title: Bru-seq from HCT116 (ENCSR664LAL)

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: CRISPR RNA-seq from K562 (ENCSR667JRK)

status: Public on Dec 04 2022

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Expression profiling by high throughput sequencing

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CAT. (CAT-BGKcLV26)

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


title: CRISPR RNA-seq from HepG2 (ENCSR234UAM)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGHcLV29-B)

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


title: CRISPR RNA-seq from HepG2 (ENCSR232ERY)

summary:
Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV32)

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


title: CRISPR RNA-seq from K562 (ENCSR233MJI)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGKcLV26)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR233IVG)

summary:
human_brain_Rush ID_E3332236_BS97_ENC4_cDNA674

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


title: CRISPR RNA-seq from HepG2 (ENCSR224XSS)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CPSF2. (CPSF2-BGHcLV29)

For data usage terms and conditions, please refer to http://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 K562 (ENCSR223DWL)

summary:
Homo sapiens K562 treated with Bortezomib for 48 hours

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


title: BruChase-seq from endothelial cell of umbilical vein (ENCSR656QKV)


title: CRISPR RNA-seq from K562 (ENCSR218ITU)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SEC31A. (SEC31A-BGKcLV33)

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


title: Bru-seq from HCT116 (ENCSR651PJF)


title: long read RNA-seq from C2C12 (ENCSR221XGR)

summary:
C2C12 Myoblast

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


title: CRISPR RNA-seq from K562 (ENCSR220DTX)

summary:
Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV28)

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


title: CRISPR RNA-seq from K562 (ENCSR654SOD)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against AGFG1. (AGFG1-BGKcLV26)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR216RNR)

summary:
human_brain_Rush ID_E8259623_BS127_ENC4_cDNA689

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


title: long read RNA-seq from layer of hippocampus (ENCSR214HSG)

summary:
Hippocampus1 from 6 mo C57BL/6 male

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


title: CRISPR RNA-seq from HepG2 (ENCSR213ILK)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against LARS. (LARS-BGHcLV24)

For data usage terms and conditions, please refer to http://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 motor neuron (ENCSR215KUO)

summary:
RNA-seq on human motor neuron cell lines

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR209TIR)

summary:
human_brain_Rush ID_E7886851_BS164_ENC4_cDNA714

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR650SDA)

summary:
human_brain_Rush ID_E1805112_BS175_ENC4_cDNA729

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


title: CRISPR RNA-seq from HepG2 (ENCSR650TTU)

summary:
Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV27)

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


title: microRNA-seq from middle frontal area 46 (ENCSR211KOS)

type: Non-coding RNA profiling by high throughput sequencing

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from HepG2 (ENCSR207GTU)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGHcLV31)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR648JOK)

summary:
human_brain_Rush ID_4933693_BS56_ENC4_cDNA652

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


title: microRNA-seq from middle frontal area 46 (ENCSR650DHI)


title: total RNA-seq from K562 (ENCSR206KFV)

summary:
Homo sapiens K562 treated with Galeterone for 4 hours

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


title: microRNA-seq from HL-60 (ENCSR645VXJ)

summary:
RNA Evaluation HL-60 derived M0 macrophages microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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-seq from HCT116 (ENCSR222XCG)

summary:
PRO-seq in SMARCA5_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: CRISPR RNA-seq from HepG2 (ENCSR206ICZ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CHCHD3. (CHCHD3-BGHcLV29)

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


title: CRISPR RNA-seq from K562 (ENCSR642RCV)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against ALDH18A1. (ALDH18A1-BGKcLV26)

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


title: Bru-seq from endothelial cell of umbilical vein (ENCSR651FWH)

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


title: long read RNA-seq from left cerebral cortex (ENCSR644GDT)

summary:
Cortex from 6 mo C57BL/6 male

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR198QAJ)

summary:
human_brain_Rush ID_3002106_BS114_ENC4_cDNA664

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


title: CRISPR RNA-seq from HepG2 (ENCSR199WMC)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against REXO2. (REXO2-BGHcLV32)

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


title: CRISPR RNA-seq from K562 (ENCSR642LZB)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SPAG9. (SPAG9-BGKcLV33)

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR197JLW)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in POLR2A_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: total RNA-seq from T-cell (ENCSR196KBV)

summary:
CD3+_DONOR 4: 0 hour no activation

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR642FZN)

summary:
human_brain_Rush ID_E5410646_BS203_ENC4_cDNA758

For data usage terms and conditions, please refer to http://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 K562 (ENCSR195JRH)

summary:
Homo sapiens K562 treated with JQ1 for 12 hours

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


title: CRISPR RNA-seq from HepG2 (ENCSR191LWZ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ARHGEF2. (ARHGEF2-BGHcLV29)

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


title: microRNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR641JYN)

summary:
RNA Evaluation human naive CD8+ T cell microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR641XXD)

summary:
human_brain_Rush ID_E3760550_BS198_ENC4_cDNA753

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


title: microRNA-seq from left cerebral cortex (ENCSR640XEJ)

summary:
RNA Evaluation mouse PND25 male left cortex microRNA-seq from Mortazavi

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


title: Bru-seq from MCF 10A (ENCSR188PRS)


title: CRISPR RNA-seq from K562 (ENCSR639XFV)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGKcLV33)

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


title: CRISPR RNA-seq from K562 (ENCSR183WOW)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SMG5. (SMG5-BGKcLV33)

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


title: microRNA-seq from Caco-2 (ENCSR638OIX)

summary:
RNA Evaluation human Caco-2 cell line microRNA-seq from Mortazavi

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


title: Bru-seq from WTC11 (ENCSR637ZTH)


title: total RNA-seq from adrenal gland (ENCSR173MHB)

summary:
B6 X Cast adrenal gland_8-10 months female

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


title: microRNA-seq from adrenal gland (ENCSR178KAF)

summary:
RNA Evaluation 5xFAD/Cast mouse male adrenal microRNA-seq from Mortazavi

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


title: microRNA-seq from heart (ENCSR173OTH)

summary:
RNA Evaluation mouse PND36 months female heart microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 layer of hippocampus (ENCSR637GLC)

summary:
B6 X Cast hippocampus_8-10 months female

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR171ZNI)

summary:
human_brain_Rush ID_E1005516_BS117_ENC4_cDNA679

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR634JQK)

summary:
human_brain_Rush ID_9867116_BS108_ENC4_cDNA662

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


title: CRISPR RNA-seq from K562 (ENCSR166VYI)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGKcLV28)

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR635SXX)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in RAD21_U.

