title: Ankrd11 deficiency reverses the dysfunction of chronic HBV-specific T-cell [ATAC-seq]

first: Wei

last: Xu

summary: To investigate the impact of Ankrd11 deficiency on chromatin accessibility in CD8 T cells, we performed ATAC-seq to analyze differences in chromatin openness between Ankrd11-knockout CD8 T cells and wild-type CD8 T cells.

overall_design: Ankrd11 KO and Control cells were generated by retroviral transduction. sgRNA-positive cells (NGFR+) were sorted 5 days post-transduction with >95% purity for subsequent ATAC-seq.

first: Xuyu

last: Zhou


title: capture Hi-C from HepG2 (ENCSR374AJQ)

status: Public on Jul 24 2026

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

summary:
promoter capture Hi-C in HepG2 cells

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


title: capture Hi-C from K562 (ENCSR193DKN)

summary:
promoter capture Hi-C in K562 cells

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


title: total RNA-seq from HG03129 (ENCSR998MYO)

type: Expression profiling by high throughput sequencing

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: long read RNA-seq from right lung (ENCSR997XFO)


title: total RNA-seq from GM19449 (ENCSR997LSS)


title: long read RNA-seq from large intestine (ENCSR992UMK)


title: total RNA-seq from T-helper 1 cell (ENCSR997HFD)


title: long read RNA-seq from stomach (ENCSR993RKQ)


title: total RNA-seq from T-cell (ENCSR990GHM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR992FYQ)


title: total RNA-seq from GM21775 (ENCSR989SXC)


title: long read RNA-seq from muscle of arm (ENCSR989PGQ)


title: snATAC-seq from heart left ventricle (ENCSR987PQH)

type: Genome binding/occupancy profiling by high throughput sequencing


title: snATAC-seq from SK-N-SH (ENCSR989MQQ)

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

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


title: total RNA-seq from GM19020 (ENCSR984PRR)


title: TF ChIP-seq from K562 (ENCSR985RPY)

summary:
TEAD4 ChIP-seq on K562 cells treated with shRNA targeting GATA1

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR983YCJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR982RIX)


title: total RNA-seq from GM19037 (ENCSR983OGO)


title: total RNA-seq from GM19437 (ENCSR982AOX)


title: Control ChIP-seq from HepG2 (ENCSR981UIH)

summary:
TEAD4 ChIP-seq on HepG2 cells treated with vector control shRNA

For data usage terms and conditions, please refer to http://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 HG03369 (ENCSR981CYF)


title: long read RNA-seq from muscle of leg (ENCSR979UPD)


title: total RNA-seq from HG03268 (ENCSR979JWV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR979GPU)


title: snATAC-seq from heart (ENCSR978JAI)


title: total RNA-seq from GM19321 (ENCSR978HDN)


title: total RNA-seq from HG03069 (ENCSR976HAT)


title: snATAC-seq from astrocyte (ENCSR986YGY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR975NWR)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR975MXT)


title: total RNA-seq from HG03169 (ENCSR971RIR)


title: snATAC-seq from Panc1 (ENCSR974TUB)


title: total RNA-seq from GM21600 (ENCSR973GTG)


title: total RNA-seq from HG03378 (ENCSR974SWF)


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR971LSO)


title: total RNA-seq from T-cell (ENCSR969WFV)


title: total RNA-seq from inflammatory macrophage (ENCSR971KZD)


title: total RNA-seq from GM21417 (ENCSR967LOO)


title: snATAC-seq from HepG2 (ENCSR967HFR)

summary:
scATAC-seq on human cell line HepG2

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


title: long read RNA-seq from testis (ENCSR966PBL)


title: total RNA-seq from HG02464 (ENCSR966FVT)


title: TF ChIP-seq from K562 (ENCSR965UZJ)

summary:
CEBPB ChIP-seq on K562 cells treated with shRNA targeting MAFF

For data usage terms and conditions, please refer to http://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 GM21441 (ENCSR965QXB)


title: snATAC-seq from gastrocnemius (ENCSR964PUM)


title: total RNA-seq from GM21478 (ENCSR964NYB)


title: total RNA-seq from HG03086 (ENCSR963SQT)


title: total RNA-seq from GM21739 (ENCSR962PNR)


title: snATAC-seq from psoas muscle (ENCSR963HLE)

summary:
scATAC-seq on human 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 GM19431 (ENCSR963NSP)


title: long read RNA-seq from renal cortex interstitium (ENCSR961RJV)


title: total RNA-seq from GM21529 (ENCSR961HMI)


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR961UKV)


title: snATAC-seq from heart left ventricle (ENCSR960IDI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR961CKN)


title: long read RNA-seq from spinal cord (ENCSR959XNI)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR961BYL)


title: total RNA-seq from GM21390 (ENCSR959ULL)


title: total RNA-seq from GM18522 (ENCSR959BHR)


title: snATAC-seq from heart left ventricle (ENCSR958FFE)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR955XIA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR953MDI)


title: total RNA-seq from GM21336 (ENCSR954KWV)


title: total RNA-seq from inflammatory macrophage (ENCSR951TBV)


title: total RNA-seq from HG03052 (ENCSR952FHK)


title: long read RNA-seq from muscle of back (ENCSR952SBK)


title: snATAC-seq from heart left ventricle (ENCSR951AID)


title: total RNA-seq from HG03027 (ENCSR950VCC)


title: total RNA-seq from GM21519 (ENCSR947TOB)


title: polyA plus RNA-seq from GM19147 (ENCSR946IFS)

summary:
GM19147 RNA Seq

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


title: Control ChIP-seq from HepG2 (ENCSR943SJY)

summary:
JUND ChIP-seq on HepG2 cells treated with control sgRNA

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


title: polyA plus RNA-seq from GM19238 (ENCSR955MJB)

summary:
GM19238 RNA Seq

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


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR955OOH)


title: total RNA-seq from HG02760 (ENCSR940SIV)


title: total RNA-seq from HG02840 (ENCSR952TUJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR940NCC)


title: total RNA-seq from GM21367 (ENCSR940RSZ)


title: long read RNA-seq from kidney (ENCSR941IFA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR940DDA)


title: total RNA-seq from GM21693 (ENCSR939PUS)


title: total RNA-seq from GM19401 (ENCSR939BEP)


title: total RNA-seq from HG03557 (ENCSR938GML)


title: total RNA-seq from GM21458 (ENCSR937CYO)


title: long read RNA-seq from heart (ENCSR934VNZ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR934JNT)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR932JIV)


title: snATAC-seq from T-helper 2 cell (ENCSR932LAJ)


title: total RNA-seq from GM21493 (ENCSR931TXM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR931NIE)


title: snATAC-seq from left cerebral cortex (ENCSR931EJA)


title: long read RNA-seq from heart (ENCSR930RNO)


title: total RNA-seq from GM21300 (ENCSR929NBE)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR928QLV)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR930GNS)


title: snATAC-seq from mucosa of urinary bladder (ENCSR927MVL)

summary:
scATAC-seq on human mucosa of urinary bladder

For data usage terms and conditions, please refer to http://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 HG02611 (ENCSR924QLE)


title: total RNA-seq from HG03469 (ENCSR924HWA)


title: snATAC-seq from left cerebral cortex (ENCSR924ZXU)


title: total RNA-seq from GM21580 (ENCSR922VBQ)


title: total RNA-seq from GM21578 (ENCSR923SGT)


title: snATAC-seq from mucosa of descending colon (ENCSR922FEK)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR460MGC).

For data usage terms and conditions, please refer to http://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 HG02595 (ENCSR921UIK)


title: total RNA-seq from CD14-positive monocyte (ENCSR921XFY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR920XLL)


title: snATAC-seq from left cerebral cortex (ENCSR921EFB)


title: polyA plus RNA-seq from GM12282 (ENCSR919QJN)

summary:
GM12282 RNA Seq

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


title: snATAC-seq from heart left ventricle (ENCSR918VTH)

summary:
scATAC on left heart ventricle. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR755CIF).

For data usage terms and conditions, please refer to http://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 HG02837 (ENCSR917OYF)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR918XMD)


title: total RNA-seq from GM19030 (ENCSR916XPW)


title: snATAC-seq from psoas muscle (ENCSR916EDP)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR203THX).

For data usage terms and conditions, please refer to http://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 left colon (ENCSR916RYB)

summary:
scATAC-seq on human left 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 GM19457 (ENCSR916BPD)


title: total RNA-seq from HG02722 (ENCSR914CLE)


title: total RNA-seq from GM21733 (ENCSR913TLO)


title: total RNA-seq from HG03419 (ENCSR914JWB)


title: Control ChIP-seq from K562 (ENCSR915CFB)

summary:
CEBPB ChIP-seq on K562 cells treated with vector control shRNA

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


title: snATAC-seq from heart left ventricle (ENCSR913OAS)

summary:
scATAC-seq on human heart left ventricle

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


title: total RNA-seq from GM21479 (ENCSR913FIO)

