title: ChIP-seq from K562 (ENCSR213VUI)

summary:
TRIM25 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR200DKE)

status: Public on Jan 04 2017

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

summary:
eCLIP experiment on K562 against MTPAP

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


title: ChIP-seq from GM12878 (ENCSR205SKQ)

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
YBX1 ChIP-seq on human GM12878

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


title: eCLIP from K562 (ENCSR197NFH)

summary:
eCLIP control experiment on K562 against KHDRBS1

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


title: eCLIP from K562 (ENCSR207DWI)

summary:
eCLIP control experiment on K562 against DDX6

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


title: ChIP-seq from K562 (ENCSR198KYG)

summary:
Input control ChIP-seq on human eGFP-TAF7 tagged K562 cell line.

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


title: eCLIP from HepG2 (ENCSR197LHH)

summary:
eCLIP control experiment on HepG2 against DKC1

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


title: ChIP-seq from MCF-7 (ENCSR200CUA)

summary:
HDGF ChIP-seq on human MCF-7

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


title: eCLIP from K562 (ENCSR196INN)

summary:
eCLIP experiment on K562 against RBM15

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


title: eCLIP from K562 (ENCSR195IWB)

summary:
eCLIP control experiment on K562 against DDX24

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


title: ChIP-seq from IMR-90 (ENCSR197WGI)

summary:
NFE2L2 ChIP-seq on human IMR90

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


title: eCLIP from K562 (ENCSR197INS)

summary:
eCLIP experiment on K562 against PPIL4

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


title: eCLIP from K562 (ENCSR194AVW)

summary:
eCLIP control experiment on K562 against RBM27

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


title: eCLIP from HepG2 (ENCSR192PUP)

summary:
eCLIP control experiment on HepG2 against LARP4

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


title: ChIP-seq from K562 (ENCSR197ALX)

summary:
HDGF ChIP-seq on human K562

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


title: eCLIP from HepG2 (ENCSR182AEG)

summary:
eCLIP control experiment on HepG2 against AGGF1

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


title: eCLIP from K562 (ENCSR200SAU)

summary:
eCLIP control experiment on K562 against DDX42

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


title: ChIP-seq from HEK293 (ENCSR185FOY)

summary:
eGFP-ZNF341 ChIP-seq on human HEK293 cells.

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


title: eCLIP from K562 (ENCSR180EJY)

summary:
eCLIP control experiment on K562 against DDX55

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


title: eCLIP from K562 (ENCSR170XQH)

summary:
eCLIP control experiment on K562 against XRN2

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


title: eCLIP from HepG2 (ENCSR167OYL)

summary:
eCLIP control experiment on HepG2 against SND1

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


title: ChIP-seq from K562 (ENCSR173USI)

summary:
Control ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR189PYJ)

summary:
SMAD2 ChIP-seq on human K562

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


title: ChIP-seq from limb (ENCSR164BWS)

summary:
Chip-Seq on e14.5 limb-mouse (fragmentation date: 2014-09-30)

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


title: ChIP-seq from MCF-7 (ENCSR176EXN)

summary:
JUN ChIP-seq on human MCF-7

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


title: ChIP-seq from K562 (ENCSR175SZH)

summary:
ZSCAN29 ChIP-seq on human K562

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


title: ChIP-seq from MCF-7 (ENCSR197DJH)

summary:
SREBF1 ChIP-seq on human MCF-7

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


title: ChIP-seq from K562 (ENCSR167KBO)

summary:
ZNF316 ChIP-seq on human K562

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


title: ChIP-seq from HepG2 (ENCSR157CAU)

summary:
ZKSCAN1 ChIP-seq on human HepG2

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


title: eCLIP from K562 (ENCSR154HRN)

summary:
eCLIP experiment on K562 against HNRNPA1

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


title: eCLIP from HepG2 (ENCSR151MPZ)