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR171CLQ)

summary:
human_brain_Rush ID_E8685549_BS169_ENC4_cDNA719

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


title: CRISPR RNA-seq from K562 (ENCSR633RMN)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CAPRIN1. (CAPRIN1-BGKcLV26)

For data usage terms and conditions, please refer to http://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 K562 (ENCSR165EQJ)

summary:
Homo sapiens K562 treated with MB-3 for 4 hours

For data usage terms and conditions, please refer to http://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-seq from HCT116 (ENCSR163WLJ)

summary:
PRO-seq in SUPT16H_U

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR165QKR)

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

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


title: CRISPR RNA-seq from K562 (ENCSR164POA)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGKcLV28)

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


title: microRNA-seq from MCF 10A (ENCSR165HDP)

summary:
RNA Evaluation human MCF10A cell line microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 K562 (ENCSR165GPK)

summary:
Homo sapiens K562 treated with AR-42 for 48 hours

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR162SPJ)

summary:
human_brain_Rush ID_E6018011_BS156_ENC4_cDNA706

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


title: CRISPR RNA-seq from K562 (ENCSR163RXI)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RBM8A. (RBM8A-BGKcLV30)

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


title: microRNA-seq from middle frontal area 46 (ENCSR160XES)

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

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


title: total RNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR177CWW)

summary:
h.CD4.Naive_DONOR 5: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR631GOR)

summary:
human_brain_Rush ID_E7469354_BS162_ENC4_cDNA712

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


title: microRNA-seq from middle frontal area 46 (ENCSR630RSK)


title: CRISPR RNA-seq from K562 (ENCSR159HPD)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CAST. (CAST-BGKcLV26)

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


title: CRISPR RNA-seq from K562 (ENCSR632RWY)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RECQL5. (RECQL5-BGKcLV30)

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


title: CRISPR RNA-seq from K562 (ENCSR631NIZ)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RNPC3. (RNPC3-BGKcLV30)

For data usage terms and conditions, please refer to http://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 K562 (ENCSR161RSX)

summary:
Homo sapiens K562 treated with MB-3 for 24 hours

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR158VWD)

summary:
human_brain_Rush ID_E7623847_BS163_ENC4_cDNA713

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


title: Bru-seq from HCT116 (ENCSR626FRT)

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: CRISPR RNA-seq from K562 (ENCSR157IJG)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SMG7. (SMG7-BGKcLV33)

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


title: microRNA-seq from middle frontal area 46 (ENCSR158OEV)


title: total RNA-seq from middle frontal area 46 (ENCSR158IHB)

summary:
human_brain_Rush ID_E6590998_BS170_ENC4_cDNA720

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


title: microRNA-seq from layer of hippocampus (ENCSR625RML)

summary:
RNA Evaluation mouse PND25 female hippocampus microRNA-seq from Mortazavi

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


title: microRNA-seq from middle frontal area 46 (ENCSR630MSF)


title: BruChase-seq from endothelial cell of umbilical vein (ENCSR624MRE)


title: microRNA-seq from HL-60 (ENCSR617YSI)

summary:
RNA Evaluation HL-60 derived M2 macrophages (differentiated 12hr) microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR154PNU)

summary:
human_brain_Rush ID_E5387473_BS202_ENC4_cDNA757

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


title: CRISPR RNA-seq from HepG2 (ENCSR153WFE)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against RUVBL2. (RUVBL2-BGHcLV31)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR620YAV)

summary:
human_brain_Rush ID_E1311604_BS172_ENC4_cDNA726

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


title: CRISPR RNA-seq from K562 (ENCSR613ZVB)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against DDX17. (DDX17-BGKcLV28)

For data usage terms and conditions, please refer to http://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 A549 (ENCSR155ZTO)


title: microRNA-seq from middle frontal area 46 (ENCSR153PPA)

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

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


title: microRNA-seq from middle frontal area 46 (ENCSR153LFS)


title: PRO-cap from K562 (ENCSR149ZRX)

summary:
CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and PCR amplification was performed before sequencing.

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


title: CRISPR RNA-seq from K562 (ENCSR608WYZ)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RIOK1. (RIOK1-BGKcLV30)

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


title: CRISPR RNA-seq from HepG2 (ENCSR146ITQ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCTN2. (DCTN2-BGHcLV29)

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


title: microRNA-seq from middle frontal area 46 (ENCSR142LHL)


title: CRISPR RNA-seq from HepG2 (ENCSR608WXK)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF6. (EIF6-BGHcLV24)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR138MMB)

summary:
human_brain_Rush ID_E4646042_BS99_ENC4_cDNA676

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


title: Bru-seq from PC-9 (ENCSR137XKP)


title: polyA plus RNA-seq from left cerebral cortex (ENCSR137GMB)

summary:
Cortex from 6 mo C57BL/6 male

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


title: CRISPR RNA-seq from K562 (ENCSR146YRO)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CTTN. (CTTN-BGKcLV28)

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


title: CRISPR RNA-seq from HepG2 (ENCSR608CUI)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against PSMA1. (PSMA1-BGHcLV25)

For data usage terms and conditions, please refer to http://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 K562 (ENCSR604EBH)

summary:
CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and no PCR amplification was done.