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 heart left ventricle (ENCSR912XZH)


title: total RNA-seq from T-cell (ENCSR910HYR)


title: long read RNA-seq from muscle of arm (ENCSR910OEU)


title: total RNA-seq from HG02943 (ENCSR911ZBO)


title: total RNA-seq from GM21512 (ENCSR911SHG)


title: total RNA-seq from GM21473 (ENCSR910GKE)


title: total RNA-seq from GM19379 (ENCSR909EGF)


title: A unique Mitochondrial Quality Control (MQC) mechanism reverses the phagosome maturation arrest caused by Mycobacterium tuberculosis

status: Public on Jul 31 2026

city: New Delhi

first: Dhiraj

last: Kumar

address: Aruna Asaf Ali Marg,

country: India

institute: International Centre for Genetic Engineering and Biotechnology

summary: Phagosome maturation arrest (PMA) imposed by Mycobacterium tuberculosis (Mtb) is among the classic tools that helps Mtb evade macrophage anti-bacterial response. Here we report a unique crosstalk between mitochondrial quality control (MQC) pathways and the phagosome maturation pathway, which unblocks the PMA and results in the efficient killing of Mtb. Depletion of p62/SQSTM1, a major autophagy adaptor, in human macrophages enhances Mtb killing. However, depletion of p62/SQSTM1 does not impact mitochondrial quality, despite an apparent block in mitophagy flux. Interestingly, in p62KD cells, MQC is ensured via TOM20+-mitochondria-derived vesicles (MDVs). MDVs, being dependent on RAB7 for maturation, are heavily recruited on Mtb-phagosomes in p62KD cells inadvertently aiding RAB7 recruitment on Mtb-phagosomes thereby releasing the PMA that facilitates efficient lysosomal delivery and killing of Mtb. Finally, blocking MQC in the p62KD cells, augments bacterial killing, underscoring the crosstalk between MQC and host-antibacterial mechanisms, providing an unexplored host-directed therapy strategy against tuberculosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from THP1 monocytes derived macrophages.

first: Surbhi

last: Verma

first: Mrinmoy

last: Das


title: Chronic stress accelerates pancreatic cancer tumorigenesis via promoting the acinar induced increasing of Slc6a2 in nerve

city: Xi’an

first: Weikun

last: Qian

address: 277 West Yanta Road

country: China

institute: The First Affiliated Hospital of Xi’an Jiaotong University

summary: Background: Chronic psychosomatic stress has been regarded as a critical risk factor for the development of pancreatic cancer, and the interaction between nerve and tumor seems contributed to this situation. In this study, we aim to find out the possible mechanisms on how tumor-nerve crosstalk promote the pancreatic tumorigenesis in stress condition. Methods: A transgenic mice harbored spontaneous pancreatic cancer and a restraint model were used in vivo, and the 3-dimensional acinar culture and PC12 cell were adopted as the in vitro model. High throughput mRNA sequencing was used to explore and the western blotting was adopted to verify the possible mechanisms involved in this process. Results: From the clinical data we reveled that pancreatic cancer patients harbored a higher level of psychosomatic stress. Similarly, iv vivo model showed chronic restraint stress facilitated the tumorigenesis of pancreatic cancer and stress hormone promoted the formation of acinar-to-ductal metaplasia (ADM) in vitro. Besides, we also found that nerve inhibition suppressed the chronic stress driven rapid developing of pancreatic cancer. Indeed, the results suggested that the nerve derived Slc6a2 may the key of chronic stress induced pancreatic initiation acceleration, and its upregulation in nerve was due to stress induced activating of Notch1-NGF axis in pancreatic precancerous cell. What’s more, we found duloxetine, a Slc6a2 blocker, could suppresses the tumorigenesis of pancreatic cancer in chronic stress. Conclusion: Chronic stress accelerates the development of pancreatic cancer via promoting the nerve derived Slc6a2 stimulated by the Notch1-NGF axis in pancreatic precancerous cell.

overall_design:
To investigate the role of innervating pancreatic sympathetic nerve elements on the chronic stress induced pancreatic cancer tumor growth, we established a sympathetic neurotomy (targeting sympathetic nerve that peri-coeliac artery and superior mesenteric artery) models based on the chronic restraint stress mice (which harbored the orthotropic transplanted tumor of pancreatic cancer).
We then performed gene expression profiling analysis using data obtain from RNA-seq of 6 different tumor samples at two groups (3 of each).
Comparative gene expression profiling analysis of RNA-seq data for the pancreatic tumor tissues from stress orthotropic mice and its derivatives (sympathetic neurotomy).

first: Xueni

last: Wang

first: Zeen

last: Zhu

first: Zheng


title: Gene expression data from epithelial and mesenchymal tumor cells isolated from E-A14 mouse mammary tumors grown in immunodeficient and immunocompetent mice

city: LYON

first: Amélien

last: SANLAVILLE

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

summary: Epithelial-mesenchymal transition (EMT) is a central oncogenic mechanism, contributing to transformation and metastatic dissemination. Several reports described that inflammation and innate immune cells favor EMT induction, contrasting with an understudied role of adaptive immunity in EMT promotion. Using an original murine mammary tumor model, we demonstrated that tumor cells maintain their epithelial phenotype in mice deficient for adaptive immune response but undergo EMT in the presence of T-cell mediated immunity. CD4 but not CD8 T cell depletion prevents EMT, undoubtedly demonstrating that CD4 T cell-mediated immunity favors EMT induction. Immune infiltrate and transcriptomic analyses revealed an inverse correlation between mesenchymal tumor cell and intratumoral neutrophil proportions, due to the reduced ability of mesenchymal cells to recruit neutrophils. Moreover, we demonstrated also the pro-EMT role of neutrophils. Last, transcriptomic database analysis of human breast tumors further strengthens the notion of a cooperation between CD4 T cells and neutrophils in EMT promotion.

overall_design: To perform a comparative transcriptomic analysis of both epithelial and mesenchymal tumor cells from mouse mammary tumors grown in immunodeficient and immunocompetent mice, Her2-expressing E-A14 tumor cells were injected into the mammary fat pad of CD4 and CD8 double-depleted mice (N=6) or isotype (Rat IgG2a and Rat IgG2b) control-injected mice (N=6). When tumors reached their growth end-point, 20 days post-injection in CD4/CD8-depleted mice versus 47 days post-injection in control mice, E-A14 tumors were harvested and Her2(+)EpCAM(+) versus Her2(+)EpCAM(-) tumor cells were sorted from each murine tumors to perform RNA sequencing analysis. Two replicates of in vitro culture E-A14 cells were also included in this RNAseq analysis. After principal-component analysis, epithelial-mesenchymal transition (EMT) score was calculated for each tumor cell sample to analyze its EMT status. A pathway enrichment analysis of differentially expressed genes (DEGs) between EpCAM(-) and EpCAM(+) tumor cells isolated from immunocompetent (control) mice was also performed to highlight immune-related gene pathways differentially regulated according to EMT status.

last: Sanlaville

first: Dominique

last: Poujol

first: Margaux

last: Hubert

first: Isabelle

last: Durand

first: Christophe

last: Caux

last: Puisieux


title: Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

summary: Clinical presentations that develop in response to infection are the culmination of interactions that occur between the pathogen and the ensuing defenses of the host. SARS-CoV-2, the aetiologic agent of COVID-19, directly antagonizes these defenses, resulting in a delay of immune engagement in the lungs that materializes only as cells succumb to infection and are phagocytosed. Leveraging the golden hamster model of COVID-19, we sought to understand the dynamics between SARS-CoV2 infection in the airways and the systemic host response that ensues. We find that early SARS-CoV-2 replication is largely confined to the respiratory tract and olfaction system, and, to a lesser extent, the heart and GI tract, but generates a host antiviral response that can be observed in every organ as a result of circulating type I and III interferons (IFN-I/-III).  Moreover, we show that diminishing the response in the airways by immunosuppression or administration of SARS-CoV-2 intravenously, results in a loss of immune priming, viremia, and an increase in viral tropism, including productive infection of the liver, kidney, spleen, and brain. Finally, we show that productive infection of the airways is required for mounting an effective and system-wide antiviral response. Together, these data illustrate how COVID-19 can result in diverse clinical presentations where disease outcomes can be a byproduct of the speed and strength of immune engagement. These studies provide additional evidence to the mechanistic insights of the diverse clinical presentations of COVID-19 and highlight the unique ability of the respiratory tract to generate a systemic immune defense following pathogen recognition.

overall_design: Differential gene expression analysis on RNA-Seq data from lungs and kidneys of golden hamsters PBS- or SARS-CoV-2 infected with SARS-CoV-2, and vehicle-or dexamethasone-treated.

first: Lucia

last: Carrau

first: Benjamin

middle: R

last: tenOever


title: Molecular force-induced supraphysiological liberation of transforming growth factor-beta (TGF-β) remodels the spleen for liver tissue growth

city: Nanjing

first: Zhenzhen

address: 163 Xianlin Avenue, Qixia District

department: School of Life Sciences

institute: Nanjing University

summary: Although the spleen is one potential transplantation site in liver regeneration, its native microenvironment is adverse for the stabilisation of epithelial hepatocytes after transplantation, due to the scanty collagen therein could not provide sufficient adhesion anchorage sites. Based on the crucial role of TGF-β in increasing collagen, its unique physiological status in the spleen, and its special mechanical force-mediated activation, we speculated the active TGF-β could be exploited from the storehouse of LLC in spleen by mimicking the procedure of TGF-β release. Thus, we designed a bifunctional sHA-X biomaterial integrating with the capacity of binding with LTBP1 and providing mechanical force. The network effectively enhanced the release of TGF-β from LLC, remodelled the spleen microenvironment in situ by increasing collagen abundance, promoted the adhesion and growth of hepatocytes, and then achieved the hepatisation of the spleen. The hepatised spleen could display liver-like function and survive in the liver metabolic diseases model and after liver resection. Our study confirmed the feasibility and advantages of in situ regulating TGF-β bioavailability in remodelling spleen niches and liver regeneration. Our study, for the first time, demonstrates an engineered approach to harness endogenous TGF-β functions for ectopic tissue regeneration, through mechanical manipulation of its unique mechanism of activation.

overall_design:
To remodel the spleen into the site suitable for hepatocyte transplantion, we injected sHA-X biomaterial four  times, with PBS group.
To evaluate whether the sHA-X-remodelled spleen could support the settlement of transplanted liver cells, hepatocytes were injected into spleen tissue.
At 30 days post-transplantation of hepatocytes, the spleens of two groups (PBS or sHA-X group) were extracted to analyze the difference of genes responsible for hepatic functions, including drug, glucose, fatty acid, and cholesterol metabolism.