summary:
eCLIP control experiment on HepG2 against DHX30

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


title: ChIP-seq from K562 (ENCSR155KHM)

summary:
ARNT ChIP-seq on human K562

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


title: ChIP-seq from hindbrain (ENCSR150RGT)

summary:
Chip-Seq on CTCF-mouse

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


title: ChIP-seq from K562 (ENCSR157TCS)

summary:
SMARCE1 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR157BRV)

summary:
eCLIP control experiment on K562 against GTF2F1

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


title: ChIP-seq from K562 (ENCSR167JBG)

summary:
eGFP-DIDO1 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR145PHJ)

summary:
eCLIP control experiment on K562 against SRSF7

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


title: ChIP-seq from GM12878 (ENCSR145XQO)

summary:
HDGF ChIP-seq on human GM12878

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


title: eCLIP from HepG2 (ENCSR141OIM)

summary:
eCLIP experiment on HepG2 against DDX6

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


title: ChIP-seq from kidney (ENCSR143WOK)


title: eCLIP from HepG2 (ENCSR161TFX)

summary:
eCLIP control experiment on HepG2 against UCHL5

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


title: ChIP-seq from HEK293 (ENCSR162MTR)

summary:
eGFP-ZNF346 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from HEK293 (ENCSR141PZA)

summary:
eGFP-SP3 ChIP-seq on human HEK293 cells.

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


title: eCLIP from HepG2 (ENCSR135VMS)

summary:
eCLIP experiment on HepG2 against LSM11

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


title: ChIP-seq from K562 (ENCSR138FUZ)

summary:
RING1 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR133QEA)

summary:
eCLIP experiment on K562 against SF3B1

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


title: ChIP-seq from K562 (ENCSR137ZMQ)

summary:
REST ChIP-seq on human K562

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


title: ChIP-seq from HeLa-S3 (ENCSR140DSL)

summary:
MAFF ChIP-seq on human HeLa-S3

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


title: eCLIP from HepG2 (ENCSR130TOJ)

summary:
eCLIP control experiment on HepG2 against QKI

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


title: ChIP-seq from MCF-7 (ENCSR135ANT)

summary:
NRF1 ChIP-seq on human MCF-7

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


title: ChIP-seq from HEK293 (ENCSR134QIE)

summary:
eGFP-ZFP3 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from K562 (ENCSR130PDE)

summary:
eGFP-NR4A1 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR130HEG)

summary:
COPS2 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR128VXC)

summary:
eCLIP experiment on K562 against SND1

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


title: ChIP-seq from HEK293 (ENCSR123TVS)

summary:
Input ChIP-seq on eGFP-ZFP62 tagged human HEK293 cells.

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


title: eCLIP from K562 (ENCSR125CLF)

summary:
eCLIP control experiment on K562 against IGF2BP1

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


title: eCLIP from K562 (ENCSR121GQH)

summary:
eCLIP experiment on K562 against SERBP1

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


title: eCLIP from HepG2 (ENCSR121NVA)

summary:
eCLIP experiment on HepG2 against PRPF8

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


title: ChIP-seq from K562 (ENCSR126FZN)

summary:
eGFP-PTRF ChIP-seq on human K562

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


title: ChIP-seq from HEK293 (ENCSR121EZR)

summary:
eGFP-ZNF71 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from HEK293 (ENCSR125DNC)

summary:
eGFP-ZNF394 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from GM12878 (ENCSR189YYK)

summary:
ZBTB40 ChIP-seq on human GM12878

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


title: ChIP-seq from HepG2 (ENCSR121CWV)

summary:
Control ChIP-seq on human HepG2

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


title: ChIP-seq from K562 (ENCSR124BJR)

summary:
ETV6 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR119AFY)

summary:
eCLIP control experiment on K562 against FASTKD2

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


title: ChIP-seq from K562 (ENCSR117WTM)

summary:
eGFP-ZNF24 ChIP-seq on human K562

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


title: ChIP-seq from HEK293 (ENCSR159GFL)

summary:
eGFP-ZNF518A ChIP-seq on human HEK293 cells.