For data usage terms and conditions, please refer to http://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 K562 (ENCSR601DZY)

summary:
Homo sapiens K562 treated with DMSO for 12 hours

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


title: microRNA-seq from middle frontal area 46 (ENCSR135RRX)


title: total RNA-seq from middle frontal area 46 (ENCSR133PLR)

summary:
human_brain_Rush ID_E1703237_BS141_ENC4_cDNA691

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


title: microRNA-seq from middle frontal area 46 (ENCSR134UWT)


title: total RNA-seq from A549 (ENCSR599BTG)

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


title: total RNA-seq from adrenal gland (ENCSR129DEA)

summary:
5xFAD X Cast adrenal gland_8-10 months male

For data usage terms and conditions, please refer to http://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 K562 (ENCSR124KOZ)

summary:
Homo sapiens K562 treated with Galeterone for 24 hours

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR596KAH)

summary:
human_brain_Rush ID_6207143_BS26_ENC4_cDNA655

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


title: CRISPR RNA-seq from K562 (ENCSR122RJE)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGKcLV26)

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


title: microRNA-seq from OCI-LY7 (ENCSR596ZXX)

summary:
RNA Evaluation human OCI-LY7 cell line microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from K562 (ENCSR119PLU)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RUVBL1. (RUVBL1-BGKcLV33)

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


title: CRISPR RNA-seq from K562 (ENCSR593NFA)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against DBNL. (DBNL-BGKcLV28)

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


title: CRISPR RNA-seq from HepG2 (ENCSR119RXN)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPS15A. (RPS15A-BGHcLV32)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR591ZCN)

summary:
human_brain_Rush ID_E6315900_BS205_ENC4_cDNA760

For data usage terms and conditions, please refer to http://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 K562 (ENCSR115PIZ)

summary:
Homo sapiens K562 treated with Chaetocin for 48 hours

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR591NFI)

summary:
human_brain_Rush ID_E2987977_BS146_ENC4_cDNA696

For data usage terms and conditions, please refer to http://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 K562 (ENCSR114HGS)

summary:
CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and PCR amplification was performed before sequencing.

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


title: microRNA-seq from middle frontal area 46 (ENCSR105ZCZ)

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 K562 (ENCSR114LNC)

summary:
Homo sapiens K562 treated with Vorinostat for 4 hours

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


title: microRNA-seq from heart (ENCSR108XJW)

summary:
RNA Evaluation mouse PND 18-20 months male heart microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 K562 (ENCSR105NQB)

summary:
Homo sapiens K562 treated with Vorinostat for 12 hours

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


title: BruChase-seq from Calu3 (ENCSR591KLL)

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: CRISPR RNA-seq from HepG2 (ENCSR104RTM)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against BARD1. (BARD1-BGHcLV25)

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


title: total RNA-seq from T-helper 2 cell (ENCSR588TIV)

summary:
CD4 N (RA+ MACS sort)Th2 (aIFNg 5ug/ml+IL-4 100ng/ml)(day 14)

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


title: total RNA-seq from K562 (ENCSR591KOB)

summary:
Homo sapiens K562 treated with Crizotinib for 24 hours

For data usage terms and conditions, please refer to http://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 left cerebral cortex (ENCSR588BJN)

summary:
B6 X Cast L. cortex (brain)_8-10 months female

For data usage terms and conditions, please refer to http://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 K562 (ENCSR100VUY)

summary:
Homo sapiens K562 treated with Chaetocin for 24 hours

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR102NWB)

summary:
human_brain_Rush ID_E7584572_BS209_ENC4_cDNA764

For data usage terms and conditions, please refer to http://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 K562 (ENCSR100JNS)

summary:
Homo sapiens K562 treated with DMSO for 24 hours

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


title: CRISPR RNA-seq from K562 (ENCSR585UBH)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against ATXN2L. (ATXN2L-BGKcLV26)

For data usage terms and conditions, please refer to http://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 Caco-2 (ENCSR100LIJ)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CACO2.

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR100EDZ)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in RAD21_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: total RNA-seq from middle frontal area 46 (ENCSR096YLM)

summary:
human_brain_Rush ID_E2804864_BS180_ENC4_cDNA734

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


title: CRISPR RNA-seq from K562 (ENCSR096JMV)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RBM26. (RBM26-BGKcLV30)

For data usage terms and conditions, please refer to http://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 endothelial cell of umbilical vein (ENCSR098LLB)

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

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


title: CRISPR RNA-seq from HepG2 (ENCSR585MSI)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against API5. (API5-BGHcLV27)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR585EUI)

summary:
human_brain_Rush ID_E2904121_BS150_ENC4_cDNA700

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


title: Bru-seq from HCT116 (ENCSR093FVX)


title: total RNA-seq from A549 (ENCSR584OXW)


title: CRISPR RNA-seq from HepG2 (ENCSR094AES)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGHcLV31)

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


title: total RNA-seq from heart (ENCSR584OSM)

summary:
5xFAD X Cast heart_8-10 months male

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR090RYJ)

summary:
human_brain_Rush ID_E9716765_BS218_ENC4_cDNA773

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


title: CRISPR RNA-seq from HepG2 (ENCSR085GSF)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGHcLV29)

For data usage terms and conditions, please refer to http://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 gastrocnemius (ENCSR086MHH)

summary:
5xFAD X Cast gastrocnemius_8-10 months male

For data usage terms and conditions, please refer to http://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 natural killer cell (ENCSR584CVV)

summary:
h.CD56+_DONOR 3: 0 hour no activation

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


title: long read RNA-seq from forelimb (ENCSR082JMB)

summary:
Mus musculus strain B6NCrl embryo (13 days) forelimb tissue

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


title: total RNA-seq from middle frontal area 46 (ENCSR080VMJ)

summary:
human_brain_Rush ID_E7244764_BS160_ENC4_cDNA710

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


title: CRISPR RNA-seq from K562 (ENCSR082BCP)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SEC63. (SEC63-BGKcLV33)