first: Ziyu

last: Zhai

first: Xuejiao

last: Tian

first: Lei

last: Dong

first: Chunming


title: total RNA-seq from GM19375 (ENCSR908UDN)

first: ENCODE

last: DCC


title: snATAC-seq from Caco-2 (ENCSR908RCU)


title: total RNA-seq from HG03072 (ENCSR908KTG)


title: long read RNA-seq from muscle of arm (ENCSR908EKJ)


title: snATAC-seq from mucosa of gallbladder (ENCSR908HQW)

summary:
scATAC-seq on human mucosa of gallbladder

For data usage terms and conditions, please refer to http://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 HG03057 (ENCSR907GXX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR907DLX)


title: long read RNA-seq from right kidney (ENCSR907BCF)


title: total RNA-seq from T-cell (ENCSR906TQE)


title: long read RNA-seq from left lung (ENCSR906DLM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR905XYH)


title: total RNA-seq from GM19452 (ENCSR905MYA)


title: total RNA-seq from HG03342 (ENCSR906CBF)


title: total RNA-seq from GM21381 (ENCSR901WQE)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR899YQW)


title: total RNA-seq from GM21378 (ENCSR899TLB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR902DVO)


title: total RNA-seq from HG02807 (ENCSR896WTR)


title: snATAC-seq from left colon (ENCSR904WIW)


title: snATAC-seq from heart left ventricle (ENCSR895LPX)


title: long read RNA-seq from muscle of leg (ENCSR899FUU)


title: total RNA-seq from inflammatory macrophage (ENCSR894RTM)


title: long read RNA-seq from adrenal gland (ENCSR891GFR)


title: total RNA-seq from GM21685 (ENCSR890BUJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR898IYQ)


title: snATAC-seq from layer of hippocampus (ENCSR888UYM)


title: total RNA-seq from HG03297 (ENCSR889ALH)


title: long read RNA-seq from thymus (ENCSR888AJG)


title: long read RNA-seq from brain (ENCSR887OJA)


title: snATAC-seq from heart left ventricle (ENCSR886PUY)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR887GNN)


title: total RNA-seq from GM21523 (ENCSR886FYI)


title: long read RNA-seq from renal pelvis (ENCSR885ASQ)


title: polyA plus RNA-seq from GM19141 (ENCSR882MBJ)

summary:
GM19141 RNA Seq

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


title: snATAC-seq from heart left ventricle (ENCSR878VJS)


title: total RNA-seq from GM19454 (ENCSR880BTX)


title: total RNA-seq from HG02583 (ENCSR884LIM)


title: total RNA-seq from GM19399 (ENCSR875USR)


title: total RNA-seq from GM19309 (ENCSR875LVT)


title: total RNA-seq from T-cell (ENCSR872YOT)


title: total RNA-seq from HG03195 (ENCSR874LLG)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR872RMM)


title: total RNA-seq from HG02703 (ENCSR878HUP)


title: snATAC-seq from psoas muscle (ENCSR869LEV)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR281RIH).

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


title: long read RNA-seq from placenta (ENCSR868WMK)


title: total RNA-seq from GM19455 (ENCSR876BFJ)


title: long read RNA-seq from renal pelvis (ENCSR870FIJ)


title: total RNA-seq from HG03446 (ENCSR868HHH)


title: total RNA-seq from T-cell (ENCSR869DEC)


title: total RNA-seq from GM21620 (ENCSR867IMW)


title: total RNA-seq from GM21689 (ENCSR865CQJ)


title: total RNA-seq from GM21365 (ENCSR866TNS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR864XZO)


title: long read RNA-seq from large intestine (ENCSR863ZSG)


title: total RNA-seq from T-helper 9 cell (ENCSR863GGC)


title: total RNA-seq from GM21486 (ENCSR863NTY)


title: snATAC-seq from heart left ventricle (ENCSR862IWS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR864WDM)


title: long read RNA-seq from right kidney (ENCSR861CLZ)


title: total RNA-seq from GM21385 (ENCSR860JQH)


title: total RNA-seq from HG03097 (ENCSR861WHN)


title: snATAC-seq from pancreas (ENCSR862WHQ)

summary:
scATAC-seq 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: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR859LMY)


title: snATAC-seq from adrenal gland (ENCSR858YSB)


title: total RNA-seq from T-cell (ENCSR858IYV)


title: total RNA-seq from HG03117 (ENCSR857HDM)


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR857LPX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR855QFJ)


title: long read RNA-seq from renal cortex interstitium (ENCSR856JRV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR855NNT)


title: total RNA-seq from suppressor macrophage (ENCSR852WOP)


title: total RNA-seq from HG03130 (ENCSR852WYF)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR854HMF)


title: long read RNA-seq from brain (ENCSR852YUV)


title: total RNA-seq from HG03428 (ENCSR851YSK)


title: total RNA-seq from HG03298 (ENCSR851JLM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR852CMR)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR851VJK)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR849CMG)


title: polyA plus RNA-seq from GM20506 (ENCSR847UYP)

summary:
GM20506 RNA Seq

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


title: total RNA-seq from GM21582 (ENCSR848SDO)


title: total RNA-seq from GM21457 (ENCSR845YVK)


title: long read RNA-seq from renal cortex interstitium (ENCSR847IOQ)


title: polyA plus RNA-seq from GM18508 (ENCSR843URE)

summary:
GM18508 RNA Seq

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


title: total RNA-seq from T-cell (ENCSR844IHN)


title: snATAC-seq from heart (ENCSR847HTC)


title: total RNA-seq from HG03539 (ENCSR842QJZ)


title: total RNA-seq from GM19376 (ENCSR841IRK)


title: long read RNA-seq from renal cortex interstitium (ENCSR845JAP)


title: snATAC-seq from HCT116 (ENCSR840IWM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR843USK)


title: total RNA-seq from HG02816 (ENCSR840JAN)


title: total RNA-seq from GM19351 (ENCSR838MLK)


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR837NVN)


title: total RNA-seq from GM21723 (ENCSR836GCO)


title: polyA plus RNA-seq from GM20530 (ENCSR835TRJ)

summary:
GM20530 RNA Seq

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


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR834LNO)


title: total RNA-seq from GM19042 (ENCSR835EWA)


title: snATAC-seq from adrenal gland (ENCSR834NRP)


title: total RNA-seq from inflammatory macrophage (ENCSR835ZHL)


title: total RNA-seq from HG02666 (ENCSR833GYF)


title: total RNA-seq from GM21353 (ENCSR833FBP)


title: total RNA-seq from HG02870 (ENCSR833RNK)


title: snATAC-seq from bile duct (ENCSR833BMK)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR060SEA).

For data usage terms and conditions, please refer to http://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 lobe of right lung (ENCSR830CXR)

summary:
scATAC-seq on human lower lobe of right 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 left colon (ENCSR830FPR)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR289ANH).

For data usage terms and conditions, please refer to http://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 GM21409 (ENCSR830BZO)


title: total RNA-seq from GM21338 (ENCSR828IRM)


title: snATAC-seq from uterus (ENCSR828HVB)


title: total RNA-seq from HG03135 (ENCSR829SDI)


title: total RNA-seq from T-cell (ENCSR827SLT)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR827MSR)


title: total RNA-seq from HG02976 (ENCSR829JXN)


title: polyA plus RNA-seq from GM18519 (ENCSR829TTU)

summary:
GM18519 RNA Seq

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


title: long read RNA-seq from thymus (ENCSR861YGQ)

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, alpha-beta T cell (ENCSR864ZKS)


title: total RNA-seq from GM19308 (ENCSR827CFV)


title: total RNA-seq from HG02614 (ENCSR861ROC)


title: long read RNA-seq from brain (ENCSR859DYW)


title: snATAC-seq from layer of hippocampus (ENCSR826NKW)


title: snATAC-seq from pancreas (ENCSR868CRK)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR281NBH).

For data usage terms and conditions, please refer to http://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 (ENCSR826BSW)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR825GMS)


title: total RNA-seq from inflammatory macrophage (ENCSR823VKN)


title: snATAC-seq from upper lobe of left lung (ENCSR824OCY)


title: long read RNA-seq from left kidney (ENCSR822NSX)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR821QTU)


title: total RNA-seq from HG03484 (ENCSR819LXM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR823OVQ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR838MLG)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR819DXL)


title: long read RNA-seq from testis (ENCSR819LQD)


title: total RNA-seq from HG03112 (ENCSR818OVU)


title: total RNA-seq from HG03190 (ENCSR817XKF)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR817PKK)


title: snATAC-seq from heart right ventricle (ENCSR814OLA)

summary:
scATAC-seq on human 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: total RNA-seq from HG03054 (ENCSR813PJF)


title: total RNA-seq from HG02855 (ENCSR814OFI)


title: polyA plus RNA-seq from GM19225 (ENCSR817BUE)

summary:
GM19225 RNA Seq

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


title: polyA plus RNA-seq from GM18486 (ENCSR849TZZ)

summary:
GM18486 RNA Seq

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


title: long read RNA-seq from muscle of leg (ENCSR813KVN)


title: total RNA-seq from HG03048 (ENCSR812FNH)


title: snATAC-seq from left lung (ENCSR816NWE)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR966DDY).

