title: PRO-cap from pancreas (ENCSR744JVA)

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

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR744SBK)

status: Public on Feb 28 2026

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy 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: DNase-seq from immature natural killer cell (ENCSR748KVP)


title: long read scRNA-seq from adrenal gland (ENCSR744DDC)

type: Expression profiling by high throughput sequencing

summary:
ONT long-read B6/Cast F1 adrenal P4 female ont_match 2k

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


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR744GUN)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR742TYK)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR743TBE)


title: long read scRNA-seq from adrenal gland (ENCSR741JGK)

summary:
PacBio long-read B6/Cast F1 adrenal P25 female normal 2k

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


title: DNase-seq from inflammatory macrophage (ENCSR741KNG)


title: PRO-cap from body of pancreas (ENCSR739MOQ)

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

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


title: DNase-seq from K562 (ENCSR736XRU)


title: DNase-seq from suppressor macrophage (ENCSR737KFS)


title: DNase-seq from NCI-H1930 (ENCSR736SEF)


title: DNase-seq from MCF-7 (ENCSR736LVS)


title: DNase-seq from T47D (ENCSR736LZX)


title: DNase-seq from inflammatory macrophage (ENCSR735SMO)


title: DNase-seq from cerebellum (ENCSR732DJI)


title: DNase-seq from HUDEP-2 (ENCSR736XWN)


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR730VZO)


title: DNase-seq from inflammatory macrophage (ENCSR735HHO)


title: proliferation CRISPR screen from MDA-MB-231 (ENCSR730NOM)

summary:
Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.

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


title: PRO-cap from peripheral blood mononuclear cell (ENCSR740DLY)

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

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


title: DNase-seq from UT-7 (ENCSR732TYX)


title: Flow-FISH CRISPR screen from K562 (ENCSR735KFG)


title: DNase-seq from suppressor macrophage (ENCSR730ACX)


title: DNase-seq from activated B cell (ENCSR729RAF)


title: long read scRNA-seq from adrenal gland (ENCSR728BUZ)

summary:
ONT long-read B6/Cast F1 adrenal P18-20mo female ont_match 2k

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


title: STARR-seq from K562 (ENCSR729EGU)

summary:
Human gDNA fragments were selected based on DHS data, GRO-cap data, and/or histone marks in K562 cells and tested for their enhancer activity with eSTARR-seq. The RNAs derived from the transfected plasmids were sequenced and reported here.

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


title: DNase-seq from T47D (ENCSR730DKS)


title: Flow-FISH CRISPR screen from K562 (ENCSR732MPX)


title: DNase-seq from common myeloid progenitor, CD34-positive (ENCSR727QHM)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR726ZEY)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR726RYN)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR724OUB)


title: DNase-seq from naive B cell (ENCSR723JLO)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR726XQP)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR726KJM)


title: DNase-seq from muscle of leg (ENCSR721NHV)


title: Flow-FISH CRISPR screen from K562 (ENCSR721QHU)


title: DNase-seq from KG1 (ENCSR719XPR)


title: PRO-cap from T-cell (ENCSR723NVI)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in T cells from T1D donor.

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


title: DNase-seq from K562 (ENCSR719SDH)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR724QRE)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR725JPJ)


title: total RNA-seq from regulatory T cell (ENCSR720CUD)


title: Flow-FISH CRISPR screen from K562 (ENCSR718ZYP)


title: DNase-seq from MCF-7 (ENCSR719NFU)


title: DNase-seq from putamen (ENCSR716RVT)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR725ZZX)


title: PRO-cap from peripheral blood mononuclear cell (ENCSR723JIC)


title: DNase-seq from inflammatory macrophage (ENCSR715DPJ)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR715WRI)


title: DNase-seq from common myeloid progenitor, CD34-positive (ENCSR722QLI)


title: Flow-FISH CRISPR screen from K562 (ENCSR721QSX)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR713PIT)


title: PRO-cap from Metastatic Liver Carcinoma in the Lung (ENCSR720EXP)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR719TQI)


title: DNase-seq from immature natural killer cell (ENCSR711KOI)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR712CJF)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR718SCQ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR712GQL)


title: Flow-FISH CRISPR screen from K562 (ENCSR713SMA)

summary:
FADS3

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


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR718UUG)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR718KCD)


title: DNase-seq from liver (ENCSR198EIO)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR718CZL)


title: DNase-seq from activated B cell (ENCSR719XDW)


title: PRO-cap from HCT116 (ENCSR718AQM)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in MED14_T.

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


title: Flow-FISH CRISPR screen from K562 (ENCSR717BYY)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR708BGC)


title: Flow-FISH CRISPR screen from K562 (ENCSR710CKZ)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR196PES)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR194LBI)


title: DNase-seq from GDM1 (ENCSR705NFY)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR194IDR)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR712DRN)


title: Flow-FISH CRISPR screen from Jurkat (ENCSR715NMM)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR711PYQ)


title: PRO-cap from T-cell (ENCSR701MOE)


title: DNase-seq from immature natural killer cell (ENCSR194AQB)


title: DNase-seq from NCI-H1436 (ENCSR707CBD)


title: DNase-seq from CD14-positive monocyte (ENCSR700VUT)


title: DNase-seq from breast epithelium (ENCSR708IUB)


title: PRO-cap from peripheral blood mononuclear cell (ENCSR712UDA)


title: DNase-seq from inflammatory macrophage (ENCSR714TXO)


title: DNase-seq from HUDEP-2 (ENCSR701KRI)


title: Flow-FISH CRISPR screen from K562 (ENCSR711ODF)


title: Flow-FISH CRISPR screen from K562 (ENCSR708OJT)


title: Control CRISPR screen from MCF-7 (ENCSR198LPZ)


title: Flow-FISH CRISPR screen from K562 (ENCSR192ZOX)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR197JOR)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR704CZH)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR708HNS)


title: DNase-seq from K562 (ENCSR710DKJ)


title: DNase-seq from activated B cell (ENCSR194PUL)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR191UKK)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR193CKS)


title: Control CRISPR screen from DU 145 (ENCSR193FCX)


title: FACS CRISPR screen from F123 (ENCSR705PWZ)


title: Flow-FISH CRISPR screen from K562 (ENCSR191YNB)


title: DNase-seq from kidney glomerular epithelial cell (ENCSR704QAK)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR191ADB)


title: DNase-seq from activated T-cell (ENCSR699SPK)


title: Flow-FISH CRISPR screen from K562 (ENCSR190MQK)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR699FZG)


title: DNase-seq from HUDEP-2 (ENCSR190EBK)


title: DNase-seq from DMS53 (ENCSR185JSG)


title: DNase-seq from activated T-cell (ENCSR189TCO)


title: PRO-cap from right lobe of liver (ENCSR694RPO)

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

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


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR698VCR)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR698MMQ)


title: Flow-FISH CRISPR screen from K562 (ENCSR698GAC)


title: FACS CRISPR screen from WTC11 (ENCSR191ECR)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR190OQD)


title: DNase-seq from MCF-7 (ENCSR692MSO)


title: Flow-FISH CRISPR screen from K562 (ENCSR185JLM)


title: DNase-seq from HUDEP-2 (ENCSR187NRI)


title: proliferation CRISPR screen from HepG2 (ENCSR694XBP)


title: Flow-FISH CRISPR screen from K562 (ENCSR185LPT)


title: DNase-seq from inflammatory macrophage (ENCSR184EVK)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR697VRN)


title: DNase-seq from stimulated activated naive CD4-positive, alpha-beta T cell (ENCSR188KVY)


title: DNase-seq from K562 (ENCSR183WIP)


title: DNase-seq from suppressor macrophage (ENCSR694OIL)


title: DNase-seq from colonic mucosa (ENCSR693EXF)


title: Control CRISPR screen from K562 (ENCSR692ZUM)


title: DNase-seq from HUDEP-2 (ENCSR184KYF)


title: DNase-seq from HCT116 (ENCSR690JTP)


title: DNase-seq from HUDEP-2 (ENCSR183LCI)


title: DNase-seq from immature natural killer cell (ENCSR189TKI)


title: proliferation CRISPR screen from OCI-AML2 (ENCSR689KVW)

summary:
CRISPR-dCas9-based epigenomic regulatory element screening (CERES) technology to screen a subset of putative non-coding regulatory elements identified in human K562 leukemia cells from whole genome discovery screen (validation). This validation screen was performed in OCI-AML2 acute myeloid leukemia cells