For data usage terms and conditions, please refer to http://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 gastrocnemius (ENCSR093SMP)

summary:
5xFAD X Cast gastrocnemius_8-10 months female

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


title: microRNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR077VTG)

summary:
RNA Evaluation human naive CD4+ T cells (activated day 7) microRNA-seq from Mortazavi

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


title: total RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR077EAM)

summary:
h.CD4.Treg_DONOR 4: 0 hour no activation

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


title: CRISPR RNA-seq from HepG2 (ENCSR077MFQ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARS. (CARS-BGHcLV27)

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


title: CRISPR RNA-seq from HepG2 (ENCSR583SHC)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CCDC47. (CCDC47-BGHcLV27)

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


title: microRNA-seq from endothelial cell of umbilical vein (ENCSR076EJO)

summary:
RNA Evaluation human HUVEC primary cells microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR082XSF)

summary:
human_brain_Rush ID_E9620322_BS190_ENC4_cDNA744

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


title: CRISPR RNA-seq from K562 (ENCSR071DBC)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGKcLV26)

For data usage terms and conditions, please refer to http://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 HCT116 (ENCSR074XOP)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in POLR2A_U.

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR078WNY)

summary:
human_brain_Rush ID_E6329379_BS157_ENC4_cDNA707

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


title: microRNA-seq from CD8-positive, alpha-beta T cell (ENCSR583BQO)

summary:
RNA Evaluation human CD8+ T cell microRNA-seq from Mortazavi

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


title: microRNA-seq from activated CD8-positive, alpha-beta T cell (ENCSR092HEE)

summary:
RNA Evaluation human CD8+ T cells (activated day 7) microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from HepG2 (ENCSR076LFC)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGHcLV24)

For data usage terms and conditions, please refer to http://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 OCI-LY7 (ENCSR073XFZ)

summary:
OCI-LY7 for bru-seq comparison

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


title: microRNA-seq from layer of hippocampus (ENCSR076IZU)

summary:
RNA Evaluation 5xFAD/Cast mouse male hippocampus microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from K562 (ENCSR582AOQ)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CWF19L2. (CWF19L2-BGKcLV28)

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


title: CRISPR RNA-seq from K562 (ENCSR068YPI)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGKcLV33)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR067GOC)

summary:
human_brain_Rush ID_E8522907_BS214_ENC4_cDNA769

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR579KTN)

summary:
human_brain_Rush ID_E1488495_BS121_ENC4_cDNA683

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


title: microRNA-seq from middle frontal area 46 (ENCSR067CHU)

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

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


title: microRNA-seq from heart (ENCSR576VFQ)

summary:
RNA Evaluation mouse PND14 months male heart microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR061RDC)

summary:
human_brain_Rush ID_2585111_BS94_ENC4_cDNA671

For data usage terms and conditions, please refer to http://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 K562 (ENCSR062FHL)

summary:
Homo sapiens K562 treated with DMSO for 4 hours

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR061HMO)

summary:
human_brain_Rush ID_4163791_BS53_ENC4_cDNA650

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


title: CRISPR RNA-seq from HepG2 (ENCSR576ASZ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGHcLV29)

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


title: CRISPR RNA-seq from HepG2 (ENCSR060SLE)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGHcLV24)

For data usage terms and conditions, please refer to http://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 motor neuron (ENCSR575MQY)

summary:
RNA-seq on human motor neuron cell lines

For data usage terms and conditions, please refer to http://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 K562 (ENCSR563ZWI)

summary:
Homo sapiens K562 treated with Bortezomib for 4 hours

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


title: CRISPR RNA-seq from K562 (ENCSR054DGN)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CCT3. (CCT3-BGKcLV28)

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


title: CRISPR RNA-seq from HepG2 (ENCSR574ZTO)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against DARS. (DARS-BGHcLV29)

For data usage terms and conditions, please refer to http://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 K562 (ENCSR056HPM)

summary:
Homo sapiens K562 treated with MB-3 for 12 hours

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR564CRW)

summary:
human_brain_Rush ID_E7334238_BS161_ENC4_cDNA711

For data usage terms and conditions, please refer to http://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 WTC11 (ENCSR056TWA)

summary:
Homo sapiens iPSCs (WTC11 cell line) differentiation into cardiomyocytes, Day 0.

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


title: total RNA-seq from activated CD4-positive, alpha-beta T cell (ENCSR052SDT)

summary:
CD4 N (RA+ MACS sort)Th0 (no diff Cytokines)(day 13)+beads (1:3) day 1

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR563SJY)

summary:
human_brain_Rush ID_E9835349_BS192_ENC4_cDNA746

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


title: CRISPR RNA-seq from K562 (ENCSR563QCQ)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGKcLV33)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR052LON)

summary:
human_brain_Rush ID_9158123_BS107_ENC4_cDNA661

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


title: CRISPR RNA-seq from HepG2 (ENCSR051BQF)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CAT. (CAT-BGHcLV27)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR562ORH)

summary:
human_brain_Rush ID_E1208017_BS171_ENC4_cDNA725

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


title: CRISPR RNA-seq from K562 (ENCSR049YEZ)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGKcLV28)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR562BUN)

summary:
human_brain_Rush ID_4163791_BS115_ENC4_cDNA665

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


title: microRNA-seq from left cerebral cortex (ENCSR560FAG)

summary:
RNA Evaluation mouse PND4 female left cortex microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from HepG2 (ENCSR051LWN)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGHcLV25)

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


title: CRISPR RNA-seq from K562 (ENCSR558XPA)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SETD1A. (SETD1A-BGKcLV33)

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


title: CRISPR RNA-seq from K562 (ENCSR046XQE)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against BRD2. (BRD2-BGKcLV26)

For data usage terms and conditions, please refer to http://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 A549 (ENCSR048LHL)

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: CRISPR RNA-seq from HepG2 (ENCSR558DZW)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADD3. (ADD3-BGHcLV25)

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


title: CRISPR RNA-seq from HepG2 (ENCSR044GQU)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CSTF3. (CSTF3-BGHcLV29)

For data usage terms and conditions, please refer to http://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 A673 (ENCSR046BCI)

summary:
A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in A673.