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


title: siRNA RNA-seq from K562 (ENCSR128HAQ)

type: Expression profiling by high throughput sequencing

summary:
Control siRNA against no target in K562 cells followed by RNA-seq.

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


title: ChIP-seq from HepG2 (ENCSR171FUX)

summary:
FOXK2 ChIP-seq on human HepG2

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


title: ChIP-seq from K562 (ENCSR121PFY)

summary:
CDC5L ChIP-seq on human K562

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


title: eCLIP from HepG2 (ENCSR114XBO)

summary:
eCLIP control experiment on HepG2 against LSM11

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


title: ChIP-seq from K562 (ENCSR108OFV)

summary:
Input control ChIP-seq on human eGFP-ZNF512 tagged K562 cell ine.

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


title: ChIP-seq from heart (ENCSR109LQX)

summary:
Chip-Seq on P0 heart-mouse (fragmentation date: 2015-02-05)

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


title: ChIP-seq from HEK293 (ENCSR110ZVM)

summary:
Input ChIP-seq on eGFP-ZNF264 tagged human HEK293 cells.

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


title: eCLIP from HepG2 (ENCSR110XNS)

summary:
eCLIP control experiment on HepG2 against HNRNPA1

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


title: eCLIP from HepG2 (ENCSR115GAA)

summary:
eCLIP control experiment on HepG2 against PCBP2

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


title: ChIP-seq from K562 (ENCSR113LAS)

summary:
MTA2 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR106FRG)

summary:
TAL1 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR107RHZ)

summary:
YBX1 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR109YGM)

summary:
CREB3L1 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR115SMW)

summary:
PKNOX1 ChIP-seq on human K562

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


title: ChIP-seq from stomach (ENCSR104QEN)

summary:
Chip-Seq on CTCF-mouse

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


title: ChIP-seq from HEK293 (ENCSR106EBH)

summary:
eGFP-ZNF366 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from K562 (ENCSR107GRP)

summary:
MLLT1 ChIP-seq on human K562

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


title: The effects of Mycobacterium avium infection on hematopoietic stem cells

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

summary: To investigate the changes in global transcriptome expression of HSCs following infection, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified HSCs (SP KSL CD150+) isolated from naive or Mycobacterium avium infected mice

overall_design: Total RNA obtained from hematopoietic stem cells isolated from naïve or Mycobacterium avium infected mice was subjected to deep sequencing, in duplicate, using Illumina Hiseq 2000

first: Deqiang

last: Sun


title: Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

type: Methylation profiling by high throughput sequencing

summary: Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation. This was shown to alter their expression and affects plant development. It is not clear why only certain body-methylated genes gain non-CpG methylation in the absence of IBM1 and others do not. We described a link between CpG methylation and the establishment of methylation in the CpHpG context that explains the two classes of body-methylated genes. We provided evidence that external cytosines of CpCpG sites can only be methylated when internal cytosines are methylated and that CpCpG sites methylated in both cytosines promote spreading of methylation in the CpHpG context in genes protected by IBM1.

overall_design: Examination of DNA methylation of 2 ibm1-1 homozigous 1st generation mutants, in Col-0 and in Ler-0 background; ibm1-1 locus was introgressed from Col-0 background by four backcrosses in Ler-0 background


title: A-to-I RNA Editing in Drosophila

first: Jin Billy

last: Li

state: California

address: 300 Pasteur Drive. Alway M303

department: Genetics

institute: Stanford University

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

sample_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis
Drosophila yakuba

overall_design: Refer to individual Series


title: WRKY transcription factors in early MAMP-triggered immunity

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research


title: WRKY transcription factors in early MAMP-triggered immunity (RNA-Seq)

summary: We determined on a genome-wide scale the flg22-induced in vivo DNA-binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40 and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Transcriptional analysis also revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes.