For data usage terms and conditions, please refer to http://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 GM19378 (ENCSR812EFD)


title: snATAC-seq from type B pancreatic cell (ENCSR811SRE)


title: snATAC-seq from glutamatergic neuron (ENCSR811QVW)


title: total RNA-seq from GM21364 (ENCSR810GEA)


title: total RNA-seq from GM19026 (ENCSR810WKR)


title: long read RNA-seq from heart (ENCSR809SJR)


title: total RNA-seq from GM19024 (ENCSR809PMO)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR824HJH)


title: total RNA-seq from GM21784 (ENCSR808WEZ)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR808TUZ)


title: total RNA-seq from GM21456 (ENCSR807DNU)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR808PWT)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR806QZX)


title: total RNA-seq from GM19391 (ENCSR806ZNR)


title: total RNA-seq from HG03133 (ENCSR806NMB)


title: polyA plus RNA-seq from GM12890 (ENCSR805MXI)

summary:
GM12890 RNA Seq

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


title: total RNA-seq from GM19312 (ENCSR805EHG)


title: total RNA-seq from HG03304 (ENCSR806PZJ)


title: long read RNA-seq from large intestine (ENCSR805BHF)


title: snATAC-seq from fallopian tube (ENCSR815FGT)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR011EDH).

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


title: snATAC-seq from heart left ventricle (ENCSR803QTN)

summary:
scATAC-seq on human heart left ventricle

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


title: total RNA-seq from HG02561 (ENCSR802PYO)


title: polyA plus RNA-seq from GM12878 (ENCSR839BHJ)

summary:
GM12878 RNA Seq

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


title: total RNA-seq from HG02715 (ENCSR840GAJ)


title: total RNA-seq from T-cell (ENCSR802LWN)


title: total RNA-seq from GM19315 (ENCSR800DDH)


title: snATAC-seq from lower lobe of left lung (ENCSR799NRE)

summary:
scATAC-seq on human 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: long read RNA-seq from kidney (ENCSR799GBH)


title: long read RNA-seq from muscle of arm (ENCSR796ZII)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR794BSV)


title: long read RNA-seq from small intestine (ENCSR793FMU)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR791VCC)


title: total RNA-seq from T-cell (ENCSR789XGM)


title: total RNA-seq from T-cell (ENCSR789HHB)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR789GYR)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR787QLY)


title: long read RNA-seq from renal pelvis (ENCSR793ODF)


title: TF ChIP-seq from K562 (ENCSR785RQR)

summary:
JUND ChIP-seq on K562 cells treated with sgRNA targeting CEBPB

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


title: snATAC-seq from heart left ventricle (ENCSR785BSP)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR727OYO).

For data usage terms and conditions, please refer to http://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 (ENCSR788RFN)


title: total RNA-seq from GM18516 (ENCSR786ALR)


title: total RNA-seq from HG02804 (ENCSR783CUF)


title: total RNA-seq from T follicular helper cell (ENCSR783TPV)


title: total RNA-seq from GM18499 (ENCSR780HOX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR779SWL)


title: snATAC-seq from IMR-90 (ENCSR778RZT)


title: snATAC-seq from left cardiac atrium (ENCSR777GVP)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR700UVN).

For data usage terms and conditions, please refer to http://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 GM21418 (ENCSR776FHJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR778BHT)


title: total RNA-seq from HG03198 (ENCSR775YXT)


title: polyA plus RNA-seq from GM18510 (ENCSR775XLU)

summary:
GM18510 RNA Seq

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


title: total RNA-seq from HG03391 (ENCSR775MWA)


title: total RNA-seq from inflammatory macrophage (ENCSR774WVH)


title: total RNA-seq from GM21513 (ENCSR775CYX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR772PIV)


title: snATAC-seq from heart right ventricle (ENCSR772BEX)


title: total RNA-seq from HG03240 (ENCSR771GMU)


title: snATAC-seq from A673 (ENCSR773HYY)


title: total RNA-seq from T-helper 17 cell (ENCSR770ZYC)


title: total RNA-seq from T-cell (ENCSR769XYT)


title: snATAC-seq from heart left ventricle (ENCSR769WLL)


title: total RNA-seq from CD14-positive monocyte (ENCSR769FIE)


title: total RNA-seq from GM19327 (ENCSR769PNT)


title: long read RNA-seq from lung (ENCSR768LJU)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR767VVE)


title: total RNA-seq from GM19463 (ENCSR767WJT)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR765JAZ)


title: total RNA-seq from T-cell (ENCSR766GLB)


title: total RNA-seq from HG02588 (ENCSR764ILD)


title: total RNA-seq from GM19472 (ENCSR763ULK)


title: total RNA-seq from GM21403 (ENCSR763FJK)


title: snATAC-seq from left cerebral cortex (ENCSR761TEQ)


title: snATAC-seq from activated T-helper 1 cell (ENCSR759OSE)


title: total RNA-seq from HG03039 (ENCSR757QTE)


title: total RNA-seq from GM19328 (ENCSR756TOK)


title: total RNA-seq from GM19307 (ENCSR757SIB)


title: snATAC-seq from PC-3 (ENCSR756HYX)


title: Control ChIP-seq from K562 (ENCSR755HEN)

summary:
TEAD4 ChIP-seq on K562 cells treated with vector control shRNA

For data usage terms and conditions, please refer to http://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 GM18879 (ENCSR754UYG)


title: snATAC-seq from MCF-7 (ENCSR754TFT)

summary:
scATAC-seq on human cell line MCF-7

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


title: Extensive Vascular Remodeling Without Widespread Blood-Brain Barrier Disruption in a Murine Model of ZFTA-RELA Ependymoma

status: Public on Jul 29 2026

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

summary:
Background: ZFTA-RELA ependymoma (EPN) is the most common supratentorial pediatric EPN subtype and is associated with poor clinical outcomes. The blood-brain barrier (BBB) is a major obstacle to effective drug delivery into the brain. Brain tumors can exhibit substantial BBB heterogeneity, and the extent to which BBB function is maintained in ZFTA-RELA EPN remains poorly understood. The aim of this study was to examine vascular architecture and BBB status of a ZFTA-RELA EPN murine model (mZRFUS-EPN).
Methods: We performed immunostaining for endothelial and BBB associated markers, transmission electron microscopy of tight junctions, in vivo vascular leakage assays, and single cell RNA-sequencing of isolated endothelial cells to compare cells from normal brain and mZRFUS-EPN.
Results: mZRFUS-EPN exhibit a dense, highly branched vascular network consistent with extensive angiogenic remodeling. Despite these vascular alterations, ultrastructural analysis, BBB marker expression, and in-vivo permeability assays demonstrated that most tumor-associated vessels retained substantial BBB integrity. Single-cell RNA sequencing identified endothelial cell-state remodeling characterized by inflammatory activation across arterial, venous, and capillary endothelial populations. mZRFUS-EPN capillary endothelial cells were enriched in cell-cycle and angiogenic tip-cell genes, consistent with proliferative and angiogenic remodeling in these tumors. Core BBB-associated transcriptional programs, including tight junction genes, transcytosis regulators, efflux transporters, and BBB specification transcription factors, remained largely preserved within tumor-associated endothelial cells.
Conclusions: These findings identify a distinct neurovascular phenotype in mZRFUS-EPN characterized by inflammatory and angiogenic endothelial remodeling with substantial preservation of BBB-associated programs. Improved understanding of BBB biology in pediatric EPN may inform future therapeutic delivery strategies.

overall_design: Single-cell RNA-sequencing (scRNA-seq) was performed on tumor endpoint tissue from ZFTA-RELA Ependymoma (EPN) brain tumor mouse model and matched control brains. This dataset contains CD31-enriched EPN tumor (n=5), CD31-depleted EPN tumor (n=5), CD31-enriched normal brain (n=3) and CD31-depleted normal brain (n=1).

middle: N

first: Sarah

middle: M

last: Reel

first: Ipsita

middle: G

last: Kundu

first: Aaron

middle: Y

last: Mochizuki


title: TF ChIP-seq from HepG2 (ENCSR752CRD)

summary:
JUND ChIP-seq on HepG2 cells treated with sgRNA targeting CEBPB

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


title: snATAC-seq from heart left ventricle (ENCSR750YRO)

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 GM21825 (ENCSR754MPP)


title: total RNA-seq from HG02462 (ENCSR751ZPV)


title: total RNA-seq from HG03159 (ENCSR748JHQ)


title: Single-cell transcriptomic landscape of neoadjuvant chemo-immunotherapy response in lung cancer

city: shanghai

first: Jian

last: Li

address: huaihai road

institute: shanghai chest hospital

summary: This study provides a high-resolution single-cell transcriptional profile of lung cancer in the context of neoadjuvant treatment. Utilizing the 10x Genomics platform, we performed single-cell RNA sequencing (scRNA-seq) on paired patient samples to investigate the cellular composition, phenotypic states, and transcriptional dynamics of the tumor microenvironment in response to the therapeutic intervention.

overall_design: Single-cell RNA sequencing was performed on paired tumor samples obtained from a single lung cancer patient, with no biological replicates. The patient was treated with a neoadjuvant regimen consisting of three cycles of combined chemotherapy and immunotherapy. Samples were collected at two distinct time points for comparative analysis: pre-treatment (baseline) and post-treatment (following the completion of the three-cycle regimen).

first: Zhouwenli

last: Meng

first: Ziming


title: total RNA-seq from T-cell (ENCSR748EWB)


title: total RNA-seq from GM21415 (ENCSR746MWO)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR744MZD)


title: total RNA-seq from HG03077 (ENCSR743UJB)


title: long read RNA-seq from renal pelvis (ENCSR746DTB)


title: total RNA-seq from T-helper 2 cell (ENCSR740VLU)


title: snATAC-seq from CD4-positive, alpha-beta memory T cell (ENCSR737VYM)


title: snATAC-seq from H9 (ENCSR737MVK)


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCSR736ZEJ)


title: long read RNA-seq from stomach (ENCSR735XFJ)


title: total RNA-seq from HG03301 (ENCSR735OOX)


title: snATAC-seq from adrenal gland (ENCSR736ABS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR735EEM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR738ZEH)


title: total RNA-seq from GM18867 (ENCSR734TIT)


title: total RNA-seq from GM21400 (ENCSR734RDY)


title: PRO-cap from HEK293T (ENCSR733DAS)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in ZNF143_T cells.

