-binding domain and a signaling-responsive domain, typical of proteins that regulate multiple biological processes. However, the comprehensive regulatory mechanisms of RmpA in hvKp remain unclear. Herein, RNA-seq showed that RmpA activates carbohydrate metabolism pathways while repressing those related to DNA replication, ribosome metabolism, and biofilm formation. ChIP-seq further confirmed RmpA’s role as a global regulator that not only enhances capsule production by activating transcripts within the capsule locus, but also upregulates the expression of key genes involved in synthesizing capsule precursors. RmpA regulates the phenotypic switch between hypermucoviscosity and biofilm formation by repressing type III fimbriae genes. In addition, Expression of RmpA in Escherichia coli induced global transcriptional changes, suggesting it functions as a global regulator across species. These findings position RmpA as a central regulator in hvKp, orchestrating metabolic pathways and phenotypic traits essential for virulence.

overall_design: ChIP-seq of RmpA in Klebsiella. The strain was Hypervirulent Klebsiella pneumoniae.

first: Shigang

last: Yao

first: Jianing

last: Geng

first: Dawei

last: Wei

first: Chao

last: Wang

first: Yuqin

last: Song

first: Gang

last: Zhang

first: Jie

last: Feng


title: Spatial transcriptomics reveals the immunomodulatory activities of an oncolytic adenovirus armed with a type I interferon in a replication-permissive immunocompetent pancreatic cancer model

city: Minneapolis

first: Julia

last: Davydova

state: MN

address: 420 Delaware St. SE, MMC 195

department: Surgery

institute: University of Minnesota

summary: Oncolytic adenoviruses (OAds) are emerging as a promising class of viro-immunotherapy. Here, we focused on a replication-competent OAd armed with a type I interferon (OAd-IFN) and assessed its immunological activities in a replication-permissive, immunocompetent Syrian hamster pancreatic cancer model. Our spatial transcriptomic analysis revealed the critical role of locally expressed type I IFN in the immunomodulatory activities of OAd-IFN in the tumor microenvironment.

overall_design: Hamsters bearing HP-1 pancreatic cancer tumors were treated intratumorally with OAd-IFN or its counterpart OAd expressing firefly luciferase (OAd-Luc). Based on the tumor volumes, hamsters treated with either of the OAds were assigned to the following criteria: Responder with a tumor volume less than 500 mm^3 and Less-responder with a tumor volume of 500-1500 mm^3. Two of four hamsters in the OAd-IFN group were classified as Responder while the other two in the OAd-IFN group and all four hamsters in the OAd-Luc group were classified as Less-responder. From them, one of the OAd-Luc, two of the OAd-IFN (Less-responder), and one of the OAd-IFN (Responder) samples were analyzed by spatial transcriptomics (Visium Spatial Gene Expression, 10x Genomics).

first: Natalia

last: Calixto Mancipe

first: Kazuho

last: Inoko


title: RmpA as a Global Regulator Modulates Switching Between Hypermucoviscosity and Biofilm in Hypervirulent Klebsiella pneumoniae [RNA-seq]

sample_organism:
Escherichia coli
Klebsiella pneumoniae

platform_organism:
Escherichia coli
Klebsiella pneumoniae

overall_design: RNA-seq of Klebsiella dCas9-sgRNA and dCas9-rmpA Escherichia PLB1K and PLB1K-rmpA strains.


title: total RNA-seq from mucosa of descending colon (ENCSR681ARR)

first: ENCODE

last: DCC

summary:
W64 mucosa of descending colon

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


title: total RNA-seq from CD4-positive naive resting alpha-beta T cell (ENCSR968ZOA)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD4 naive_spleen_F_57days

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


title: iCLIP from K562 (ENCSR984SOD)

summary:
iCLIP experiment in K562 cells against FUBP1

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


title: iCLIP from K562 (ENCSR961WWI)

summary:
iCLIP experiment in K562 cells against EIF4G1

For data usage terms and conditions, please refer to http://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 uterus (ENCSR676SRP)

summary:
W73 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: DNase-seq from liver (ENCSR961KOD)


title: Control eCLIP from K562 (ENCSR660DRN)

summary:
eCLIP control experiment on K562 against EIF4E

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR961NOR)

summary:
eCLIP control experiment on K562 against SRSF1

For data usage terms and conditions, please refer to http://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 heart right ventricle (ENCSR441IDG)

summary:
UW038 heart right ventricle

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


title: Microarray transcriptome expression of human perinatal mesenchymal stromal cells after in vitro expansion