overall_design: Three biological replicates were analysed, each consisting of 12 samples: WT and three mutant genotypes, each at 0 h (untreated), 1 h and 2 h flg22 treatment.

first: Rainer

middle: P

last: Birkenbihl

first: Imre

middle: E

last: Somssich


title: RNA-Seq of head tissue from Drosophila melanogaster Wild Type and AdarEA mutant

summary: We profiled gene expression in flies with and without A-to-I RNA editing (AdarEA mutant Drosophila melanogaster with a Canton-S background).

overall_design: mRNA profiles of heads of 3 day old male AdarEA mutant (y, sc, AdarE374A) and wild type (white Canton-S) flies

first: Rui

last: Zhang

first: Patricia

last: Deng

first: Dionna

last: Jacobson

first: Jin-Billy


title: Transcriptome profile of HepG2-expressing ATP7B-H1069Q (liver hepatocellular cells) exposed to JNK or p38 Inhibitor

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: In order to identify the effects of JNK inhibitor or p38 Inhibitor on the transcriptome of ATP7B H1069Q-overexpressing liver cells, we performed RNAseq experiments

overall_design:
Transcriptome analysis of the hepatocytes overexpressing ATP7B H1069Q, compared with hepatocytes overexpressing ATP7B WT.
Total RNA was extracted from HepG2 cells; RNA extracted from hepatocytes overexpressing ATP7B WT was used as control.

first: G

last: Chesi

first: R

middle: S

last: Polishchuk


title: The yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double stranded RNA.

city: Blacksburg

first: Kevin

last: Myles

state: VA

address: Fralin Life Science Institute 360 West Campus Drive

institute: Virginia Tech

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we describe a viral suppressor of RNA silencing encoded by the prototype flavivirus, yellow fever virus (YFV). We show that the YFV capsid protein inhibits RNA silencing in the mosquito Aedes aegypti by interfering with Dicer. These results suggest a molecular arms race between vector and pathogen underlies the continued existence of flaviviruses in nature.

overall_design: For the sequencing data we are  submitting, we used recombinant Sindbis viruses expressing the yellow fever capsid (2J_YFV_cap) or a the yellow fever capsid sequence with  the start codon removed (2J_YFV_cap_ntr). We infected mosquitoes with  the recombinant viruses, waited 96hrs and did total RNA extraction  from three pools of five mosquitoes each (each pool was a biological  replicate, thus each sample being called rep1 -3). Small RNAs (18 to 35-nt) were recovered by PAGE separation, and librarie sprepared with the Truseq small RNA sample prep kit (Illumina) according to the manufacturer's instructions.

first: Glady

middle: H

last: Samuel

first: Michael

middle: R

last: Wiley

first: Atif

last: Badawi

first: Zach

middle: N

last: Adelman

middle: M


title: ChIP-seq from GM12878 (ENCSR117KWH)

first: ENCODE

last: DCC

summary:
ZNF207 ChIP-seq on human GM12878

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


title: RNA Sequencing Reveals the Snail-Regulated Transcriptome in Head-and-Neck Squamous Cell Carcinoma.

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: The epithelial-to-mesenchymal transition (EMT) is a critical biological process in normal development and tumor progression. One of the EMT regulator, Snail is shown to suppress or activate its downstream genes to sustain migratory capacities while remodeling the tumor microenvironment. Identification of the Snail-regulated transcriptome through a robust sequencing technique will give a global direction for targeting Snail-driven malignancy.

overall_design: The stable Snail-expressing and vector control HNSCC cells are generated by lentivirus transduction. The differential expression profiles of cell established are assessed to identify the enriched biological functions and hub genes.