For data usage terms and conditions, please refer to http://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 layer of hippocampus (ENCSR549HQM)

summary:
5xFAD X Cast hippocampus_8-10 months male

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


title: microRNA-seq from gastrocnemius (ENCSR549CLV)

summary:
RNA Evaluation mouse PND 2 months male gastrocnemius microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from K562 (ENCSR041IXV)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RBM25. (RBM25-BGKcLV30)

For data usage terms and conditions, please refer to http://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-seq from HCT116 (ENCSR545GXL)

summary:
PRO-seq in POLR2A_U

For data usage terms and conditions, please refer to http://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-seq from HCT116 (ENCSR545PWV)

summary:
PRO-seq in RAD21_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: CRISPR RNA-seq from K562 (ENCSR036ZTN)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RPL29. (RPL29-BGKcLV30)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR036SUN)

summary:
human_brain_Rush ID_1863332_BS91_ENC4_cDNA668

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


title: CRISPR RNA-seq from K562 (ENCSR544ZMX)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CDC5L. (CDC5L-BGKcLV28)

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


title: CRISPR RNA-seq from HepG2 (ENCSR034VEC)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ROCK2. (ROCK2-BGHcLV32)

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


title: CRISPR RNA-seq from K562 (ENCSR034FLW)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SF3B3. (SF3B3-BGKcLV33)

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


title: CRISPR RNA-seq from HepG2 (ENCSR036HUB)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against SEPT11. (SEPT11-BGHcLV31)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR530OOO)

summary:
human_brain_Rush ID_E8243181_BS167_ENC4_cDNA717

For data usage terms and conditions, please refer to http://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 K562 (ENCSR534TGM)

summary:
Homo sapiens K562 treated with JQ1 for 48 hours

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


title: CRISPR RNA-seq from K562 (ENCSR035MKJ)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CCNT1. (CCNT1-BGKcLV26)

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


title: CRISPR RNA-seq from K562 (ENCSR535TPQ)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SPATS2. (SPATS2-BGKcLV33)

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


title: microRNA-seq from middle frontal area 46 (ENCSR027DKQ)

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from K562 (ENCSR528OVC)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against BZW2. (BZW2-BGKcLV26)

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


title: CRISPR RNA-seq from HepG2 (ENCSR029LLJ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ACTN4. (ACTN4-BGHcLV25)

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


title: Bru-seq from HCT116 (ENCSR025QKI)

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: CRISPR RNA-seq from K562 (ENCSR527XZI)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against CAND1. (CAND1-BGKcLV26)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR539OQU)

summary:
human_brain_Rush ID_E5605087_BS124_ENC4_cDNA686

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


title: CRISPR RNA-seq from HepG2 (ENCSR524NOZ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGHcLV29)

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


title: Bru-seq from Calu3 (ENCSR025EUU)


title: total RNA-seq from middle frontal area 46 (ENCSR530ESE)

summary:
human_brain_Rush ID_E7286104_BS208_ENC4_cDNA763

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


title: microRNA-seq from heart (ENCSR523CTA)

summary:
RNA Evaluation 5xFAD/Cast mouse male heart microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 A549 (ENCSR522CJR)


title: microRNA-seq from activated naive CD4-positive, alpha-beta T cell (ENCSR522TYY)

summary:
RNA Evaluation human naive CD4+ T cells (activated day 2) microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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-seq from HCT116 (ENCSR019RWT)

summary:
PRO-seq in MED14_U

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


title: microRNA-seq from middle frontal area 46 (ENCSR020RPU)


title: total RNA-seq from middle frontal area 46 (ENCSR019ICB)

summary:
human_brain_Rush ID_2327042_BS92_ENC4_cDNA669

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


title: CRISPR RNA-seq from K562 (ENCSR033MIV)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SRA1. (SRA1-BGKcLV33)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR521ZFP)

summary:
human_brain_Rush ID_E6264119_BS159_ENC4_cDNA709

For data usage terms and conditions, please refer to http://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 K562 (ENCSR015SAT)

summary:
Homo sapiens K562 treated with Crizotinib for 48 hours

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


title: microRNA-seq from middle frontal area 46 (ENCSR015QSB)


title: total RNA-seq from middle frontal area 46 (ENCSR015SAL)

summary:
human_brain_Rush ID_E4638217_BS98_ENC4_cDNA675

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR515MED)

summary:
human_brain_Rush ID_E6735279_BS207_ENC4_cDNA762

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


title: CRISPR RNA-seq from HepG2 (ENCSR513CVF)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLNS1A. (CLNS1A-BGHcLV29)

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


title: BruChase-seq from OCI-LY7 (ENCSR014FMT)


title: CRISPR RNA-seq from HepG2 (ENCSR512BIT)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against AIMP1. (AIMP1-BGHcLV27)

For data usage terms and conditions, please refer to http://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 adrenal gland (ENCSR511LAZ)

summary:
5xFAD X Cast adrenal gland_8-10 months female

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR025BZY)

summary:
human_brain_Rush ID_E5374703_BS155_ENC4_cDNA705

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR013HWB)

summary:
human_brain_Rush ID_E8325260_BS168_ENC4_cDNA718

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


title: microRNA-seq from left cerebral cortex (ENCSR013XSN)

summary:
RNA Evaluation 5xFAD/Cast mouse male left cortex microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from K562 (ENCSR012OCK)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against BYSL. (BYSL-BGKcLV26)