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

summary:
Transcriptome expression study of human mesenchymal stromal cells from three distinct perinatal tissues: cord-blood, amnios and chorion
These three samples were investigated in three distinct human individuals

overall_design: Mesenchymal stromal cells from three sources of perinatal samples (chorion, cord-blood, and amnios) for three human individuals

first: Christophe

last: Desterke

last: Martinaud

first: Marie-Caroline

last: Le Bousse-Kerdilès

first: Jean-Jacques

last: Lataillade

first: Sébastien

last: Banzet

first: Juliette

last: Peltzer


title: eCLIP from K562 (ENCSR440MSY)

summary:
eCLIP experiment on K562 against ELAC2

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


title: eCLIP from K562 (ENCSR953ZOA)

summary:
eCLIP experiment on K562 against HNRNPK

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR945VLG)

summary:
HCT116-POLR2A-clone1-untreated-new_bulk-B10

For data usage terms and conditions, please refer to http://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 monocyte (ENCSR959ZHO)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.monocytes_spleen_M_59days

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


title: WGS from transverse colon (ENCSR664TEU)

summary:
The data contained in this Experiment correspond to PacBio Sequel generated 10Kb DNA libraries of ENCODE donor ENCDO793LXB.

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR937QWU)

summary:
eCLIP control experiment on K562 against APEX1

For data usage terms and conditions, please refer to http://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 (ENCSR638QBF)

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: RIP-seq from K562 (ENCSR433RRS)


title: eCLIP from K562 (ENCSR937RSF)

summary:
eCLIP experiment on K562 against RPS10

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


title: snRNA-seq from layer of hippocampus (ENCSR075HVN)


title: Control eCLIP from K562 (ENCSR911RWF)

summary:
eCLIP control experiment on K562 against RPS6

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR931ATS)

summary:
HCT116-MED14-clone1-treated-new_bulk-4C

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


title: Targeting the 3D genome by anthracyclines for chemotherapeutic effects

city: Leiden

first: Minkang

last: Tan

address: Einthovenweg 20

department: Department of Cell and Chemical Biology

institute: Leiden University Medical Center

summary: The chromatins are folded into three-dimensional (3D) structures, and aberrant chromatin 3D folding has been shown in cancer. We performed ATAC-seq and  TOP2A ChIP-seq to profile the potential effects of different anthracyclines on the chromatin. We identified that unique anthracycline variants selectively target chromatin looping anchors via disrupting CTCF binding, suggesting an additional potential therapeutic effect on the 3D genome. We further performed Hi-C experiments, and data from K562 cells treated with the selective anthracycline drugs indicate that the global 3D chromatin organizations were disrupted dramatically, as exemplified by the disruption of distal regulation of the Myc gene. Furthermore, AML patients receiving anthracycline drugs showed altered chromatin structures around potential looping anchors, which linked to distinct clinical outcomes. Our data indicate that anthracyclines are potent and selective epigenomic targeting drugs and can further target the 3D genome for anticancer effects, which could be explored for personalized medicine to treat tumors with aberrant 3D chromatin structures.

overall_design: CTCF ChIP-seq experiments were performed using 100,000,000 K562 cells treated with 10 µM aclarubicin or daunrubicin for 4 hours.

first: Shengnan

last: Sun

first: Andrea

last: Perreault

first: Douglas

last: Phanstiel

first: Baoxu

last: Pang


title: total RNA-seq from heart right ventricle (ENCSR889IAP)

summary:
UW036 heart right ventricle

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


title: DNase-seq from liver (ENCSR887EBS)


title: Control eCLIP from K562 (ENCSR407QDZ)

summary:
eCLIP control experiment on K562 against RYBP

For data usage terms and conditions, please refer to http://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 heart left ventricle (ENCSR882RCG)

summary:
UW054 heart left ventricle

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


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCSR383XSU)


title: total RNA-seq from esophagus mucosa (ENCSR636QDK)

summary:
W71 esophagus mucosa

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


title: eCLIP from K562 (ENCSR631HUN)

summary:
eCLIP experiment on K562 against DDX47

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR856KEU)

summary:
eCLIP control experiment on K562 against FMR1

For data usage terms and conditions, please refer to http://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 psoas muscle (ENCSR629HFE)

summary:
W73 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: total RNA-seq from heart right ventricle (ENCSR854VRX)

summary:
UW076 heart right ventricle

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


title: eCLIP from K562 (ENCSR381VNR)

summary:
eCLIP experiment on K562 against SRSF9

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


title: eCLIP from HepG2 (ENCSR379GZS)

summary:
eCLIP experiment on HepG2 against NSUN2

For data usage terms and conditions, please refer to http://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 heart right ventricle (ENCSR828JSJ)

summary:
UW040 heart right ventricle

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


title: DNase-seq from spleen (ENCSR603SOS)


title: DNase-seq from monocyte (ENCSR606KBX)


title: total RNA-seq from ureter (ENCSR619DQO)

summary:
W71 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: total RNA-seq from T-cell (ENCSR377UPT)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD3_spleen_M_66days

For data usage terms and conditions, please refer to http://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 (ENCSR823GSV)

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: total RNA-seq from CD4-positive naive resting alpha-beta T cell (ENCSR835KFT)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD4 naive_spleen_M_76days