first: Hsei-Wei

last: Wang

first: Muh-Hwa

last: Yang


title: Whole transcriptome analysis of functionally distinct cell types of the jejunal intestinal epithelium of germfree and conventionalized mice [mRNA]

city: Chapel Hill

first: Bailey

last: Peck

state: NC

address: 120 Mason Farm Rd, 5100H Genetic Medicine Bldg

institute: University of North Carolina at Chapel Hill

summary: The highly characterized Sox9-EGFP transgenic mouse model, which permits the isolation and analysis of four distinct IEC populations using fluorescence-activated cell sorting (FACS) based on differing levels of cellular EGFP intensity. These are Sox9-EGFP Low (actively cycling IESCs), Sox9-EGFP Sublow (progenitor cells), Sox9-EGFP Neg (mostly differentiated enterocytes as well as goblet cells and Paneth cells), and Sox9-EGFP High (primarily EECs). We evaluated mRNA expression profiles by next-generation high-throughput RNA-sequencing in FACS purified Sox9-Low cells from germ-free (GF) and conventionalized (CV) mice.

overall_design: To assess the effect of microbiota on the intestinal epithelial stem cells population, we used four pairs of female GF Sox9-EGFP littermates. One littermate from each pair was randomly selected at 8-10 weeks of age for conventionalization. Following a two-week conventionalization, the jejunal epithelial tissue from both the CV and GF littermates were harvested and IECs were sorted by FACS. RNA was isolated from the four sorted populations from each animal, as well as from non-sorted (NS) IECs, and subject to small RNA sequencing. Additionally, Sox9-Low samples were profiled for mRNAs using mRNA-seq. Reads were aligned to the mouse genome and quantified using Salmon followed by edgeR. To avoid noise introduced by lowly expressed transcripts, we analyzed only robustly expressed transcripts defined as those with an expression of at least 10 counts per million (CPM).

middle: C

first: Praveen

last: Sethupathy

first: Pauline

middle: K

last: Lund

first: Wendy

last: Pitman


title: siRNA RNA-seq from K562 (ENCSR100ODO)

status: Public on Jan 03 2017

summary:
RNA-seq on K562 cells treated with siRNA targeting NFE2L2.

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


title: ChIP-seq from HEK293 (ENCSR103GAK)

summary:
eGFP-ZNF175 ChIP-seq on human HEK293 cells.

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


title: WRKY transcription factors in early MAMP-triggered immunity (ChIP-Seq)

first: Barbara

last: Kracher

overall_design: We analysed for each of two biological replicates 8 samples: non HA-tagged WT seedlings served as negative controls while binding  to DNA of three different WRKY-HA complementation lines were investigated ChIP-seq using an anti-HA antibody.

first: Rainer

last: Birkenbihl

first: Imre

last: Somssich


title: ChIP-seq from HepG2 (ENCSR101FJU)

summary:
ZNF384 ChIP-seq on human HepG2

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


title: eCLIP from HepG2 (ENCSR099KAK)

summary:
eCLIP control experiment on HepG2 against DDX6

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


title: eCLIP from HepG2 (ENCSR097NEE)

summary:
eCLIP experiment on HepG2 against PPIG

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


title: Near future pH conditions severely impact calcification, metabolism and nervous system in the pteropods Heliconoides inflatus