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


title: microRNA-seq from mammary epithelial cell (ENCSR022IFZ)

summary:
RNA Evaluation human HMEC cell line microRNA-seq from Mortazavi

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


title: microRNA-seq from F121-9 (ENCSR012KGU)

summary:
RNA Evaluation Cast ES cells microRNA-seq from Mortazavi

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


title: BruChase-seq from OCI-LY7 (ENCSR012JHB)

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: microRNA-seq from left cerebral cortex (ENCSR020XUQ)

summary:
RNA Evaluation mouse PND14 male left cortex microRNA-seq from Mortazavi

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


title: microRNA-seq from middle frontal area 46 (ENCSR507KCT)

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR011VQI)

summary:
h.CD4.Naive_DONOR 5: 0 hour no activation

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR501XXE)

summary:
human_brain_Rush ID_E3439501_BS153_ENC4_cDNA703

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


title: CRISPR RNA-seq from K562 (ENCSR519LZD)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RBM28. (RBM28-BGKcLV30)

For data usage terms and conditions, please refer to http://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 A549 (ENCSR018YHY)


title: total RNA-seq from K562 (ENCSR518BSQ)

summary:
Homo sapiens K562 treated with Crizotinib for 4 hours

For data usage terms and conditions, please refer to http://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-seq from HCT116 (ENCSR516VKD)

summary:
PRO-seq in SUPT16H_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: total RNA-seq from placenta (ENCSR010HIU)

summary:
Stam Placenta 11004 (redo)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR012UFU)

summary:
human_brain_Rush ID_E8969200_BS188_ENC4_cDNA742

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


title: BruChase-seq from mammary epithelial cell (ENCSR497HPX)


title: total RNA-seq from K562 (ENCSR492KRY)

summary:
Homo sapiens K562 treated with Chaetocin for 4 hours

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


title: microRNA-seq from HL-60 (ENCSR496QLS)

summary:
RNA Evaluation HL-60 derived M1 macrophages (differentiated 12hr) microRNA-seq from Mortazavi

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


title: CRISPR RNA-seq from K562 (ENCSR507WAD)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against DDX23. (DDX23-BGKcLV28)

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


title: CRISPR RNA-seq from HepG2 (ENCSR511EKJ)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against ELAC2. (ELAC2-BGHcLV24)

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


title: CRISPR RNA-seq from HepG2 (ENCSR489DNH)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against APTX. (APTX-BGHcLV24)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR483IHO)

summary:
human_brain_Rush ID_7948794_BS24_ENC4_cDNA657

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


title: CRISPR RNA-seq from K562 (ENCSR002JOW)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against RNASEH2A. (RNASEH2A-BGKcLV30)

For data usage terms and conditions, please refer to http://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 K562 (ENCSR006EBD)

summary:
Homo sapiens K562 treated with GSK J4 for 4 hours

For data usage terms and conditions, please refer to http://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 gastrocnemius (ENCSR000OCV)

summary:
B6 X Cast gastrocnemius_8-10 months male

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


title: microRNA-seq from middle frontal area 46 (ENCSR010OLA)

summary:
RNA Evaluation human Rush brain microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://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 motor neuron (ENCSR499AEH)

summary:
RNA-seq on human motor neuron cell lines

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


title: Identification of circularRNAs in neutrophil of type 2 diabetic mice

status: Public on Dec 03 2022

city: Kitakyushu

first: Takahiro

last: Umehara

address: 1-1 Iseigaoka Yahatanishiku

country: Japan

institute: University of Occupational and Environmental Health

summary: To clarify the molecular mechanism of inflammatory control in diabetic-derived neutrophils, we screened for changes of circRNA expression in diabetic-derived neutrophils using microarrays.

overall_design: non-db-derived neutrophils vs db-derived neutrophils


title: Bru-seq from HCT116 (ENCSR008ZZZ)

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


title: total RNA-seq from middle frontal area 46 (ENCSR497KUU)

summary:
human_brain_Rush ID_E3666162_BS197_ENC4_cDNA752

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


title: A broadly conserved fungal alcohol oxidase (AOX) facilitates fungal invasion of plants

status: Public on Dec 02 2022

city: Madison

first: Mehdi

last: Kabbage

state: WI

address: 1630 Linden Drive

institute: UW Madison

summary: Alcohol oxidases are ecologically important enzymes which facilitate a number of plant-fungal interactions. Within Ascomycota they are primarily associated with methylotrophy, as a peroxisomal alcohol oxidase (AOX) catalyzing the conversion of methanol to formaldehyde in methylotrophic yeast. In this study we demonstrate that AOX orthologs are phylogenetically conserved proteins which are common in the genomes of non-methylotrophic, plant-associating fungi. Additionally, AOX orthologs are highly expressed during infection in a range of diverse pathosystems. To study the role of AOX in plant colonization, AOX knockout mutants were generated in the broad host range pathogen Sclerotinia sclerotiorum. Disease assays in soybean showed that these mutants had a significant virulence defect as evidenced by markedly reduced stem lesions and mortality rates. Chemical genomics suggest that SsAOX may function as an aromatic alcohol oxidase, and growth assays demonstrate that ΔSsAOX is incapable of properly utilizing plant extract as a nutrient source. Profiling of known aromatic alcohols point towards the monolignol coniferyl alcohol (CoA) as a possible substrate for SsAOX. As CoA and other monolignols are ubiquitous among land plants, the presence of highly conserved AOX orthologs throughout Ascomycota imply that this is a broadly conserved protein used by ascomycete fungi during plant colonization.

overall_design: WT (1980) and ΔSsAOX S. sclerotiorum was grown in 1% glucose minimal media (GMM) for three days, before being transferred to fresh 1% GMM containing 1% soybean stem extract. Cultures were grown for an additional 4 hours before being flash frozen in liquid nitrogen and subjected to RNA extraction using a Maxwell RSC Plant RNA kit.

first: Nathaniel

last: Westrick


title: microRNA-seq from middle frontal area 46 (ENCSR493UZT)


title: Migration deficits of neural crest caused by CXADR triplication in a Human Down Syndrome Stem Cell Model

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

country: China

institute: Sun Yat-sen university

summary: Here, Down syndrome-specific hiPSCs (DS1-hiPSCs and DS2-hiPSCs) were induced to differentiate to neural crest stem cells (NCSCs). We sequenced mRNA samples of DS1-NCSCs and DS2-NCSCs to generate the gene expression profiles of these cells.

overall_design: mRNA samples of DS1-NCSCs and DS2-NCSCs were sequenced and analyzed.

first: Huanyao

last: Liu

first: Huiyan

last: Wang

first: Weijun

last: Huang


title: High-definition spatiotemporal atlas of cholestatic injury and repair.