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


title: total RNA-seq from GM21576 (ENCSR732QBN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR730CSH)


title: long read RNA-seq from thymus (ENCSR728RUN)


title: long read RNA-seq from right kidney (ENCSR729EEX)


title: long read RNA-seq from renal cortex interstitium (ENCSR728OMS)


title: Transcripts identified by microarray analysis that were deregulated in E12.5+18h cultures of murine ureters upon treatment with BIO.

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in murine E12.5+18h ureters upon treatment with BIO.

overall_design: Ureters of NMRI embryos (E12.5) were dissected and cultured for 18h in medium containing 10 µM BIO or in medium without BIO. Total RNA from these ureters was analyzed by microarray analysis.

first: Andreas

last: Kispert


title: long read RNA-seq from left lung (ENCSR730RYS)


title: snATAC-seq from heart (ENCSR727ZZE)


title: total RNA-seq from HG03225 (ENCSR725PAU)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR727RLJ)


title: snATAC-seq from adrenal gland (ENCSR725OFZ)

summary:
scATAC-seq on human adrenal gland

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR725BGI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR723XYM)


title: snATAC-seq from heart left ventricle (ENCSR722PYH)


title: long read RNA-seq from renal pelvis (ENCSR720KOH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR719BLV)


title: total RNA-seq from HG03476 (ENCSR718AKC)


title: total RNA-seq from HG02771 (ENCSR717DMZ)


title: total RNA-seq from T-helper 1 cell (ENCSR716NJG)


title: long read RNA-seq from muscle of arm (ENCSR759MRC)


title: total RNA-seq from GM18504 (ENCSR714BPF)


title: total RNA-seq from HG03085 (ENCSR713PRS)


title: total RNA-seq from HG03096 (ENCSR714BDB)


title: total RNA-seq from GM18881 (ENCSR713NKF)


title: long read RNA-seq from stomach (ENCSR710UTX)


title: total RNA-seq from HG02635 (ENCSR710WEB)


title: total RNA-seq from GM21743 (ENCSR736GHI)


title: long read RNA-seq from muscle of leg (ENCSR710TAV)


title: long read RNA-seq from muscle of arm (ENCSR735BJF)


title: snATAC-seq from natural killer cell (ENCSR710NDM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR710NBJ)


title: long read RNA-seq from renal pelvis (ENCSR709ZJR)


title: total RNA-seq from HG02981 (ENCSR707SQE)


title: polyA plus RNA-seq from GM19099 (ENCSR707NLA)

summary:
GM19099 RNA Seq

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


title: total RNA-seq from GM21485 (ENCSR725LYY)


title: total RNA-seq from GM21786 (ENCSR706CRD)


title: total RNA-seq from GM19466 (ENCSR705FZP)


title: snATAC-seq from activated B cell (ENCSR719QGN)


title: total RNA-seq from HG02805 (ENCSR703LWN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR702QOF)


title: snATAC-seq from heart left ventricle (ENCSR702ELN)


title: snATAC-seq from heart left ventricle (ENCSR701JAT)


title: total RNA-seq from GM19383 (ENCSR699ZYI)


title: total RNA-seq from CD14-positive monocyte (ENCSR699PTC)


title: total RNA-seq from HG02585 (ENCSR699NMP)


title: total RNA-seq from HG03376 (ENCSR698TQK)


title: total RNA-seq from CD14-positive monocyte (ENCSR698REG)


title: total RNA-seq from GM19473 (ENCSR697ZMH)


title: long read RNA-seq from thymus (ENCSR697CGA)


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR697DWS)


title: total RNA-seq from T-helper 2 cell (ENCSR696RIJ)


title: snATAC-seq from HCT116 (ENCSR694GIR)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR692XQE)


title: snATAC-seq from adrenal gland (ENCSR693GAD)

summary:
scATAC on human adrenal gland. Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR724KET)

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


title: long read RNA-seq from muscle of back (ENCSR707LOP)


title: total RNA-seq from GM18874 (ENCSR705UHV)


title: snATAC-seq from heart (ENCSR692IEP)


title: total RNA-seq from HG03209 (ENCSR691PGY)


title: snATAC-seq from activated T-helper 2 cell (ENCSR704RYV)


title: total RNA-seq from GM21613 (ENCSR691LPK)


title: total RNA-seq from GM21742 (ENCSR691EYW)


title: total RNA-seq from GM19435 (ENCSR761GMR)


title: total RNA-seq from GM21744 (ENCSR758CZU)


title: long read RNA-seq from renal cortex interstitium (ENCSR760VAB)


title: snATAC-seq from heart right ventricle (ENCSR690TAY)

summary:
scATAC-seq on human 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: snATAC-seq from pancreas (ENCSR690NZI)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR478FQR).

For data usage terms and conditions, please refer to http://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 fallopian tube (ENCSR690KGJ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR642GFM).

For data usage terms and conditions, please refer to http://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 GM19017 (ENCSR689XHD)


title: total RNA-seq from GM19428 (ENCSR689WRU)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR689TCH)


title: total RNA-seq from inflammatory macrophage (ENCSR689CVI)


title: total RNA-seq from HG03577 (ENCSR750GPT)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR687NTR)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR686VCH)


title: total RNA-seq from HG03455 (ENCSR687YKX)


title: total RNA-seq from HG03397 (ENCSR687FSO)


title: long read RNA-seq from heart (ENCSR746FEO)


title: snATAC-seq from neural crest cell (ENCSR740EIL)


title: total RNA-seq from GM19462 (ENCSR685VLL)


title: long read RNA-seq from small intestine (ENCSR683JMZ)


title: total RNA-seq from HG03259 (ENCSR684FTN)


title: polyA plus RNA-seq from GM19138 (ENCSR682NEW)

summary:
GM19138 RNA Seq

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


title: long read RNA-seq from thymus (ENCSR736GCG)


title: total RNA-seq from T-cell (ENCSR681UBL)


title: snATAC-seq from heart right ventricle (ENCSR681OLJ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR258SZI).

For data usage terms and conditions, please refer to http://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, alpha-beta T cell (ENCSR681CQP)


title: total RNA-seq from GM18870 (ENCSR677VZY)


title: long read RNA-seq from left lung (ENCSR681DGI)


title: snATAC-seq from GM12878 (ENCSR680NPV)


title: total RNA-seq from GM19393 (ENCSR679JYP)


title: total RNA-seq from GM18868 (ENCSR676MJV)


title: snATAC-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR675DJV)


title: total RNA-seq from GM21424 (ENCSR734PKC)


title: snATAC-seq from layer of hippocampus (ENCSR672YNE)


title: total RNA-seq from inflammatory macrophage (ENCSR730DLN)


title: snATAC-seq from HCT116 (ENCSR672VKC)


title: Control ChIP-seq from HepG2 (ENCSR670SEW)

summary:
Input for HepG2 cells treated with sgRNA targeting CEBPB

For data usage terms and conditions, please refer to http://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 CD8-positive, alpha-beta T cell (ENCSR675AMF)


title: total RNA-seq from GM21619 (ENCSR669ZCF)


title: total RNA-seq from GM21683 (ENCSR669PMY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR665YFR)


title: total RNA-seq from GM21647 (ENCSR665XVN)


title: total RNA-seq from GM21732 (ENCSR664DTO)


title: long read RNA-seq from muscle of back (ENCSR663LFJ)


title: snATAC-seq from heart left ventricle (ENCSR686FZG)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR662GSD)


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR662SUW)


title: total RNA-seq from GM19474 (ENCSR662FDP)


title: total RNA-seq from GM19429 (ENCSR661DLG)


title: total RNA-seq from GM18501 (ENCSR660XUE)


title: total RNA-seq from GM21295 (ENCSR660NVC)


title: total RNA-seq from inflammatory macrophage (ENCSR660JYJ)


title: long read RNA-seq from left kidney (ENCSR660EZD)


title: snATAC-seq from left cerebral cortex (ENCSR657LRM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR656FTZ)


title: snATAC-seq from heart left ventricle (ENCSR657WLS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR655SGT)


title: Spatial transcriptomics of bone taken from two PRF1-/-  B16F10-injected  and one PRF1-/-  healthy control- bone tissues using Xenium

status: Public on Jul 28 2026

first: Morgan

last: Huse

address: 417 E 68th St

institute: Sloan Kettering Institute

summary: Spatial transcriptomic profiling was performed on bone tissue from perforin-deficient (Prf1⁻/⁻) mice following bone injection and from Prf1⁻/⁻ uninjected control bone tissue using the 10x Genomics Xenium platform. The study aimed to characterize spatially resolved gene expression changes associated with tumor or cell injection in the absence of perforin-mediated cytotoxic immunity.

overall_design: This study used spatial transcriptomics to investigate gene expression changes in the bone microenvironment under perforin-deficient conditions. Bone tissues were collected from Prf1⁻/⁻ mice following bone injection (Prf1⁻/⁻ injected group) and from Prf1⁻/⁻ uninjected control mice. Spatial gene expression profiling was performed using the 10x Genomics Xenium platform to generate high-resolution, cell-resolved transcriptomic maps of bone tissue architecture.

first: Elbanna

last: Yassmin A

first: Huse

last: Morgan


title: Identification of species differences in structure and function of COMMD3-BMI1 loci in neural stem cells