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


title: Flow-FISH CRISPR screen from Jurkat (ENCSR691FHE)


title: DNase-seq from immature natural killer cell (ENCSR183SNL)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR688KJW)


title: DNase-seq from brain (ENCSR182NVY)


title: FACS CRISPR screen from K562 (ENCSR689CKC)

summary:
CRISPR screen targeting candidate CREs following FACS high

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


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR182DLC)


title: total RNA-seq from regulatory T cell (ENCSR687HLO)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR690DEH)


title: Control CRISPR screen from F123 (ENCSR180JKQ)


title: DNase-seq from brain (ENCSR181VRE)


title: DNase-seq from inflammatory macrophage (ENCSR687GAA)


title: DNase-seq from HUDEP-2 (ENCSR182CAW)


title: DNase-seq from suppressor macrophage (ENCSR179UUK)


title: DNase-seq from cerebellar nuclear complex (ENCSR179ZAO)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR179DAP)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR187PYU)


title: PRO-cap from sigmoid colon (ENCSR179FHG)

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

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


title: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCSR687HZX)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR687CFN)

summary:
CAT

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


title: STARR-seq from A549 (ENCSR687CTB)

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: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCSR180NBV)


title: Control STARR-seq from K562 (ENCSR686XII)

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

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


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR686FHJ)


title: PRO-cap from WTC11 (ENCSR178XKL)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in WTC11.

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


title: proliferation CRISPR screen from K562 (ENCSR686WRO)

summary:
Tiling, dCas9/CRISPRd proliferation screen at the GATA1, MYB, and ZMYND8 loci

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


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR178QSI)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR178XIU)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR177UBF)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR685ZOX)


title: Flow-FISH CRISPR screen from K562 (ENCSR176HTB)


title: STARR-seq from A549 (ENCSR176UAM)


title: DNase-seq from immature natural killer cell (ENCSR182RCX)


title: DNase-seq from HUDEP-2 (ENCSR685WFY)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR685FKP)


title: Flow-FISH CRISPR screen from K562 (ENCSR684QJT)


title: PRO-cap from helper T cell (ENCSR683YVU)

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

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


title: PRO-cap from Pfeiffer (ENCSR683YIA)

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

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


title: DNase-seq from T47D (ENCSR683VUZ)


title: PRO-cap from mesenteric fat pad (ENCSR683FOJ)

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

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


title: long read scRNA-seq from layer of hippocampus (ENCSR683IIF)

summary:
PacBio long-read B6/Cast F1 hippocampus P2mo female normal 2k

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


title: DNase-seq from MCF-7 (ENCSR175QCV)


title: DNase-seq from brain (ENCSR172LRR)


title: DNase-seq from T47D (ENCSR681OAY)


title: Flow-FISH CRISPR screen from K562 (ENCSR175QLP)


title: Flow-FISH CRISPR screen from K562 (ENCSR679QMQ)


title: Flow-FISH CRISPR screen from K562 (ENCSR680YMO)


title: PRO-cap from Metastatic Pancreatic Carcinoma in the Ovary (ENCSR175VMO)

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

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


title: DNase-seq from HUDEP-2 (ENCSR171DQX)


title: DNase-seq from amniotic stem cell (ENCSR174DZU)


title: proliferation CRISPR screen from K562 (ENCSR680PDZ)

summary:
CRISPR screen targeting candidate CREs following survival

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


title: DNase-seq from suppressor macrophage (ENCSR679BYA)


title: DNase-seq from K562 (ENCSR680QDV)


title: DNase-seq from T47D (ENCSR174YEX)


title: DNase-seq from T47D (ENCSR175CXB)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR684OCJ)


title: long read scRNA-seq from layer of hippocampus (ENCSR170VWE)

summary:
PacBio long-read B6/Cast F1 hippocampus P36 male normal 2k

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


title: DNase-seq from T47D (ENCSR685GGU)


title: DNase-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR172RHL)


title: Flow-FISH CRISPR screen from THP-1 (ENCSR171CNP)


title: DNase-seq from HCT116 (ENCSR170ALH)


title: PRO-cap from heart left ventricle (ENCSR676YGJ)

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

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


title: FACS CRISPR screen from glutamatergic neuron (ENCSR678GDA)


title: DNase-seq from CD8-positive, alpha-beta memory T cell (ENCSR677CYJ)


title: Flow-FISH CRISPR screen from K562 (ENCSR169CXG)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR675FHK)


title: total RNA-seq from T-helper 17 cell (ENCSR169MYZ)


title: PRO-cap from testis (ENCSR679CMZ)

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

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


title: long read scRNA-seq from adrenal gland (ENCSR673ZVY)

summary:
PacBio long-read B6/Cast F1 adrenal P18-20mo female normal 2k

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


title: PRO-cap from cerebral cortex (ENCSR675RBN)

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

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR674LCO)


title: DNase-seq from HUDEP-2 (ENCSR674CYS)


title: long read scRNA-seq from layer of hippocampus (ENCSR674HUF)

summary:
PacBio long-read B6/Cast F1 hippocampus P2mo male normal 2k

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


title: DNase-seq from HCT116 (ENCSR671TYL)


title: DNase-seq from NCI-H2081 (ENCSR670QLZ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR670KEJ)


title: DNase-seq from T47D (ENCSR167FNW)


title: Flow-FISH CRISPR screen from K562 (ENCSR169ALP)

summary:
HDAC6

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


title: PRO-cap from Metastatic Lung Carcinoma in the Adrenal Gland (ENCSR673CJC)

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

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


title: FACS CRISPR screen from WTC11 (ENCSR669TMQ)

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


title: DNase-seq from HUDEP-2 (ENCSR167ITZ)


title: DNase-seq from T47D (ENCSR167JCP)


title: DNase-seq from MOLM-13 (ENCSR165WVZ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR670JXY)


title: DNase-seq from immature natural killer cell (ENCSR667XOX)


title: Flow-FISH CRISPR screen from BJAB (ENCSR670JOB)


title: Flow-FISH CRISPR screen from THP-1 (ENCSR664UQJ)


title: DNase-seq from UT-7 (ENCSR668NUT)


title: PRO-cap from Colon Carcinoma Metastatic in the Lung (ENCSR666GXV)

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

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


title: DNase-seq from MCF-7 (ENCSR165ZEV)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR671PJK)


title: DNase-seq from T1000 (ENCSR165VNH)


title: DNase-seq from central memory CD8-positive, alpha-beta T cell (ENCSR665ZKM)


title: DNase-seq from MCF-7 (ENCSR167RKK)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR664QPP)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR664DPC)


title: FACS CRISPR screen from WTC11 (ENCSR662MTS)


title: Flow-FISH CRISPR screen from K562 (ENCSR165TJK)


title: Flow-FISH CRISPR screen from K562 (ENCSR164TJP)


title: STARR-seq from K562 (ENCSR661FOW)


title: Flow-FISH CRISPR screen from K562 (ENCSR662HLC)


title: DNase-seq from urinary bladder (ENCSR160PRT)


title: proliferation CRISPR screen from K562 (ENCSR162HMH)

summary:
CRISPR-dCas9-based epigenomic regulatory element screening (CERES) technology to screen all >100,000 putative non-coding regulatory elements defined by open chromatin sites in human K562 leukemia cells for their role in regulating essential cellular processes (whole genome).