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: Cholestatic injuries, featured with regional damage around the periportal, cause considerable mortality without curative therapies. It is technically challenging to dissect regional cell-cell interactions and molecular changes to fully understand cholangiopathies. Here, we generated a high-definition atlas of spatiotemporal transcriptome during cholestatic injury and repair. Remarkably, cholangiocytes functioned as a periportal hub by integrating signals from neighboring cells. We also dissected periportal damage, spatial heterogenous reprogramming and zonal regeneration, which appeared to be strongly associated with cholangiocyte. Moreover, spatiotemporal analyses revealed a key inhibitory rheostat for hepatocyte proliferation. Together, our study provides a comprehensive resource that is instrumental to demarcate regional cholestatic injury.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for resting hepatocytes (shNC) and its knockdown derivatives (shAtoh8) after DDC diet for 17 days.

first: Baihua

last: Wu

first: Xinyi

last: Shentu

first: Haitao

first: Pengcheng

last: Guo

first: Shijie

last: Hao

first: Jiangshan

last: Xu

first: Shuncheng

last: Shangguan

first: Lei

last: Cui

first: Qiuting

last: Deng

first: Yan

first: Chang

first: Yumo

last: Song

first: Xiumei

last: Lin

first: Zhifeng

first: Yue

last: Yuan

first: Wen

last: Ma

first: Ronghai

first: Wensi

last: Du

first: Tingting

last: Lai

first: Tao

last: Yang

first: Chuanyu

first: Yiwei

first: Longqi

first: Miguel

middle: A

last: Esteban


title: Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: CRISPR RNA-seq from K562 (ENCSR008ECN)

first: ENCODE

last: DCC

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SEC62. (SEC62-BGKcLV33)

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


title: Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm [ATAC-seq]

summary: Genome-wide identification of gene regulatory networks for murine cardiac conduction system (CCS)

overall_design: We demonstrate successful isolation of cell type-specific nuclei (Isolation of Nuclei TAgged in specific Cell Types (INTACT)) from CCS followed by magnet-assisted nuclear immunoprecipitation (MAN-IP) in conjunction with a suite of CCS compartment-specific Cre driver lines,which we refer to here as CCS-INTACT from the fibrous adult murine heart.  We generated a robust compendium of gene regulatory elements for each CCS compartment (SAN, AVN, and VCS) by ATAC-seq on nuclei purified by CCS-INTACT.

first: Samadrita

last: Bhattacharyya

first: Rahul

middle: K

last: Kollipara


title: CRISPR RNA-seq from HepG2 (ENCSR485ZHW)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against RIOK2. (RIOK2-BGHcLV32-B)

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR007SVQ)

summary:
human_brain_Rush ID_E1121653_BS119_ENC4_cDNA681

For data usage terms and conditions, please refer to http://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 middle frontal area 46 (ENCSR001QSI)

summary:
human_brain_Rush ID_E2504543_BS178_ENC4_cDNA732

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


title: CRISPR RNA-seq from K562 (ENCSR002ODC)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against DDX10. (DDX10-BGKcLV28)

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


title: Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm [RNA-seq]


title: CRISPR RNA-seq from HepG2 (ENCSR470SBK)

summary:
RNA-seq on HepG2 cells treated with a CRISPR gRNA against CDK9. (CDK9-BGHcLV29)

For data usage terms and conditions, please refer to http://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 and proteome profiling of activated cardiac fibroblasts supports target prioritization in cardiac fibrosis

status: Public on Dec 01 2022

city: Oeiras

first: Daniel

last: Simão

address: Av. República, Qta. do Marquês, Estação Agronómica Nacional, Edificio IBET/ITQB

country: Portugal

institute: iBET, Instituto de Biologia Experimental e Biológica

summary: Activated cardiac fibroblasts (CF) play a central role in cardiac fibrosis, a condition associated with most cardiovascular diseases. Conversion of quiescent into activated CF sustains heart integrity upon injury. However, permanence of CF in active state inflicts deleterious heart function effects. Mechanisms underlying this cell state conversion are still not fully disclosed, contributing to a limited target space and lack of effective anti-fibrotic therapies. To prioritize targets for drug development, we studied CF remodeling upon activation at transcriptomic and proteomic levels, using three different cell sources: primary adult CF (aHCF), primary fetal CF (fHCF), and induced pluripotent stem cells derived CF (hiPSC-CF). All cell sources showed a convergent response upon activation, with clear morphological and molecular remodeling associated with cell-cell and cell-matrix interactions. Quantitative proteomic analysis identified known cardiac fibrosis markers, such as FN1, CCN2 and Serpine1, but also revealed targets not previously associated with this condition, including MRC2, IGFBP7 and NT5DC2. Exploring such targets to modulate CF phenotype represents a valuable opportunity for development of anti-fibrotic therapies. Also, we demonstrate that hiPSC-CF is a suitable cell source for preclinical research, displaying significantly lower basal activation level relative to primary cells, while being able to elicit a convergent response upon stimuli.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for quiescent and activated cardiac fibroblasts (CF) from three different sources (human adult primary CF, human fetal primary CF, human induced pluripotent stem cell-derived CF)

first: Maria

middle: R

last: Moita

first: Marta

middle: M

last: Silva

first: Cláudia

last: Diniz

first: Margarida

last: Serra

first: René

last: Hoet

first: Ana

last: Barbas


title: Gene expression analysis in mouse mature T-cells either upon knockdown of L3MBTL3 or rescue with RBPJ WT or F261A/A284V mutant