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

country: Japan

institute: Hiroshima University

summary: Human cerebral development is supported by the continuous proliferation of neural stem cells (NSCs), a process that morphologically and functionally distinguishes humans from other mammals. Several human brain-specific genes are known to contribute to the formation of such species differences. We hypothesize that differences at the epigenomic level also play a role in shaping species-dependent NSC behaviors. In this study, we examined structural interspecies differences in the components of protein regulator of cytokinesis 1 (PRC1), an important transcriptional repressor complex that functions in cortical development. We found that, for BMI1, diversity emerged in the fusion with COMMD3, generating three COMMD3-BMI1 transcripts (COMMD3-BMI1_1-3). We performed a series of knockdown experiments using AF22 cells, a human iPS cell-derived neural stem cell line, and found that the human-specific isoform, COMMD3-BMI1_3, showed the highest NSC proliferative activity, that was comparable to BMI1. These results suggest that the evolutionary acquisition of the human-specific COMMD3-BMI1 isoform has constituted species differences in cerebral development through the enhancement of NSC proliferative activity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AF22 NSCs and BMI1/COMMD3-BMI1 KD derivative.

first: Arisa

last: Makimura

first: Boyang

first: Sota

last: Nishida

first: Tomonori

last: Kameda

first: Fumihiro

last: Morishita

first: Mizuki

last: Honda

first: Takuya

last: Imamura


title: total RNA-seq from HG03028 (ENCSR652AOQ)

first: ENCODE

last: DCC


title: Combination AURKA and WEE1 inhibition exhibits efficacy in EGFR or pan-ERBB inhibitor resistant head and neck squamous cell carcinoma

city: PHILADELPHIA

first: Flaviane

middle: Nunes da

last: Silva

state: PENNSYLVANIA

address: 333 COTTMAN AVENUE

institute: Fox Chase Cancer Center

summary: Over 600,000 cases of head and neck squamous cell carcinoma (HNSCC) are diagnosed globally each year. Many HNSCCs overexpress the ERBB family member EGFR, and EGFR inhibitors (EGFRis) and pan-ERBB inhibitors (ERBBis) are clinically active in treatment of locally advanced, metastatic or recurrent HNSCC. However, resistance to these inhibitors typically develops, often associated with epithelial-mesenchymal transition (EMT). Aurora kinase A (AURKA), a mitotic regulator with expanded signaling functions in tumors, has been reported to reverse EGFR resistance in EGFR-mutated lung cancer. To identify strategies to overcome resistance in HNSCC, we developed HNSCC cell models that were treatment-naïve parental, or selected for resistance to the EGFRi erlotinib, or the ERBBi afatinib. The resistant HNSCC models had typically undergone partial EMT, consistent with clinical resistance, associated with upregulation of the AURKA partner protein NEDD9. Synergy of the AURKA inhibitor VIC-1911 with erlotinib or afatinib in parental models was reduced in resistant models in short term growth assays. In longer term clonogenic assays and in vivo, cells selected for EGFRi/ERBBi resistance showed heightened sensitivity to VIC-1911, contributing to reduced synergy. Based on increased AURKA dependence, we compared combination of VIC-1911 with adavosertib, an inhibitor of the cell cycle checkpoint regulator WEE1, in parental versus resistant models. These showed a combination effect both in vitro and in vivo, that was retained in ERBBi-resistant xenografts, suggesting the potential value of combined AURKA and WEE1 inhibitor use in patients with ERBB inhibitor-resistant HNSCC.

overall_design: To assess transcriptional changes associated with EGFR inhibitor resistance, RNA-seq profiling was conducted on afatinib- and erlotinib-sensitive FaDu and CAL27 parental cell lines and their corresponding EGFR inhibitor–resistant derivatives.

first: Jong

middle: W

last: Lee

first: Theodore

middle: T

last: Nguyen

first: Tetyana

last: Bagnyukova

first: Fiona

last: Goeckel

first: Erica

middle: A

last: Golemis

first: Barbara

last: Burtness

first: Hossein

last: Borghaei


title: total RNA-seq from GM19238 (ENCSR650NFP)


title: total RNA-seq from HG03385 (ENCSR650KFI)


title: total RNA-seq from HG03115 (ENCSR649IOK)


title: long read RNA-seq from muscle of arm (ENCSR649UAP)


title: total RNA-seq from HG02885 (ENCSR649ABR)


title: total RNA-seq from HG03433 (ENCSR644XIP)


title: snATAC-seq from kidney (ENCSR643EOZ)

summary:
scATAC-seq on human kidney

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


title: snATAC-seq from heart left ventricle (ENCSR642ZIC)

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: long read RNA-seq from renal cortex interstitium (ENCSR645EEX)


title: total RNA-seq from HG02938 (ENCSR642VUY)


title: total RNA-seq from suppressor macrophage (ENCSR641VNR)


title: total RNA-seq from suppressor macrophage (ENCSR640LYV)


title: long read RNA-seq from placenta (ENCSR638WIV)


title: long read RNA-seq from renal pelvis (ENCSR639PHC)


title: snATAC-seq from esophagus mucosa (ENCSR639HAJ)

summary:
scATAC-seq on human 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: total RNA-seq from GM21399 (ENCSR638ASI)


title: long read RNA-seq from heart (ENCSR636RRH)


title: total RNA-seq from GM19317 (ENCSR636IKH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR635VLR)


title: snATAC-seq from GM12878 (ENCSR635OKA)

summary:
scATAC-seq on human cell line GM12878

For data usage terms and conditions, please refer to http://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 GM21574 (ENCSR635HYR)


title: snATAC-seq from gastrocnemius (ENCSR634YIW)


title: total RNA-seq from HG03064 (ENCSR633TYQ)


title: total RNA-seq from suppressor macrophage (ENCSR633DOW)


title: total RNA-seq from T-cell (ENCSR632GUZ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR631SUM)


title: total RNA-seq from HG03294 (ENCSR631LSU)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR631KDU)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR631PKY)


title: snATAC-seq from right lobe of liver (ENCSR630YEA)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR367YUX).

For data usage terms and conditions, please refer to http://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 HG02861 (ENCSR629ODY)


title: snATAC-seq from Right ventricle myocardium inferior (ENCSR628POB)

summary:
scATAC on human right ventricle myocardium inferior. Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR151ONW)

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


title: snATAC-seq from activated CD4-positive, alpha-beta T cell (ENCSR628NXO)


title: snATAC-seq from heart left ventricle (ENCSR627IOJ)


title: total RNA-seq from T-helper 1 cell (ENCSR626GTK)


title: snATAC-seq from A549 (ENCSR624OTN)

summary:
scATAC-seq on human cell line A549

For data usage terms and conditions, please refer to http://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 HG03461 (ENCSR628GXS)


title: total RNA-seq from GM21333 (ENCSR623JKQ)


title: total RNA-seq from GM18488 (ENCSR623ENT)


title: total RNA-seq from HG02814 (ENCSR623CFL)


title: total RNA-seq from GM19041 (ENCSR622YIA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR622RGO)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR621JBA)


title: total RNA-seq from HG03103 (ENCSR621PQS)


title: total RNA-seq from GM19355 (ENCSR619NZQ)


title: snATAC-seq from heart left ventricle (ENCSR617IKC)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR616VHK)


title: long read RNA-seq from lung (ENCSR616YXE)


title: snATAC-seq from heart right ventricle (ENCSR615TSN)


title: total RNA-seq from GM21587 (ENCSR615WDX)


title: snATAC-seq from SK-N-SH (ENCSR615PXV)

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

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR615FXW)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR614CXA)


title: total RNA-seq from GM21355 (ENCSR614BQR)


title: total RNA-seq from GM21782 (ENCSR613SZQ)


title: total RNA-seq from GM21583 (ENCSR612PZD)


title: total RNA-seq from HG03166 (ENCSR610MWX)


title: total RNA-seq from HG02676 (ENCSR609WDD)


title: polyA plus RNA-seq from GM12154 (ENCSR609DRM)

summary:
GM12154 RNA Seq

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


title: total RNA-seq from GM21306 (ENCSR608WYC)


title: snATAC-seq from right cardiac atrium (ENCSR607OJR)


title: total RNA-seq from HG03311 (ENCSR608DIJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR607OCT)


title: snATAC-seq from left lung (ENCSR606VJQ)

summary:
scATAC-seq on human 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: total RNA-seq from HG03567 (ENCSR605OJJ)


title: total RNA-seq from HG02759 (ENCSR605FKR)


title: snATAC-seq from heart right ventricle (ENCSR604PDO)

summary:
scATAC-seq on human 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: snATAC-seq from mucosa of descending colon (ENCSR605FGF)

summary:
scATAC-seq on human 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 HG02465 (ENCSR604JSF)


title: long read RNA-seq from right lung (ENCSR602XVJ)


title: total RNA-seq from HG02623 (ENCSR602HXV)


title: long read RNA-seq from spleen (ENCSR602MDH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR598XPW)


title: long read RNA-seq from brain (ENCSR598UIY)


title: total RNA-seq from GM21320 (ENCSR671CAO)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR598HFA)


title: total RNA-seq from HG03479 (ENCSR670PDC)


title: long read RNA-seq from right lung (ENCSR598BKD)


title: snATAC-seq from heart left ventricle (ENCSR668XPI)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR012APQ).

For data usage terms and conditions, please refer to http://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 adrenal gland (ENCSR668VPD)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR667LBE)


title: total RNA-seq from GM21526 (ENCSR667JGU)


title: snATAC-seq from activated CD4-positive, alpha-beta T cell (ENCSR597YWW)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR597FRN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR595BNL)


title: total RNA-seq from HG03300 (ENCSR597QGT)


title: snATAC-seq from heart left ventricle (ENCSR594WKI)


title: total RNA-seq from GM19331 (ENCSR594LOZ)


title: total RNA-seq from GM19446 (ENCSR594AQY)


title: snATAC-seq from colonic mucosa (ENCSR593FCC)

summary:
scATAC-seq on human colonic 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 lower lobe of left lung (ENCSR592WYM)

summary:
scATAC-seq on human 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: long read RNA-seq from right kidney (ENCSR592OXC)


title: total RNA-seq from HG02817 (ENCSR592AEV)


title: total RNA-seq from HG02808 (ENCSR588YMV)


title: snATAC-seq from heart right ventricle (ENCSR588PEE)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR060ZXZ).