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


title: RIP-seq from GM12878 (ENCSR593SOD)


title: Control eCLIP from K562 (ENCSR585TQT)

summary:
eCLIP control experiment on K562 against POLR2G

For data usage terms and conditions, please refer to http://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 (ENCSR809OXS)


title: DNase-seq from natural killer cell (ENCSR573LKK)


title: Control eCLIP from K562 (ENCSR816TOM)

summary:
eCLIP control experiment on K562 against DDX43

For data usage terms and conditions, please refer to http://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 psoas muscle (ENCSR870IUI)

summary:
W62 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: Control eCLIP from K562 (ENCSR344GAQ)

summary:
eCLIP control experiment on K562 against EEF2

For data usage terms and conditions, please refer to http://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 lower lobe of left lung (ENCSR568UGZ)

summary:
W80 lower 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 natural killer cell (ENCSR803VYN)


title: Control eCLIP from K562 (ENCSR567ZND)

summary:
eCLIP control experiment on K562 against RPS24

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


title: eCLIP from K562 (ENCSR391BBA)

summary:
eCLIP experiment on K562 against EIF4E

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


title: icLASER from K562 (ENCSR623ICN)

summary:
K562 icLASER experiment

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


title: Control eCLIP from K562 (ENCSR561QXJ)

summary:
eCLIP control experiment on K562 against DDX1

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


title: RIP-seq from GM12878 (ENCSR551YTL)


title: Control eCLIP from K562 (ENCSR325HDY)

summary:
eCLIP control experiment on K562 against FXR2

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


title: eCLIP from K562 (ENCSR554UVB)

summary:
eCLIP experiment on K562 against FMR1

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR546JKS)

summary:
eCLIP control experiment on K562 against ADAT1

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR545KBT)

summary:
eCLIP control experiment on K562 against ELAC2

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR821ESG)

summary:
eCLIP control experiment on K562 against NFX1

For data usage terms and conditions, please refer to http://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 neutrophil (ENCSR309GVQ)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_F_83days

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR790SPV)

summary:
eCLIP control experiment on K562 against MORC2

For data usage terms and conditions, please refer to http://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 heart left ventricle (ENCSR790BBE)

summary:
UW068 heart left ventricle

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


title: total RNA-seq from heart left ventricle (ENCSR570DQR)

summary:
UW076 heart left ventricle

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


title: total RNA-seq from B cell (ENCSR788PEE)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD19_spleen_F_67days

For data usage terms and conditions, please refer to http://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 monocyte (ENCSR536HHA)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.monocytes_spleen_F_59days

For data usage terms and conditions, please refer to http://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 (ENCSR541RQH)

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: total RNA-seq from HCT116 (ENCSR294AKN)

summary:
HCT116-CDK7-untreated-new_bulk-A4

For data usage terms and conditions, please refer to http://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 (ENCSR300NZA)


title: total RNA-seq from CD8-positive naive resting alpha-beta T cell (ENCSR769LJY)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.CD8 naive_spleen_M_57days

For data usage terms and conditions, please refer to http://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 eCLIP from K562 (ENCSR327BBW)

summary:
eCLIP control experiment on K562 against ELAVL1

For data usage terms and conditions, please refer to http://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 neutrophil (ENCSR293FRO)

summary:
MouseF1 of C57BL/6 (f) x CAST Eij (m)_m.neutrophil_spleen_F_59days

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


title: eCLIP from K562 (ENCSR293FWY)

summary:
eCLIP experiment on K562 against DDX1

For data usage terms and conditions, please refer to http://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 eCLIP from HepG2 (ENCSR293CFE)

summary:
eCLIP control experiment on HepG2 against NSUN2

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


title: eCLIP from K562 (ENCSR321PWZ)

summary:
eCLIP experiment on K562 against SRSF1

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR275SNI)

summary:
HCT116-BRD4-clone1-treated-new_bulk-1F

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR267FRL)

summary:
HCT116-BRD4-clone1-untreated-new_bulk-1F

For data usage terms and conditions, please refer to http://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 B cell (ENCSR499UQO)


title: total RNA-seq from HCT116 (ENCSR800KLD)

summary:
HCT116-RAD21-clone1-untreated-new_bulk-C1

For data usage terms and conditions, please refer to http://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 naive resting alpha-beta T cell (ENCSR300SJS)


title: total RNA-seq from right lobe of liver (ENCSR534OAS)

summary:
W82 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: total RNA-seq from HCT116 (ENCSR266SBI)

summary:
HCT116-CTCF-treated-new_bulk-D12

For data usage terms and conditions, please refer to http://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 monocyte (ENCSR526NSY)


title: eCLIP from K562 (ENCSR521GON)

summary:
eCLIP experiment on K562 against EXOSC10

For data usage terms and conditions, please refer to http://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 1 cell (ENCSR743TJZ)

summary:
CD4 N (RA+ MACS sort)Th1 (aIL-4 1ug/ml+IL-12 30ng/ml)(day 14)

For data usage terms and conditions, please refer to http://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 (ENCSR260SFQ)