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: We identified genes upregulated upon depletion of L3MBTL3 in mouse mature T-cells (MT). Additionally, we identified genes downregulated upon rescue with RBPJ WT but not with an L3MBTL3-interacting defecting mutant (F261A/A284V) in MT cells depleted of RBPJ using the CRISPR/Cas9 technology.

overall_design: RNA-seq analysis of mouse mature T-cells either upon knockdown of L3MBTL3 or rescue with RBPJ WT or F261A/A284V mutant.

first: Marek

last: Bartkuhn

first: Benedetto

middle: D

last: Giaimo

first: Francesca

last: Ferrante


title: Comparison of oocyte vitrification using a semi-automated or a manual closed system in human siblings

city: DIJON

first: Bastien

last: Ducreux

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

country: France

institute: Inserm U1231

summary: To study the efficiency of a semi-automated technique of oocyte vitrification as compared with a manual method and transcriptomic landscape associated with the oocyte vitrification.

overall_design: Sibling oocytes were randomized between fresh, manual or semi-automated vitrification groups for transcriptome profiling using single-cell RNA-sequencing technology

first: Julie

last: Barberet

first: Céline

last: Bruno

first: Magali

last: Guilleman

first: Adrien

last: Guilloteau

first: Déborah

last: Bourc’his

first: Patricia

last: Fauque


title: Podocalyxin-Like Protein 1 Regulates Extended and Primed Pluripotency through the Cholesterol Biosynthesis Pathway

city: Nankang

first: Jean

last: Lu

state: Taipei

address: 128 Academia Road, Section 2, IBMS, N401F

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: We utilized scRNA-seq to study the human-mouse chimera transcriptomic regulation at peri-implantation embryo stage. Single-cell RNA sequencing revealed PODXL overexpression boosted chimerism between human cells in mouse host embryos and the potential cell-cell communication interactions in human-mouse chimeras.  Potential cell-cell communications were identified to optimize cell-cell contact interaction for reducing the xenogeneic barrier in the interspecies chimeras in future studies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We generated Tet-on-PODXL hEPSC lines that stably expressed tdTomato (tdT) florescence protein. We generated human-mouse chimeric embryos by incorporating one 8C embryo with ~8-10 cells of Dox-treated or untreated control hEPSCs using an aggregation method. The embryos were cultured for additional ~37 hours to the late blastocyst stage.

first: Wei-Ju

last: Chen


title: Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development

city: New York

first: Nadejda

last: Tsankova

state: New York

address: 1245 Madison Avenue

department: Pathology

institute: Icahn School of Medicine at Mount Sinai

summary: Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors.

overall_design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex.

first: Ramos

last: Susana

first: Mussa

last: Zarmeen

first: Falk

last: Elisa

first: Pai

last: Balagopal

first: Giotti

first: Sebra

last: Robert

first: Beaumont

last: Kristin

first: Tsankov

last: Alexander

first: Tsankova

last: Nadejda


title: Early response evaluation by single cell signaling profiling in acute myeloid leukemia

city: Bergen

first: Bjørn Tore

last: Gjertsen

address: Klinisk institutt 2 Postboks 7804

department: Clinical science

country: Norway

institute: University of Bergen

summary: Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a cohort of 32 acute myeloid leukemia (AML) patients, using 36-dimensional mass cytometry. Through supervised and unsupervised machine learning approaches, we find that reduction of extracellular-signal-regulated kinase (ERK) 1/2 and p38 mitogen-activated protein kinase (MAPK) phosphorylation in the myeloid cell compartment 24h post-chemotherapy is a significant predictor of patient 5-year overall survival in this cohort. Validation by RNA sequencing show induction of MAPK target gene expression in patients with high phospho-ERK1/2 24h post-chemotherapy, while proteomics confirms an increase of the p38 prime target MAPK activated protein kinase 2 (MAPKAPK2). In this study, we demonstrate that mass cytometry can be a valuable tool for early response evaluation in AML and elucidate the potential of functional signaling analyses in precision oncology diagnostics.

overall_design: In this study we investigate the singlaing response to standard induction therapy in a cohort of 32 acute myeloid leukemia (AML) patients. Samples were taken at pre-treatment (0h), 4 hours and 24 hours after start of chemotherapy. We validated our results by proteomics and RNA-sequencing. RNA sequencing was performed for some of these patients at all tiempoints available.

first: Bjørn

last: Tore Gjertsen

first: Benedicte

last: Sjo Tislevoll

first: Aashish

last: Srivastava

first: Monica

last: Hellesøy


title: Samples from prospectively enrolled patients with histologically confirmed primary Head and Neck squamous cell carcinoma (HNSCC) were analyzed for miRNA profiling

status: Public on Nov 30 2022

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary: miRNA profiling in HNSCC, including 66 paired normal, peritumor and tumor tissues from the same patients, and additional 55 unpaired tumor tissues

overall_design: The study involved 121 prospectively enrolled patients with histologically confirmed primary Head and Neck squamous cell carcinoma (HNSCC), not previously treated by adjuvant therapy. 66 paired normal, peritumor and tumor samples were hybridized on “Human miRNA Microarray (V2) 8x15K” slides, containing probes for 723 human miRNAs,   while 55 additional tumor samples were hybridized on “SurePrint G3 Human v16 miRNA 8x60K” slides, containing probes for 1205 human miRNAs

first: F

last: Ganci

first: G

last: Blandino

first: A

last: Sacconi