For data usage terms and conditions, please refer to http://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 HG03224 (ENCSR588GAR)


title: snATAC-seq from HCT116 (ENCSR587XSM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR587LNN)


title: total RNA-seq from HG03563 (ENCSR658TVR)


title: total RNA-seq from GM21489 (ENCSR587FUD)


title: total RNA-seq from HG03025 (ENCSR586WMW)


title: total RNA-seq from GM21447 (ENCSR655WZX)


title: long read RNA-seq from right kidney (ENCSR655VWF)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR586OMC)


title: long read RNA-seq from left lung (ENCSR585QNX)


title: total RNA-seq from HG02852 (ENCSR585APF)


title: total RNA-seq from HG03439 (ENCSR654AWV)


title: total RNA-seq from GM21440 (ENCSR584IVB)


title: total RNA-seq from GM21631 (ENCSR584DEF)


title: long read RNA-seq from brain (ENCSR582TMC)


title: total RNA-seq from T-helper 2 cell (ENCSR582NNM)


title: total RNA-seq from HG02634 (ENCSR581YIF)


title: polyA plus RNA-seq from GM18861 (ENCSR581EYM)

summary:
GM18861 RNA Seq

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


title: total RNA-seq from T-cell (ENCSR580MYI)


title: snATAC-seq from heart right ventricle (ENCSR579TPC)


title: total RNA-seq from GM18520 (ENCSR578QTT)


title: total RNA-seq from HG03246 (ENCSR578BUG)


title: total RNA-seq from HG02716 (ENCSR577MFW)


title: total RNA-seq from suppressor macrophage (ENCSR577HZI)


title: long read RNA-seq from muscle of leg (ENCSR646BMO)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR575WTO)


title: snATAC-seq from chondrocyte (ENCSR575LID)


title: total RNA-seq from GM21584 (ENCSR575WIT)


title: total RNA-seq from GM21387 (ENCSR573PQE)


title: total RNA-seq from HG03548 (ENCSR572HTN)


title: polyA plus RNA-seq from GM18907 (ENCSR571CLM)

summary:
GM18907 RNA Seq

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


title: snATAC-seq from right lobe of liver (ENCSR568XID)

summary:
scATAC-seq on human right lobe of liver

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


title: total RNA-seq from GM21382 (ENCSR568WYT)

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 HG03136 (ENCSR573ZDH)


title: long read RNA-seq from thymus (ENCSR562KIZ)


title: Control ChIP-seq from K562 (ENCSR562EHT)

summary:
Input for K562 cells treated with shRNA targeting GATA1

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


title: long read RNA-seq from right lung (ENCSR588HDZ)


title: long read RNA-seq from muscle of back (ENCSR559DWD)


title: polyA plus RNA-seq from GM19257 (ENCSR558XAR)

summary:
GM19257 RNA Seq

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


title: long read RNA-seq from muscle of back (ENCSR557ZVE)


title: snATAC-seq from heart left ventricle (ENCSR556UHL)

summary:
scATAC-seq on human heart left ventricle

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


title: total RNA-seq from GM19036 (ENCSR553DGY)


title: long read RNA-seq from renal pelvis (ENCSR558FSR)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR551PHJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR550SAN)


title: total RNA-seq from HG03045 (ENCSR549XOL)


title: total RNA-seq from HG02878 (ENCSR548FDO)


title: snATAC-seq from Right ventricle myocardium superior (ENCSR548IRG)

summary:
scATAC on human right ventricle myocardium superior. Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR813PWQ)

For data usage terms and conditions, please refer to http://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 lobe of right lung (ENCSR548BXU)

summary:
scATAC-seq on human lower lobe of right 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: total RNA-seq from HG03074 (ENCSR547MCI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR547BMD)


title: snATAC-seq from heart left ventricle (ENCSR546WZB)


title: snATAC-seq from gastrocnemius (ENCSR546WNG)


title: total RNA-seq from HG03559 (ENCSR545PEL)


title: total RNA-seq from suppressor macrophage (ENCSR545EEX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR544WYT)


title: total RNA-seq from GM18517 (ENCSR544JRP)


title: total RNA-seq from GM21307 (ENCSR543HAT)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR542LAG)


title: total RNA-seq from HG02646 (ENCSR541YPB)


title: total RNA-seq from HG03394 (ENCSR542GVY)


title: long read RNA-seq from small intestine (ENCSR541NRY)


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCSR541BVY)


title: long read RNA-seq from muscle of back (ENCSR540GZD)


title: total RNA-seq from HG02628 (ENCSR539RRG)


title: Control ChIP-seq from K562 (ENCSR538UCE)

summary:
Input for K562 cells treated with shRNA targeting MAFF

For data usage terms and conditions, please refer to http://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 GM21435 (ENCSR538PUW)


title: total RNA-seq from HG03126 (ENCSR536ION)


title: snATAC-seq from heart right ventricle (ENCSR534KYJ)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR534JDX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR533VJD)


title: snATAC-seq from ovary (ENCSR533CSY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR532WIC)


title: snATAC-seq from heart left ventricle (ENCSR531ZKI)


title: snATAC-seq from gastrocnemius (ENCSR531ZFB)


title: total RNA-seq from GM19395 (ENCSR531ROT)


title: total RNA-seq from GM21362 (ENCSR530TPK)


title: total RNA-seq from GM19404 (ENCSR528NAL)


title: long read RNA-seq from small intestine (ENCSR527XXI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR527RCU)


title: long read RNA-seq from thymus (ENCSR526NUC)


title: total RNA-seq from GM18878 (ENCSR527ODW)


title: total RNA-seq from HG02582 (ENCSR524JBZ)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR524GMW)


title: snATAC-seq from left cerebral cortex (ENCSR521RLW)


title: snATAC-seq from heart right ventricle (ENCSR520ZUD)


title: total RNA-seq from GM19451 (ENCSR520VJV)


title: total RNA-seq from HG02799 (ENCSR520TJP)


title: total RNA-seq from T-helper 1 cell (ENCSR520OSH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR519ARV)


title: total RNA-seq from GM21391 (ENCSR518RPJ)


title: snATAC-seq from adrenal gland (ENCSR525WPH)


title: total RNA-seq from T-cell (ENCSR518BIO)


title: total RNA-seq from T-cell (ENCSR517VKJ)


title: snATAC-seq from layer of hippocampus (ENCSR568LCP)


title: total RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR521WKX)


title: total RNA-seq from GM21686 (ENCSR567XFT)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR563HOA)


title: long read RNA-seq from placenta (ENCSR567LHH)


title: snATAC-seq from heart right ventricle (ENCSR517QNQ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR517QID)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR555ZBQ)


title: total RNA-seq from HG03295 (ENCSR555MCF)


title: polyA plus RNA-seq from GM19204 (ENCSR517FYU)

summary:
GM19204 RNA Seq

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


title: long read RNA-seq from large intestine (ENCSR555FAZ)


title: long read RNA-seq from left kidney (ENCSR555RBI)


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR516UIC)


title: total RNA-seq from HG02811 (ENCSR516NOS)


title: total RNA-seq from HG03267 (ENCSR516MIQ)


title: total RNA-seq from HG03279 (ENCSR552OBZ)


title: total RNA-seq from GM21616 (ENCSR516JGC)


title: snATAC-seq from endothelial cell of umbilical vein (ENCSR516MHK)


title: total RNA-seq from HG02772 (ENCSR515QLF)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR515XBO)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR515OTH)


title: total RNA-seq from HG03547 (ENCSR511HXI)


title: total RNA-seq from GM19028 (ENCSR514RNJ)


title: snATAC-seq from heart left ventricle (ENCSR511VYN)


title: total RNA-seq from central memory CD4-positive, alpha-beta T cell (ENCSR509WMO)


title: total RNA-seq from HG02757 (ENCSR512SSW)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR508LYC)


title: long read RNA-seq from heart (ENCSR508BRD)


title: snATAC-seq from dendritic cell (ENCSR507ZEN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR507PXP)


title: total RNA-seq from HG02895 (ENCSR506UQN)


title: snATAC-seq from heart left ventricle (ENCSR506ROZ)


title: total RNA-seq from HG03370 (ENCSR506SHB)


title: total RNA-seq from HG02574 (ENCSR506DRH)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR545NOS)


title: total RNA-seq from HG03518 (ENCSR505PII)


title: long read RNA-seq from ovary (ENCSR504FSC)


title: long read RNA-seq from muscle of trunk (ENCSR504PXZ)


title: total RNA-seq from GM19380 (ENCSR503MHN)


title: long read RNA-seq from renal pelvis (ENCSR503DHX)


title: snATAC-seq from left cerebral cortex (ENCSR502SUM)


title: Control ChIP-seq from K562 (ENCSR500KIT)

summary:
JUND ChIP-seq on K562 cells treated with control sgRNA

For data usage terms and conditions, please refer to http://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 cardiac atrium (ENCSR499VTJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR499DSM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR497SHC)


title: snATAC-seq from pancreas (ENCSR496XXB)

summary:
scATAC on human pancreas. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR261BXB).

For data usage terms and conditions, please refer to http://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 GM21450 (ENCSR496IWD)


title: total RNA-seq from HG03193 (ENCSR495VON)


title: total RNA-seq from HG02941 (ENCSR495UGE)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR495IOL)


title: snATAC-seq from heart left ventricle (ENCSR495SMB)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR493UEI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR493ROS)


title: snATAC-seq from CD8-positive, alpha-beta memory T cell (ENCSR493QJO)


title: total RNA-seq from GM18858 (ENCSR493LPB)


title: total RNA-seq from HG03499 (ENCSR492IOQ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR491OTO)


title: snATAC-seq from left cardiac atrium (ENCSR491LSZ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR463EEP).