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


title: DNase-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR162NNR)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR164OGQ)


title: DNase-seq from K562 (ENCSR160FPV)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR164QVW)


title: PRO-cap from left lung (ENCSR659YNL)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in 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: Flow-FISH CRISPR screen from K562 (ENCSR657SHO)


title: PRO-cap from heart left ventricle (ENCSR656ZDH)


title: PRO-cap from uterus (ENCSR657RPS)

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

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


title: DNase-seq from COLO668 (ENCSR660IDG)


title: PRO-cap from kidney (ENCSR660UDB)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in 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: Flow-FISH CRISPR screen from BJAB (ENCSR657SBV)


title: DNase-seq from psoas muscle (ENCSR657QWW)


title: DNase-seq from HUDEP-2 (ENCSR652TXP)


title: DNase-seq from activated B cell (ENCSR653JLD)


title: Flow-FISH CRISPR screen from K562 (ENCSR655OXC)


title: DNase-seq from K562 (ENCSR654EFD)


title: Flow-FISH CRISPR screen from K562 (ENCSR657MXN)


title: PRO-cap from aorta (ENCSR657PSE)

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

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


title: DNase-seq from T-helper 1 cell (ENCSR654RJL)


title: FACS CRISPR screen from WTC11 (ENCSR659YFO)


title: Flow-FISH CRISPR screen from K562 (ENCSR650GUQ)


title: DNase-seq from putamen (ENCSR652NYA)


title: Flow-FISH CRISPR screen from K562 (ENCSR651CKH)


title: DNase-seq from T-helper 1 cell (ENCSR650QOL)


title: DNase-seq from T47D (ENCSR652KQY)


title: DNase-seq from DMS79 (ENCSR659DSM)


title: DNase-seq from activated B cell (ENCSR642YPV)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR647HGY)


title: DNase-seq from activated T-cell (ENCSR647OEG)


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR650FUK)


title: PRO-cap from Colon Carcinoma Metastatic in the Brain (ENCSR644TYW)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR642XRC)


title: long read scRNA-seq from adrenal gland (ENCSR641RYW)

summary:
PacBio long-read B6/Cast F1 adrenal P4 male normal 2k

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR647XBL)


title: PRO-cap from tibial artery (ENCSR642TRG)

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

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR642FCN)


title: DNase-seq from immature natural killer cell (ENCSR641JOW)


title: DNase-seq from T47D (ENCSR648YHN)


title: DNase-seq from T-helper 17 cell (ENCSR641OEM)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR639HIL)


title: ATAC-seq from T-helper 17 cell (ENCSR639PPN)


title: DNase-seq from heart (ENCSR641LIG)


title: Flow-FISH CRISPR screen from K562 (ENCSR640NMZ)

summary:
NMU

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR640KVD)


title: DNase-seq from HUDEP-2 (ENCSR639ETN)


title: DNase-seq from HCT116 (ENCSR638LVT)


title: Flow-FISH CRISPR screen from K562 (ENCSR639EDX)

summary:
CAT

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


title: Flow-FISH CRISPR screen from K562 (ENCSR638GOI)


title: Flow-FISH CRISPR screen from K562 (ENCSR638HLU)


title: Flow-FISH CRISPR screen from K562 (ENCSR637ASK)


title: DNase-seq from inflammatory macrophage (ENCSR637ELM)


title: Flow-FISH CRISPR screen from K562 (ENCSR636HVY)


title: DNase-seq from T-helper 1 cell (ENCSR633ZXD)


title: PRO-cap from skeletal muscle tissue (ENCSR636RVF)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR634GWM)


title: Flow-FISH CRISPR screen from K562 (ENCSR632VQO)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR635SLV)


title: PRO-cap from pulmonary lymph node (ENCSR633OWM)

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

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


title: DNase-seq from immature natural killer cell (ENCSR633MZF)


title: Flow-FISH CRISPR screen from K562 (ENCSR630UAQ)


title: DNase-seq from CD14-positive monocyte (ENCSR629GFF)


title: long read scRNA-seq from layer of hippocampus (ENCSR637ORL)

summary:
PacBio long-read B6/Cast F1 hippocampus P14 female normal 2k

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


title: Flow-FISH CRISPR screen from K562 (ENCSR629LGG)


title: DNase-seq from T-cell (ENCSR634AMY)


title: DNase-seq from HCT116 (ENCSR638IGJ)


title: DNase-seq from MCF-7 (ENCSR625NVM)


title: long read scRNA-seq from adrenal gland (ENCSR628CKI)

summary:
PacBio long-read B6/Cast F1 adrenal P10 female normal 2k

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


title: DNase-seq from K562 (ENCSR625KXT)


title: PRO-cap from peritoneum (ENCSR624CVP)

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

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


title: DNase-seq from HUDEP-2 (ENCSR620HHG)

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


title: DNase-seq from T-cell (ENCSR619JBY)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR629CES)


title: DNase-seq from HUDEP-2 (ENCSR619HAW)


title: CRISPR screen from K562 (ENCSR631KBC)

summary:
CRISPR screen targeting candidate CREs following survival

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


title: PRO-cap from ileum (ENCSR618ZHM)

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

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


title: DNase-seq from K562 (ENCSR621ZDQ)


title: Control CRISPR screen from K562 (ENCSR625TAF)


title: PRO-cap from skeletal muscle tissue (ENCSR632XIZ)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR618JKY)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR617VJH)


title: DNase-seq from natural killer cell (ENCSR618TIP)


title: proliferation CRISPR screen from A549 (ENCSR621FIC)

summary:
Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.

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


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR616AQJ)


title: long read scRNA-seq from layer of hippocampus (ENCSR157ZUT)

summary:
ONT long-read B6/Cast F1 hippocampus P14 male ont_match 2k

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


title: DNase-seq from immature natural killer cell (ENCSR611CGE)


title: Flow-FISH CRISPR screen from K562 (ENCSR615FAF)


title: DNase-seq from immature natural killer cell (ENCSR615IPZ)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR160AWN)


title: proliferation CRISPR screen from K562 (ENCSR157EQV)

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

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR156DZX)


title: Flow-FISH CRISPR screen from K562 (ENCSR609RED)


title: DNase-seq from spleen (ENCSR157WNX)


title: DNase-seq from CD14-positive monocyte (ENCSR609PYW)


title: long read scRNA-seq from adrenal gland (ENCSR604HPH)

summary:
PacBio long-read B6/Cast F1 adrenal P14 male normal 2k

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


title: PRO-cap from penis (ENCSR155NVW)

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

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


title: PRO-cap from Metastatic Breast Carcinoma in the Ovary (ENCSR617JRP)

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

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


title: DNase-seq from T47D (ENCSR155XOC)


title: DNase-seq from heart left ventricle (ENCSR606QFW)


title: DNase-seq from NK-92 (ENCSR612JUJ)


title: DNase-seq from MCF-7 (ENCSR606UTF)


title: DNase-seq from HCT116 (ENCSR153ZRJ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR616BQA)


title: PRO-cap from esophagus squamous epithelium (ENCSR153AON)

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

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


title: DNase-seq from MCF-7 (ENCSR152CUE)


title: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCSR610POV)

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

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


title: DNase-seq from K562 (ENCSR152LUV)


title: DNase-seq from kidney (ENCSR604VIY)


title: Flow-FISH CRISPR screen from K562 (ENCSR602DUU)


title: DNase-seq from T47D (ENCSR603IXL)


title: long read scRNA-seq from layer of hippocampus (ENCSR604GLK)

summary:
PacBio long-read B6/Cast F1 hippocampus P10 male normal 2k

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


title: DNase-seq from MCF-7 (ENCSR603YOQ)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR151UPI)


title: Flow-FISH CRISPR screen from K562 (ENCSR601JKO)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR601QTE)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR144JQL)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR146FHV)


title: total RNA-seq from T-helper 1 cell (ENCSR141PRV)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR151MUX)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR600PWZ)


title: DNase-seq from HUDEP-2 (ENCSR139FTB)


title: DNase-seq from MCF-7 (ENCSR150QWZ)


title: proliferation CRISPR screen from K562 (ENCSR138FGY)

summary:
Tiling, dCas9/CRISPRd proliferation screen at the GATA1, MYB, and ZMYND8 loci

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


title: DNase-seq from activated B cell (ENCSR138FUS)


title: DNase-seq from immature natural killer cell (ENCSR138CUE)


title: DNase-seq from MCF-7 (ENCSR150OSO)


title: DNase-seq from activated T-cell (ENCSR147SKP)


title: proliferation CRISPR screen from K562 (ENCSR141ZPC)

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

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


title: FACS CRISPR screen from F123 (ENCSR141PNN)


title: DNase-seq from NCI-H2107 (ENCSR134ODL)


title: total RNA-seq from T-helper 1 cell (ENCSR600QUH)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR136EXX)


title: DNase-seq from K562 (ENCSR133YRZ)


title: DNase-seq from T47D (ENCSR149SET)


title: PRO-cap from Metastatic Liver Carcinoma in the Lung (ENCSR149WMX)

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

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR136JHK)


title: DNase-seq from right lobe of liver (ENCSR131KDD)


title: DNase-seq from pancreas (ENCSR132LSC)


title: long read scRNA-seq from layer of hippocampus (ENCSR137PNB)

summary:
PacBio long-read B6/Cast F1 hippocampus P36 female normal 2k

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


title: DNase-seq from T47D (ENCSR133XWW)

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


title: DNase-seq from HUDEP-2 (ENCSR136SHW)


title: DNase-seq from NOMO-1 (ENCSR144OFT)


title: DNase-seq from CD14-positive monocyte (ENCSR601HWV)


title: Flow-FISH CRISPR screen from K562 (ENCSR130XPY)

summary:
FADS1

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


title: DNase-seq from T-helper 2 cell (ENCSR136URU)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR130SOU)


title: DNase-seq from HUDEP-2 (ENCSR139HUW)


title: DNase-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR140EQO)


title: DNase-seq from immature natural killer cell (ENCSR128IYB)


title: STARR-seq from HepG2 (ENCSR135NXN)


title: DNase-seq from T47D (ENCSR133NSP)


title: DNase-seq from activated T-cell (ENCSR131CTE)


title: Flow-FISH CRISPR screen from K562 (ENCSR126BVU)


title: Flow-FISH CRISPR screen from K562 (ENCSR129IST)

summary:
ERP29

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


title: PRO-cap from SUDHL5 (ENCSR124AWE)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SU-DHL-5.

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


title: DNase-seq from T47D (ENCSR123VCI)


title: PRO-cap from right ventricle myocardium (ENCSR124RWD)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR123OKE)


title: Flow-FISH CRISPR screen from K562 (ENCSR120GMA)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR118HJI)


title: FACS CRISPR screen from glutamatergic neuron (ENCSR119JRG)


title: DNase-seq from NCI-H748 (ENCSR119PWZ)


title: Flow-FISH CRISPR screen from K562 (ENCSR118EQS)


title: proliferation CRISPR screen from WTC11 (ENCSR117YGQ)

summary:
Cell survival-based CRISPR screen targeting genomic regions near MSH2, MSH6, MLH1, PMS2, PCNA and HPRT1 genes.

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


title: PRO-cap from T-cell (ENCSR118KGX)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in T cells from T1D donor.

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


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR117HIN)


title: Flow-FISH CRISPR screen from K562 (ENCSR116VOY)


title: PRO-cap from trachea (ENCSR117JKC)

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

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


title: Flow-FISH CRISPR screen from BJAB (ENCSR115WOS)


title: PRO-cap from colic lymph node (ENCSR122BHP)

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

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


title: FACS CRISPR screen from glutamatergic neuron (ENCSR113CEG)


title: DNase-seq from T47D (ENCSR122QWB)


title: Flow-FISH CRISPR screen from K562 (ENCSR109YFI)


title: DNase-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR116MMP)


title: DNase-seq from T47D (ENCSR118GIG)


title: DNase-seq from inflammatory macrophage (ENCSR105BTM)


title: DNase-seq from inflammatory macrophage (ENCSR111MLU)


title: DNase-seq from HUDEP-2 (ENCSR116FOP)


title: DNase-seq from NCI-H2227 (ENCSR113NAA)


title: Flow-FISH CRISPR screen from K562 (ENCSR113BJT)


title: DNase-seq from activated T-cell (ENCSR108TSN)


title: PRO-cap from pancreas (ENCSR104MSL)

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

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


title: DNase-seq from CD14-positive monocyte (ENCSR103ZWK)


title: Control CRISPR screen from K562 (ENCSR111BOI)


title: Flow-FISH CRISPR screen from Jurkat (ENCSR107RAC)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR108LRW)


title: Flow-FISH CRISPR screen from K562 (ENCSR104CUH)

summary:
CD164

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


title: DNase-seq from HUDEP-2 (ENCSR103CMW)


title: DNase-seq from right cerebral cortex (ENCSR103IUP)


title: DNase-seq from NCI-H2196 (ENCSR099EGC)


title: PRO-cap from paraaortic lymph node (ENCSR100PNA)

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

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR110WYZ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR102GSP)


title: DNase-seq from K562 (ENCSR102SPN)


title: Flow-FISH CRISPR screen from K562 (ENCSR103FXA)


title: DNase-seq from CD14-positive monocyte (ENCSR101KYT)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR098YWP)


title: total RNA-seq from T-helper 2 cell (ENCSR100YQC)


title: DNase-seq from pancreas (ENCSR102GJU)


title: Flow-FISH CRISPR screen from K562 (ENCSR097UHI)


title: DNase-seq from upper lobe of right lung (ENCSR097KCC)


title: Flow-FISH CRISPR screen from K562 (ENCSR097POB)

summary:
LMO2

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


title: DNase-seq from T47D (ENCSR103JOR)


title: Control CRISPR screen from F123 (ENCSR097OCB)


title: DNase-seq from MCF-7 (ENCSR098DVC)


title: DNase-seq from K562 (ENCSR101LUA)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR095GDO)


title: Flow-FISH CRISPR screen from K562 (ENCSR097HQT)


title: DNase-seq from NCI-H146 (ENCSR092COI)


title: PRO-cap from monocyte (ENCSR093JST)

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

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


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR090JIM)


title: DNase-seq from activated T-cell (ENCSR093YYI)


title: DNase-seq from HepG2 (ENCSR094FWH)


title: PRO-cap from T-cell (ENCSR089CQL)


title: DNase-seq from T-cell (ENCSR089GLM)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR088JFQ)


title: Flow-FISH CRISPR screen from K562 (ENCSR088XTH)


title: DNase-seq from MCF-7 (ENCSR084AQX)


title: total RNA-seq from regulatory T cell (ENCSR086CAL)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR094EAF)


title: proliferation CRISPR screen from HCT116 (ENCSR087EPN)


title: PRO-cap from ovary (ENCSR087CGY)

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

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


title: DNase-seq from MCF-7 (ENCSR087DTL)


title: DNase-seq from MCF-7 (ENCSR086GAN)


title: DNase-seq from T47D (ENCSR082VQC)


title: DNase-seq from K562 (ENCSR082TYA)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR092JBF)


title: PRO-cap from B cell (ENCSR083AMN)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR080HHB)


title: DNase-seq from CD14-positive monocyte (ENCSR083DZB)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR093BGQ)


title: DNase-seq from MCF-7 (ENCSR079WDP)


title: DNase-seq from HUDEP-2 (ENCSR079SGU)


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR079MZU)


title: proliferation CRISPR screen from K562 (ENCSR077WEU)

summary:
CRISPR screen targeting candidate CREs following survival

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


title: Flow-FISH CRISPR screen from K562 (ENCSR078IVY)

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: PRO-cap from tibial nerve (ENCSR077MAX)

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

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR076OSM)


title: total RNA-seq from T-helper 1 cell (ENCSR076CCA)


title: DNase-seq from CD14-positive monocyte (ENCSR073CPU)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR074UOT)


title: DNase-seq from posterior vena cava (ENCSR082MKK)


title: Control CRISPR screen from glutamatergic neuron (ENCSR072YHQ)


title: PRO-cap from Colon Carcinoma Metastatic in the Brain (ENCSR074XYR)

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

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


title: proliferation CRISPR screen from WTC11 (ENCSR071ZGB)


title: DNase-seq from K562 (ENCSR070GSY)


title: total RNA-seq from T-helper 1 cell (ENCSR073FPO)


title: DNase-seq from K562 (ENCSR082QLL)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR073PJU)


title: Flow-FISH CRISPR screen from K562 (ENCSR074DRW)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR067MLO)


title: Flow-FISH CRISPR screen from K562 (ENCSR065ZKH)


title: PRO-cap from cytotoxic T cell (ENCSR069DQH)