For data usage terms and conditions, please refer to http://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, alpha-beta T cell (ENCSR490SPA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR491BTW)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR490OGB)


title: total RNA-seq from GM21632 (ENCSR489ANE)


title: total RNA-seq from suppressor macrophage (ENCSR487JSW)


title: total RNA-seq from HG02675 (ENCSR488KMC)


title: snATAC-seq from right cardiac atrium (ENCSR486KVX)


title: total RNA-seq from HG03061 (ENCSR486VJZ)


title: total RNA-seq from suppressor macrophage (ENCSR484FKM)


title: total RNA-seq from GM18909 (ENCSR483DZA)


title: snATAC-seq from layer of hippocampus (ENCSR482ORB)


title: Control ChIP-seq from HepG2 (ENCSR482BUK)

summary:
Input for HepG2 cells treated with vector control shRNA

For data usage terms and conditions, please refer to http://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 activated effector memory CD4-positive, alpha-beta T cell (ENCSR480RHI)


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR479TXY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR478YJK)


title: total RNA-seq from GM19443 (ENCSR477REX)


title: long read RNA-seq from kidney (ENCSR476STT)


title: long read RNA-seq from left lung (ENCSR475XGB)


title: total RNA-seq from GM19350 (ENCSR476KJL)


title: long read RNA-seq from lung (ENCSR475SHG)


title: total RNA-seq from HG02586 (ENCSR474GTG)


title: total RNA-seq from suppressor macrophage (ENCSR473SJD)


title: total RNA-seq from HG03100 (ENCSR473POP)


title: PRO-cap from HEK293T (ENCSR473KVF)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in ZNF143_U cells.

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


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCSR473ETU)


title: total RNA-seq from GM21448 (ENCSR472BFR)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR470ZTV)


title: snATAC-seq from endodermal cell (ENCSR470TKG)


title: long read RNA-seq from kidney (ENCSR469YWQ)


title: total RNA-seq from HG03060 (ENCSR468INT)


title: total RNA-seq from HG03445 (ENCSR469UCM)


title: total RNA-seq from T-helper 1 cell (ENCSR467GYH)


title: total RNA-seq from T-helper 2 cell (ENCSR467JQS)


title: snATAC-seq from ureter (ENCSR465CKP)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR464ODS)


title: snATAC-seq from heart left ventricle (ENCSR494FFG)


title: total RNA-seq from GM18502 (ENCSR463LCS)


title: total RNA-seq from suppressor macrophage (ENCSR460NOV)


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCSR463BAI)


title: total RNA-seq from inflammatory macrophage (ENCSR459UIT)


title: polyA plus RNA-seq from GM19114 (ENCSR459TWG)

summary:
GM19114 RNA Seq

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


title: long read RNA-seq from adrenal gland (ENCSR458UIY)


title: total RNA-seq from HG02979 (ENCSR489KYR)


title: total RNA-seq from HG03571 (ENCSR457XXO)


title: total RNA-seq from GM21679 (ENCSR488HDA)


title: long read RNA-seq from renal pelvis (ENCSR457PDH)


title: long read RNA-seq from muscle of arm (ENCSR457CLX)


title: total RNA-seq from GM21414 (ENCSR456PEX)


title: total RNA-seq from HG02621 (ENCSR456LPH)


title: total RNA-seq from GM19320 (ENCSR482YTN)


title: total RNA-seq from GM18511 (ENCSR455FKV)


title: snATAC-seq from heart right ventricle (ENCSR454YDZ)

summary:
scATAC-seq on human 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: total RNA-seq from GM21359 (ENCSR454NRE)


title: snATAC-seq from pancreas (ENCSR481YWC)

summary:
scATAC-seq 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: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR451YWJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR454MAP)


title: snATAC-seq from gastrocnemius (ENCSR451PWE)


title: snATAC-seq from heart left ventricle (ENCSR450VTB)


title: long read RNA-seq from right kidney (ENCSR448TJV)


title: total RNA-seq from GM21454 (ENCSR448VFZ)


title: total RNA-seq from GM18508 (ENCSR447TKM)


title: snATAC-seq from GM23338 (ENCSR446QJT)

summary:
scATAC-seq on human cell line PGP1

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


title: long read RNA-seq from renal cortex interstitium (ENCSR446EHC)

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 GM21371 (ENCSR446ODD)


title: snATAC-seq from Calu3 (ENCSR443NJZ)


title: total RNA-seq from GM19467 (ENCSR443MSV)


title: snATAC-seq from heart right ventricle (ENCSR442RZO)


title: Control ChIP-seq from HepG2 (ENCSR441NSM)

summary:
NR2F2 ChIP-seq on HepG2 cells treated with vector control shRNA

For data usage terms and conditions, please refer to http://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 HG02884 (ENCSR440UOW)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR439ZSL)


title: total RNA-seq from GM21717 (ENCSR473GBY)


title: total RNA-seq from HG03196 (ENCSR439NNZ)


title: total RNA-seq from GM21436 (ENCSR438LON)


title: total RNA-seq from GM21634 (ENCSR439UXE)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR438JKO)


title: long read RNA-seq from thymus (ENCSR437ODI)


title: snATAC-seq from CD8-positive, alpha-beta T cell (ENCSR438DII)


title: total RNA-seq from suppressor macrophage (ENCSR470GWS)


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR436PAE)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR436BAK)


title: snATAC-seq from heart left ventricle (ENCSR435CGY)


title: total RNA-seq from GM19471 (ENCSR434DUZ)


title: total RNA-seq from GM19043 (ENCSR432YJC)


title: long read RNA-seq from stomach (ENCSR431KBL)


title: total RNA-seq from HG02819 (ENCSR430SWN)


title: total RNA-seq from GM18856 (ENCSR429OPS)


title: total RNA-seq from HG03163 (ENCSR428TVC)


title: total RNA-seq from HG03401 (ENCSR428DBM)


title: total RNA-seq from GM21298 (ENCSR427TCZ)


title: snATAC-seq from mucosa of urinary bladder (ENCSR427SIL)

summary:
scATAC-seq on human mucosa of urinary bladder

For data usage terms and conditions, please refer to http://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 activated effector memory CD4-positive, alpha-beta T cell (ENCSR427HHG)


title: polyA plus RNA-seq from GM11840 (ENCSR426RVG)

summary:
GM11840 RNA Seq

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


title: snATAC-seq from layer of hippocampus (ENCSR425RRQ)


title: total RNA-seq from GM21316 (ENCSR424DGE)


title: snATAC-seq from left ventricle myocardium superior (ENCSR425CZQ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR079LVG).

For data usage terms and conditions, please refer to http://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, alpha-beta T cell (ENCSR423XHS)


title: total RNA-seq from GM18853 (ENCSR422TPB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR422HVC)


title: total RNA-seq from HG02953 (ENCSR421OPI)


title: total RNA-seq from GM19316 (ENCSR420UKS)


title: total RNA-seq from activated gamma-delta T cell (ENCSR420NCN)


title: total RNA-seq from GM21488 (ENCSR420IZM)


title: snATAC-seq from adrenal gland (ENCSR420EWQ)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR362YDM).

For data usage terms and conditions, please refer to http://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 CD14-positive monocyte (ENCSR418PAC)


title: total RNA-seq from GM21611 (ENCSR418YCO)


title: total RNA-seq from HG02589 (ENCSR418DEZ)


title: long read RNA-seq from stomach (ENCSR414YMK)


title: total RNA-seq from GM21774 (ENCSR413TFJ)


title: long read RNA-seq from heart (ENCSR416HNH)


title: total RNA-seq from HG02881 (ENCSR413MKK)


title: snATAC-seq from progenitor cell of endocrine pancreas (ENCSR413MCQ)


title: total RNA-seq from HG03105 (ENCSR412WLP)


title: snATAC-seq from heart left ventricle (ENCSR412VTJ)


title: long read RNA-seq from large intestine (ENCSR410YNQ)


title: snATAC-seq from CD14-positive monocyte (ENCSR410OWB)


title: total RNA-seq from HG03127 (ENCSR410NCF)


title: total RNA-seq from HG02839 (ENCSR410BNC)


title: snATAC-seq from heart left ventricle (ENCSR409QLZ)


title: total RNA-seq from HG03132 (ENCSR409MNR)


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCSR409FWR)


title: total RNA-seq from HG03046 (ENCSR406EDK)


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR407ILD)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR408SVX)


title: snATAC-seq from heart left ventricle (ENCSR406CJH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR406AIN)


title: total RNA-seq from CD14-positive monocyte (ENCSR405UWS)


title: total RNA-seq from central memory CD4-positive, alpha-beta T cell (ENCSR403NDE)


title: total RNA-seq from effector CD8-positive, alpha-beta T cell (ENCSR402WEM)


title: total RNA-seq from HG03024 (ENCSR403GEW)


title: total RNA-seq from GM21577 (ENCSR402SJR)


title: snATAC-seq from right lobe of liver (ENCSR402PKA)

summary:
scATAC-seq on human right lobe of liver

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


title: Control ChIP-seq from K562 (ENCSR402HVP)

summary:
Input for K562 cells treated with vector control shRNA

For data usage terms and conditions, please refer to http://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 layer of hippocampus (ENCSR401ARG)


title: snATAC-seq from adrenal gland (ENCSR400PXQ)


title: total RNA-seq from GM21408 (ENCSR399IJT)


title: long read RNA-seq from stomach (ENCSR400AEX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR399CLZ)


title: total RNA-seq from HG03442 (ENCSR399DLV)


title: total RNA-seq from HG02570 (ENCSR398WEL)