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

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


title: DNase-seq from CD8-positive, alpha-beta memory T cell (ENCSR071CAW)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR071ZVJ)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR066BYY)


title: DNase-seq from HUDEP-2 (ENCSR069YUO)


title: PRO-cap from T-cell (ENCSR065NDB)


title: DNase-seq from UT-7 (ENCSR067YMF)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR066ARN)


title: Flow-FISH CRISPR screen from K562 (ENCSR063QSP)


title: FACS CRISPR screen from F123 (ENCSR063AQH)


title: PRO-cap from liver (ENCSR072JHG)

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

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


title: DNase-seq from HUDEP-2 (ENCSR073BNC)


title: PRO-cap from left lobe of liver (ENCSR065QHA)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left 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: long read scRNA-seq from layer of hippocampus (ENCSR068XEK)

summary:
PacBio long-read B6/Cast F1 hippocampus P18-20mo male normal 2k

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


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR062EZB)


title: Flow-FISH CRISPR screen from K562 (ENCSR061EUK)


title: PRO-cap from cerebellum (ENCSR062QYF)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR061EPE)


title: DNase-seq from HUDEP-2 (ENCSR062DKN)


title: long read scRNA-seq from adrenal gland (ENCSR062QQH)

summary:
PacBio long-read B6/Cast F1 adrenal P10 male normal 2k

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR061LMN)


title: DNase-seq from T47D (ENCSR060UTU)


title: Flow-FISH CRISPR screen from K562 (ENCSR060PQR)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR060YHM)


title: STARR-seq from HCT116 (ENCSR064KUD)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR056UNT)


title: DNase-seq from K562 (ENCSR057VNM)


title: PRO-cap from cerebellum (ENCSR053UMZ)


title: DNase-seq from T47D (ENCSR054EUF)


title: Flow-FISH CRISPR screen from K562 (ENCSR056IET)


title: Flow-FISH CRISPR screen from K562 (ENCSR059XCK)


title: DNase-seq from bone marrow (ENCSR054JPT)


title: proliferation CRISPR screen from K562 (ENCSR056FSY)

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

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


title: Flow-FISH CRISPR screen from K562 (ENCSR053OQS)


title: DNase-seq from T47D (ENCSR055VFU)


title: Control CRISPR screen from SW620 (ENCSR053SNW)

summary:
Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.

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


title: Flow-FISH CRISPR screen from K562 (ENCSR060KBF)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR051UEN)


title: DNase-seq from erythroblast (ENCSR059YWJ)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR053DYH)


title: DNase-seq from MCF-7 (ENCSR051UHK)


title: Flow-FISH CRISPR screen from K562 (ENCSR052XYV)

summary:
MEF2C

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


title: Control CRISPR screen from WTC11 (ENCSR049FQL)


title: Flow-FISH CRISPR screen from THP-1 (ENCSR050KOD)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR047OET)


title: Control CRISPR screen from K562 (ENCSR048GGL)

summary:
Control for CRISPR screen targeting candidate CREs

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


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR046CHZ)


title: DNase-seq from K562 (ENCSR047PMJ)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR045NQF)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR044QVE)


title: DNase-seq from activated T-cell (ENCSR045TEW)


title: DNase-seq from cardiac muscle cell (ENCSR041RRW)


title: DNase-seq from immature natural killer cell (ENCSR044SGH)


title: PRO-cap from urinary bladder (ENCSR045XAW)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in 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: DNase-seq from T47D (ENCSR039AWQ)


title: proliferation CRISPR screen from K562 (ENCSR039ZOS)

summary:
Functional characterization experiment for dCas9-RYBP/CRISPRi tiling proliferation screens at a subset of cCREs around essential genes

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR043OPR)


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR040VOK)


title: DNase-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR049EWR)


title: DNase-seq from T-helper 17 cell (ENCSR041OZM)


title: Flow-FISH CRISPR screen from K562 (ENCSR048WSZ)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR038NGR)


title: DNase-seq from suppressor macrophage (ENCSR038TGY)


title: DNase-seq from B cell (ENCSR040SOG)


title: DNase-seq from caudate nucleus (ENCSR038QGU)


title: DNase-seq from globus pallidus (ENCSR047NWZ)


title: DNase-seq from activated T-helper 1 cell (ENCSR040KQV)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR036ZBI)


title: DNase-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR036REG)


title: Control STARR-seq from K562 (ENCSR036YOP)

summary:
Single human gDNA fragments and concatenated pairs of such fragments were tested for their enhancer activity with eSTARR-seq. The transfected plasmids (post-transfection DNA sample) were sequenced and reported here.

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


title: total RNA-seq from T-cell (ENCSR036EDO)


title: Flow-FISH CRISPR screen from K562 (ENCSR034NTW)


title: DNase-seq from lower lobe of left lung (ENCSR033FSK)


title: DNase-seq from T47D (ENCSR033ETD)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR032SJX)


title: DNase-seq from caudate nucleus (ENCSR036HFB)


title: DNase-seq from suppressor macrophage (ENCSR031CYX)


title: DNase-seq from suppressor macrophage (ENCSR030ZGP)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR029QFS)


title: DNase-seq from MCF-7 (ENCSR029HEU)


title: DNase-seq from MCF-7 (ENCSR032UZV)


title: Flow-FISH CRISPR screen from K562 (ENCSR028IQA)


title: DNase-seq from T47D (ENCSR031EOD)


title: DNase-seq from T47D (ENCSR026QGE)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR026VVD)


title: long read scRNA-seq from adrenal gland (ENCSR027HXJ)

summary:
ONT long-read B6/Cast F1 adrenal P25 female ont_match 2k

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


title: DNase-seq from HUDEP-2 (ENCSR032WWT)

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


title: Flow-FISH CRISPR screen from K562 (ENCSR021HCT)


title: PRO-cap from right common carotid artery plus branches (ENCSR023NXW)

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

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


title: Control CRISPR screen from WTC11 (ENCSR019PDV)


title: DNase-seq from activated T-cell (ENCSR031UKN)


title: DNase-seq from inflammatory macrophage (ENCSR029DUS)


title: long read scRNA-seq from adrenal gland (ENCSR030XVR)

summary:
ONT long-read B6/Cast F1 adrenal P10 male ont_match 2k

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


title: DNase-seq from inflammatory macrophage (ENCSR023BJE)


title: DNase-seq from T-helper 9 cell (ENCSR020HZH)


title: DNase-seq from T-helper 1 cell (ENCSR019NVA)


title: DNase-seq from brain (ENCSR017MOU)


title: DNase-seq from psoas muscle (ENCSR019MYA)


title: Flow-FISH CRISPR screen from Jurkat (ENCSR018WJG)


title: long read scRNA-seq from adrenal gland (ENCSR016VQS)

summary:
ONT long-read B6/Cast F1 adrenal P4 male ont_match 2k

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


title: DNase-seq from HCT116 (ENCSR017OUV)


title: PRO-cap from uterus (ENCSR015HKC)

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

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


title: DNase-seq from cerebellar nuclear complex (ENCSR013YDQ)


title: Flow-FISH CRISPR screen from K562 (ENCSR014DAS)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR016IMD)


title: Flow-FISH CRISPR screen from K562 (ENCSR014QMX)


title: DNase-seq from inflammatory macrophage (ENCSR019QLA)


title: DNase-seq from MCF-7 (ENCSR013IKT)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR011KKH)


title: DNase-seq from MCF-7 (ENCSR010FDB)


title: Flow-FISH CRISPR screen from K562 (ENCSR009YJO)

summary:
FADS2

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


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR009UTO)


title: DNase-seq from HUDEP-2 (ENCSR013QDF)


title: DNase-seq from K562 (ENCSR010PPW)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR012LNE)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR011COH)


title: DNase-seq from inflammatory macrophage (ENCSR009WGS)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR009BPM)


title: DNase-seq from left cardiac atrium (ENCSR009OHB)


title: Flow-FISH CRISPR screen from K562 (ENCSR004RLG)


title: proliferation CRISPR screen from K562 (ENCSR007UZQ)

summary:
Functional characterization experiment for dCas9-ZNF705-KRAB/CRISPRi tiling proliferation screens at a subset of cCREs around essential genes

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


title: Flow-FISH CRISPR screen from K562 (ENCSR003ALA)


title: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCSR008TSD)

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

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


title: STARR-seq from A549 (ENCSR005XEA)


title: DNase-seq from immature natural killer cell (ENCSR008LND)


title: Flow-FISH CRISPR screen from K562 (ENCSR007DLQ)


title: DNase-seq from T-helper 1 cell (ENCSR008ZMN)


title: Flow-FISH CRISPR screen from K562 (ENCSR002RHQ)


title: DNase-seq from MCF-7 (ENCSR002YFO)


title: proliferation CRISPR screen from K562 (ENCSR013IWY)

summary:
Functional characterization experiment for dCas9-KRAB-WSR7EEE/CRISPRi tiling proliferation screens at a subset of cCREs around essential genes

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


title: total RNA-seq from T-helper 17 cell (ENCSR000YRX)


title: long read scRNA-seq from adrenal gland (ENCSR000GUP)

summary:
PacBio long-read B6/Cast F1 adrenal P14 female normal 2k

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


title: Transcriptome-wide profiling of N6-methyladenosine during shade avoidance response in Arabidopsis

city: Shanghai

first: Lin

last: Li

address: 2005 Songhu Road, Yangpu Distric

department: school of life science

country: China

institute: Fudan university

summary: Shade avoidance is a critical adaptive strategy in plants, enabling rapid growth response to access more sunlight under crowding. Despite N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA and plays critical roles in RNA stability and translation, m6A dynamics and role in shade avoidance remains unclear. To investigate the effect of shade on m6A modification, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) on wild-type Arabidopsis seedlings grown under continuous white light and subjected to 8 h of shade treatment, as well as on the phyB-9 mutant under white light. The results revealed that global m6A modification levels were significantly reduced either after shade treatment or in the phyB-9 mutant.

overall_design: 7-day-old Col-0 seedlings exposed to shade for 8 h and phyB-9 mutant grown under continuous white light

first: Fengquan


title: Identification of CD74-positive antigen presenting glioma cells in primary human tumors and murine models of NF1 high-grade glioma

city: Philadelphia

first: Thomas

last: De Raedt

state: PA

address: 3501 Civic Center boulevard CTRB 4028

institute: CHOP

summary: High-grade gliomas (HGG) arising in the context of Neurofibromatosis type 1 (NF1) present significant therapeutic challenges. To better understand the tumor microenvironment and immune interactions in these tumors, we developed and validated an immunocompetent murine allograft model. Using the NF1-HGG17 cell line, derived from sporadic gliomas in NPcis mice (Nf1/Tp53 mutant), we performed orthotopic allografting into the striatum of male B6 mice. Single-nucleus RNA sequencing (snRNA-seq) was employed to characterize the cellular composition of the tumor at 28 days post-injection.

overall_design: Orthotopic allografting of 10,000 NF1-HGG17 glioma cells into the striatum of male mice (Nf1+/- or wild-type B6). Tumors were harvested 28 days post-injection for nuclei isolation and single-nucleus RNA sequencing (10X Genomics 3' v3.1).

first: Stephanie

last: Brosius

first: Jonathan

last: Sussman

first: Seka

last: Isabelle

first: Steven

last: Foltz

first: Katherine

last: Labella

first: Isabella

last: DiStefano

first: Kai

last: Tan


title: Transcriptional and functional profiles of muscarinic cholinergic receptor-expressing neurons in the primate prefrontal cortex

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

summary: Acetylcholine modulates the anterior cingulate (ACC) and lateral prefrontal (LPFC) cortices via specific m1-m4 muscarinic receptor subtypes (mAChR) encoded by CHRM1-4 genes. Single-nucleus RNA sequencing and mRNA-protein histology in macaques revealed CHRM3 as the most enriched mAChR gene in neurons, while m1 predominates at the protein level, likely due to nuclear retention of CHRM3 and cytoplasmic trafficking of CHRM1. CHRM3 and CHRM1 showed strong co-expression and functional overlap, differing from CHRM2 mainly in calcium signaling-related genes. CHRM2 is uniquely enriched in deep layer excitatory and PVALB+ inhibitory neurons. Although CHRM+ cell distributions are similar between areas, CHRM1–3+ excitatory neurons in ACC exhibited upregulation of synaptic plasticity genes. Functional in vitro experiments confirm a more robust cholinergic-mediated decrease in excitatory:inhibitory synaptic ratio in ACC than in LPFC neurons, accompanied by compensatory changes in spine morphology. These findings highlight region-specific acetylcholine signaling essential for flexible processing, learning and memory.

overall_design: snRNA-seq of ACC and LPFC tissue from 4 adult male rhesus monkeys (Macaca mulatta; ages= 8.5, 8.9, 20.8, 24.8 y.o.)


title: STARR-seq from pancreas (ENCSR001HGB)


title: DNase-seq from CD8-positive, alpha-beta T cell (ENCSR003CJK)


title: ChIP-seq for beta-catenin, EZH2, EED, KMT2B, H3K4me3, H3K27me3 and sequential chipseq

city: Sacramento

first: Yatian

last: Yang

institute: UC Davis

summary: Genome-wide measurements of histone modifications and transcripton factors binding in different prostate cancer clinical tumors tissue, PDX tumor, and cell models to study the tumor lineage plasticity and chromatin bivalency.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq for different histone marks and transcriptional factors in LNCaP_42D, LuCaP_77_ENZR, LuCaP_35CR, MyC-CaPCR, C4-2B, LNCaP and clinical tumor tissue samples.


title: FACS CRISPR screen from F123 (ENCSR004TXD)


title: Effete and Cullin 4 affect nuclear organization of the gypsy chromatin insulator

status: Public on Feb 27 2026

city: Bethesda

first: Elissa

middle: P

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

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

overall_design: Refer to individual Series


title: Single-cell transcriptomic analyses reveal angiogenic vascular responses to chronic cerebral hypoperfusion

city: Pittsburgh

first: Xiaoming

last: Hu

address: 200 lothrop street

department: Neurology

institute: University of Pittsburgh

summary: We employed single-cell RNA sequencing to map cell populations and explore vascular responses in mouse brains collected 42 days after asymmetric common carotid artery stenosis (ACAS)-induced chronic cerebral hypoperfusion

overall_design: Brain hemispheres were collected from the ameroid constrictor side at 42 days after ACAS. Single cells were prepared and subjected to scRNAseq

first: Jun

last: Chen


title: Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk [scRNA-seq and scATAC-seq]

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

summary: Vascular smooth muscle cells contribute to heritable coronary artery disease risk and undergo complex transitions to multiple disease-related phenotypes. To investigate the genetic basis of these trajectories, we develop a dense timecourse single cell transcriptomic and epigenetic map of atherosclerosis in a murine disease model accompanied by high-plex in situ spatial data. Using temporal data and probabilistic fate modeling, we identify key transcription factors that drive cell state changes through a combination of network-based prioritization and in silico transcription factor perturbation. Parallel knockout studies of validated coronary artery disease gene Tcf21 uncover its molecular mechanisms in smooth muscle cell transition, due in part to a role regulating the transition of smooth muscle cells in the secondary heart field. Integrating the murine atlas with human coronary artery disease genetics pinpoint smooth muscle cell phenotypes that mediate disease risk, highlighting causal disease mechanisms. Together, these studies resolve atherosclerosis trajectories at single cell resolution and identify genetic causal transcriptomic and epigenomic mechanisms of coronary artery disease risk.

overall_design: We performed single cell RNA sequencing (scRNAseq) and single-nucleus assay of transposase-accessible sequencing (scATACseq) with aortic root tissue from ApoE-/- (ApoE KO) mice to characterize the complex genetic regulatory networks that control the developmental cascade of smooth muscle cell (SMC) phenotypic transitions in the context of atherosclerotic stress

first: Daniel Y


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [PEM-seq]

status: Public on Feb 26 2026

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

summary: While CRISPR/Cas9 holds therapeutic promise, broader application demands understanding complications in vast non-coding regions. We found that CRISPR/Cas9 can cause premature differentiation of neural stem cells in vivo and mouse embryonic stem cells in vitro, even when cleavage occurred at distant sites tens of kilobases away from the nearest regulatory elements. To investigate this, we employed an integrated ATAC/RNA approach (AR-seq) and identified editing-induced chromatin accessibility change, with its scale varying by cell types. Cells with stemness are most affected, experiencing perturbations that extend over a hundred kilobases. Furthermore, even local DNA perturbations can disrupt CTCF- and condensate-associated chromatin architecture, causing distal transcriptional rewiring and ultimately loss of stemness identity. To minimize chromatin perturbations and preserve cell identity we refined gene editing strategies, including distance-aware sgRNA design, pharmacological attenuation of DNA resection, and alternative editing systems. This work paves the way for safer and broader application of genome editing technologies.

overall_design: To investigate possible misinterpretation of editing-introduced effects, alongside long-read sequencing after editing, we conducted PEM-seq experiments to provide an independent view of possible large deletions or structural variations. In this study, PEM-seq was used to profile the spectrum of repair outcomes around the cut site, including deletion-size distribution and low-frequency rearrangement-like events.

first: Zhu

last: Ming

first: Yuan

last: Junsong

first: Meng

last: Qiuchen

first: Yu

last: Jiawei


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [ATAC-Seq]

overall_design: To characterize how genome editing reshapes chromatin state at and beyond the cleavage locus, we implemented an ATAC-centered design that emphasizes spatial extent and mechanistic interpretability rather than peak-level changes alone. Using the ATAC arm of AR-seq, we quantified editing-associated accessibility shifts as a distance-resolved signal (ΔATAC/ΔATAC span), enabling direct evaluation of whether chromatin perturbation decays with increasing genomic distance from the edit site. The framework was structured to distinguish local DNA damage effects from broad regulatory remodeling by integrating matched RNA outputs, repair-pathway perturbations, and orthogonal chromatin assays. In particular, the design tested whether pathway bias toward resection-prone non-cNHEJ states is linked to broader accessibility propagation, and whether these accessibility changes align with disruption of higher-order regulatory architecture.


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [Long Read Amplicon Sequencing]

overall_design: To rigorously test whether CRISPR-induced phenotypic disruption near stemness-associated regulatory regions is driven by direct structural damage at the edited locus, we implemented an orthogonal validation strategy centered on long-read amplicon Nanopore sequencing. The design rationale was to overcome the resolution limits of conventional short-read assays and gel-based screening, and to quantify the full spectrum of local repair outcomes at single-molecule scale, with particular sensitivity to larger deletion classes. Conceptually, this assay was positioned as a mechanistic discriminator: if distal transcriptional and cell-state perturbations were primarily a consequence of extensive on-target sequence loss, a substantial burden of long deletions would be expected in edited populations.  Accordingly, we profiled locus-spanning long-read amplicons from edited and matched control samples, then quantified deletion-length distributions relative to the nuclease cut site. The analytical framework was designed to distinguish rare large-deletion events from the dominant indel background while controlling for amplification-related representation bias, enabling robust estimation of the structural contribution to phenotype. In parallel with PEM-seq and targeted off-target interrogation, this design provided convergent evidence for interpreting causality: structural lesions were detectable but limited in prevalence, supporting a model in which widespread chromatin/transcriptional rewiring cannot be explained solely by frequent large on-target deletions.


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [Cut&Tag]

overall_design: To investigate whether editing-induced chromatin effects involved changes in active regulatory marks, we performed histone CUT&Tag profiling after genome editing as an orthogonal epigenomic readout. In this study, histone CUT&Tag was used to evaluate how active chromatin signatures around edited loci and nearby regulatory elements changed in relation to the observed accessibility and transcriptional shifts. To investigate whether editing could alter higher-order regulatory architecture through boundary-associated factors, we performed CTCF CUT&Tag after genome editing. Here, CTCF CUT&Tag was designed to measure the extent and direction of CTCF occupancy changes around edited sites, and to test whether these changes were consistent with the chromatin and transcriptional patterns observed in matched samples. We used this assay conservatively as an architectural readout, together with other datasets, to assess whether displacement or reduction of CTCF-linked regulation was a plausible contributor to distal expression changes.


title: scRNAseq analysis of human bronchial epithelial cell air liquid interface cultures infected with the A/Perth/16/2009 H3N2 with and without PA-X

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

summary: The goal of this analysis was to examine the impact of PA-X activity during infection in a model of the human airway epithelium, using primary airway cells from two different donors. We profiled the effects of infection and PA-X activity in various airway epithelial cell types. Donor H1: Male, 21, Caucasian, no health issues noted. Donor H2: Male, 55, Caucasian, no health issues noted.

overall_design: Air liquid interface culture models of the human airway epithelium were differentiated for 3-4 weeks post air lift. Then they were either mock-infected or infected at an MOI of 0.1 with wild type or PA-X deficient A/Perth/16/2009 H3N2. Basal media was replaced and apical surfaces were washed every 24 hours post infection. At 1 and 3 days post infection, cells were trypsinized and dead cells were depleted using an Annexin V binding kit (Stemcell). Viable single cell suspensions were collected and fixed using the Parse Evercode Fixation Kit v3. Library preparation was performed with Parse Evercode WT kit and sequenced on a NovaSeq X Plus 100 cycle 10B flow cell. About 69,000 cells were detected, with a depth of approximately 20,000 reads/cell.

first: Marta Maria

first: Alessandra

last: Setaro


title: Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina

first: Matthew

middle: J

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI


title: Characterization of transcriptomic changes across Coccidioides morphologies using RiboMarker-enhanced RNA sequencing

city: Santa Cruz

first: Deanna

last: Fedash

address: 2125 Delaware Ave

institute: RealSeq Biosciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Coccidioides is a dimorphic, pathogenic fungus responsible for transmission of the mammalian disease colloquially known as “Valley fever”. To better understand the molecular basis of Coccidioides pathogenesis, previous studies have characterized transcriptomes that define transitions between the saprobic and pathogenic life stages of the two species that cause Valley fever - Coccidioides immitis and Coccidioides posadasii. However, none of these studies have focused on small RNA profiles, which have been shown in several pathogenic fungi to play crucial roles in host-pathogen communication, affecting virulence and infectivity. In this study, we analyzed changes in small RNA expression across three major morphologies of C. posadasii: arthroconidia, mycelia, and spherules, from both intracellular and extracellular fractions. Utilizing RiboMarker® small RNA and RNA fragment library preparation, we show enhanced coverage across the transcriptome by increasing incorporation of normally incompatible RNAs into the sequencing pool. Using these data, we observed transcriptomic shifts during the transition of arthroconidia to either mycelia or spherules, marked largely by changes in both protein-coding, tRNA, and unannotated loci. As little is known regarding the mechanisms governing these life stage transitions, these data provide better insight into those small RNA- and fragment-producing genes and loci that may be required for progression between Coccidioides saprobic and parasitic life cycles. Additionally, analysis of fragmentation patterns across all morphologies suggests unique patterns of RNA fragmentation across a cohort of RNA species that correlate with a given ecotype. Finally, we noted evidence of RNA export to the extracellular space, particularly regarding snRNA and tRNA-derived fragments as well as mRNA-derived transcripts, during the transition to either mycelia or spherules, which may play roles in cell-cell, and/or host-pathogen communication. Going forward, this newly established intra- and extracellular Coccidioides sRNA atlas will provide a foundation for potential biomarker discovery and contribute to our understanding of the molecular basis for virulence in Valley fever.

sample_organism:
unidentified
Coccidioides posadasii

platform_organism:
unidentified
Coccidioides posadasii

overall_design: The study investigates how small RNAs change during key life stage transitions in Coccidioides posadasii, the fungus behind Valley fever. A Comparative analysis of intracellular and extracellular small RNA profiles using NGS in three morphologies—arthroconidia, mycelia, and spherules—using a specialized RiboMarker® library preparation to enhance transcriptome coverage.

first: Jonathan

middle: M

last: Howard

first: Aidan

middle: C

last: Manning

first: Rachel

last: Clark

first: Tahirah

last: Williams

first: Clarissa

last: Nobile

first: Sergei

last: Kazakov

first: Sergio

last: Barberan-Soler


title: RNA-seq data from GBM patients and paired organoids

status: Public on Feb 25 2026

city: Pozuelo de Alarcon

first: Angel

middle: Ayuso

last: Sacido

state: Madrid

address: Ctra. Pozuelo-Majadahonda KM 1.800.

department: Faculty of Experimental Sciences

country: Spain

institute: Universidad Francisco de Vitoria

summary: In this study, we have investigated the possibility of using patient derived organoids from GBM patients in order to select personalised treatments. As part of this study, we have performed RNA-seq on 11 paired tumors and their derived organoids without any treatment.

overall_design: This study contain 11 paired samples from GBM patients and their respctive derived organoids after 2 weeks in culture, all untreted. We wanted to investigate the similarities between the original tissue and the paired organoids

last: Ayuso Sacido

first: Noemi

last: Garcia Romero

first: Alvaro

last: Monago Sanchez


title: BALF gene expression profiling reveals innate immune activation bias in persistent post-COVID-19 ILD

city: Voutes

first: Eliza

last: Tsitoura

state: Crete

address: Voutes 70013, Heraklion, Greece

department: Medical School

country: Greece

institute: University of Crete

summary: Survivors of COVID-19 can experience long-term lung complications (pulmonary sequelae), but the underlying mechanisms remain unclear. While most patients with major COVID-19 lung injury eventually recover essentially completely, some experience significant residual damage.   To investigate the underlying differences, we analyzed, using bronchoalveolar lavage fluid (BALF), the alveolar immune cell compartments of a group of patients with post-COVID-19 interstitial lung disease (ILD) six months after acute COVID-19. Patients were categorized into two groups, based on High-Resolution Computed Tomography (HRCT) evaluation a year later: those with persistent HRCT abnormalities compatible with fibrosis (persistent post-COVID-19 ILD, n=6) and those with resolved lung lesions (resolved post-COVID-19 ILD, n=13). Additionally, 6 patients with pre-existing ILD were included in the study, after recovery from COVID-19.  Bulk RNA transcriptomics analyses of BALF cells revealed pathways of neutrophil and monocyte chemotaxis to be enriched in patients with persistent HRCT abnormalities, consistent with increased monocyte-like cell recruitment in the lungs. Furthermore, increased gene expression of markers of pro-fibrotic macrophages/monocytes, such as SPP1 and pro-inflammatory cytokines, such as Il-1b, was also observed. Conversely, patients with resolved post-COVID-19 ILD displayed BALF cell gene expression signatures indicative of T-cell activation. Additionally, BALF gene expression patterns associated with pro-fibrotic macrophage activation, neutrophil chemotaxis and downregulation of T-cell activation were also observed in patients with pre-existing fibrotic ILD following COVID-19.   These findings suggest that immune response imbalance leading to prolonged activation of innate immunity and subdued adaptive immune responses may be associated with persistent post-COVID-19 ILD.

overall_design: We analysed the BALF cells from patients with residual lung abnormalities on average 6 months post severe COVID-19 that were categorized into two groups, based on High-Resolution Computed Tomography (HRCT) evaluation a year later: those with persistent HRCT abnormalities compatible with fibrosis (persistent post-COVID-19 ILD, n=6) and those with resolved lung lesions (resolved post-COVID-19 ILD, n=13). Additionally, 6 patients with pre-existing ILD were included in the study, after recovery from COVID-19.

first: Katerina

last: Antoniou

first: Eirini

last: Vasarmidi


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [RNA-Seq]

first: Jiawei

last: Yu

overall_design: To define the transcriptional consequences of genome editing at regulatory-adjacent non-coding loci, we designed an RNA-centered framework that prioritizes spatially resolved, mechanism-informative readouts rather than endpoint differential expression alone. Specifically, we used the RNA arm of AR-seq to quantify locus-proximal and distal expression perturbation after editing, and formalized these effects as a distance-aware metric (ΔRNA/ΔRNA span) to test whether transcriptional disruption propagates outward from the cut site. This design was coupled to matched chromatin measurements and perturbation controls (including p53 inhibition and repair-pathway modulation) to separate generic stress responses from editing-linked regulatory rewiring. We further integrated 3D genome context to evaluate whether genes proximal in chromatin contact space are preferentially affected relative to genes closer only in linear genomic distance. In aggregate, this study design enables a causal interpretation in which editing-induced transcriptional changes are modeled as structured, distance- and architecture-dependent regulatory perturbations, rather than as nonspecific global expression drift.

first: Zhu

last: Ming

first: Yuan

last: Junsong

first: Meng

last: Qiuchen

first: Yu

last: Jiawei


title: CATCH-seq analysis of 2PN, P1PN, Parthenogenetic, and Androgenetic zygotes.

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

summary: Embryogenesis begins with a zygote, a single cell with two pronuclei that separately enclose maternal and paternal chromosomes. The functional significance of the separation of parental chromosomes into distinct pronuclei remains unexplored, despite the fact that one-pronuclear biparental zygotes are used clinically. Here, using a combination of mouse zygote manipulation, quantitative imaging and theoretical approaches, we show a cytoplasm-mediated competition mechanism between separate parental pronuclei that ensures developmental potential. This mechanism limits pronuclear volume and prevents epigenetic mark dysregulation, including loss of maternal trimethylated histones. One-pronuclear biparental zygotes lack this mechanism, resulting in a reduced rate of development to term. This low developmental potential can be rescued by competition-based or drug-based restoration of epigenetic marks. This study provides a spatial mechanism linking fertilization to the establishment of the full developmental potential for the next generation, highlighting caveats in clinical use of one-pronuclear biparental zygotes.

overall_design: 2PN, P1PN, Parthenogenetic, and Androgenetic zygotes were analyzed by CATCH-seq for H3K4me3 and H3K27me3.

first: Tappei

last: Mishina

first: Tomoya

middle: S

last: Kitajima

first: Masahiro

last: Matsuwaka

first: Mami

last: Kumon

first: Azusa

last: Inoue


title: Individual RNA-seq for different prostate cancer cells, tumors treated by LGK974, ENZ, EPZ6438, EED226 or by CTNNB1 gene knockdown and overexpression, and BRN2 gene knockdown

first: Yatian

last: Yang

summary: Gene expression profile of different prostate cancer clinical tumors and adjacent normal tissue, PDX tumor, and cell models to study the tumor lineage plasticity and chromatin bivalency.

overall_design: RNA-seq for LNCaP, C42B, LNCaP_42D, LuCaP_35CR, MyC-CaP with different treatment.


title: MafB is a conserved transcriptional regulator of macrophage development and identity across tissues and species [CUT&RUN 2]

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

summary: Resident tissue macrophages (RTM) are characterized by a remarkable diversity but also share common features that are thought to be driven by conserved transcriptional programs. While the transcription factor MafB is highly expressed in the macrophage lineage, little is known about its role in establishing RTM identities. Here, we show that the absence of MafB results in a profound imbalance across many RTM populations and in a disruption of global and tissue-specific RTM signatures in mice. Furthermore, we found that MafB was required for the differentiation of bone-marrow-derived macrophages (BMDMs) ex vivo and of RTM populations from monocytes in vivo. Mechanistically, epigenetic profiling of MafB binding sites in BMDMs revealed that MafB directly regulated expression of key RTM differentiation and identity genes, including Csf1r and Fcgr1. Finally, in silico analyses showed that MafB binding sites were highly conserved across vertebrates. Our findings demonstrate the crucial and evolutionarily conserved role of MafB as regulator of RTM development and identity, connecting MafB-dependent transcriptional programs with unique defining features of RTM.

overall_design: To quantify transcriptional activity at MafB binding sites we performed CUT&RUN for H3K27ac on BMDM from Lyz2CreMafbfl/fl (Mafb KO) and Mafbfl/fl littermate controls (Mafb WT).

first: Domien

last: Vanneste

first: Joan

last: Abinet