city: Townsville

first: Aurelie

last: Moya

state: QLD

address: James Cook drive

department: ARC Centre of Excellence for Coral Reefs Studies

country: Australia

institute: James Cook University

summary: Shelled pteropods play key roles in the global carbon cycle and foodwebs of various ecosystems. Their thin external shell is extremely sensitive to changes in pH and shell dissolution has already been observed in areas where aragonite saturation state is ~ 1. A decline in pteropod abundance has the potential to disrupt trophic networks and directly impact commercial fisheries. Therefore it is crucial to understand how pteropods will be affected by global environmental change, particularly ocean acidification. In the present study, physiological and molecular approaches were used to investigate the response of the Mediterranean pteropod, Heliconoides inflatus, to pH values projected for 2100 under a moderate emissions trajectory (RCP6.0). Pteropods were subjected to pHT 7.9 for 3d and gene expression levels, calcification and respiration rates measured relative to pHT 8.1 controls. Gross calcification decreased markedly under low pH conditions, while genes potentially involved in calcification were up-regulated, reflecting the inability of pteropods to maintain calcification rates. Gene expression data imply that under low pH conditions both metabolic processes and protein synthesis may be compromised, while genes involved in acid-base regulation were up-regulated. A large number of genes related to nervous system structure and function were also up-regulated in the low pH treatment, including a GABAA receptor subunit. This is particularly interesting because GABAA receptor disturbances, leading to altered behaviour, have been documented in several other marine animals after exposure to elevated CO2. The up-regulation of many genes involved in nervous system function suggests that, in addition to its impacts on other aspects of biology, exposure to low pH could have major effects on pteropod behavior. This study not only illustrates the utility of combining physiological and molecular approaches, but also highlights the desirability of including behavioural analyses in studies aimed at understanding the impacts of low pH on marine animals.

overall_design: Six biological samples were sequenced, 3 replicates for the control condition and 3 replicates for the treatment. All samples were sequenced twice except the replicate treatment #3.

first: Ella

middle: L

last: Howes

first: Thomas

last: Lacoue-Labarthe

first: Sylvain

last: Forêt

first: Bishoy

last: Hanna

first: Mónica

last: Medina

first: Philip

last: Munday

first: Jue-Sheng

last: Ong

first: Jean-Louis

last: Teyssié

first: Gergely

last: Torda

first: Sue-Ann

last: Watson

first: David

middle: J

last: Miller

first: Jelle

last: Bijma

first: Jean-Pierre

last: Gattuso


title: Identification and Characterization of the Glucose Dual-transporter System: Pleiotropic Roles in Nutrient Transport, Signaling, and Carbon Catabolite Repression in Neurospora crassa

city: Tianjin

first: Bang

last: Wang

address: 32 Xi Qi Dao, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary:
  The glucose dual-affinity transport system (low- and high-affinity) is a conserved strategy exerted by microorganisms to cope with the naturally fluctuating availability of nutrients in the environment. The glucose sensing and uptaking process were believed to be tightly involved in cellulases expression regulation in cellulolytic fungi. However, both the identities and functions of the major molecular components of this evolutionarily conserved system in filamentous fungi remain elusive. Here, we conducted a systematic identification and characterization of the glucose dual-affinity transport system in the model fungus Neurospora crassa.
  Using RNA sequencing coupled with functional transport analyses, we were able to assign GLT-1 (Km = 18.42 ± 3.38 mM) and HGT-1/-2 (Km = 16.13 ± 0.95 µM and 98.97 ± 22.02 µM) to low- and high-affinity glucose transport systems, respectively. The high-affinity transporters hgt-1/-2 were able to complement a moderate growth defect under high glucose when glt-1 was deleted. Simultaneous deletion of hgt-1/-2 led to extensive derepression of genes for plant cell wall deconstruction on cellulose. This suppression by HGT-1/-2 was connected to both carbon catabolite repression (CCR) and the cyclic adenosine monophosphate-protein kinase A pathway. Alteration of a residue conserved across taxa for hexose-transporters was found to result in a loss of glucose-transporting function, whereas CCR signal transduction was retained, indicating a dual function for HGT-1/-2 as “transceptors”.
  In this study, GLT-1 and HGT-1/-2 are identified as the key components of the glucose dual-affinity transport system, which play diverse roles in glucose transport and carbon metabolism. Given their wide conservation across fungal species, the glucose dual-affinity transport components and their pleiotropic roles revealed in this study would shed extensive new light on the molecular basis of nutrient transport, signaling, and plant cell wall degradation in fungi.

overall_design: Conidia of Neurospora crass wild type were inoculated with 10e6 conidia/mL into 100 mL 1×Vogel’s salts with 2% (w/v) sucrose pregrown for 16 h and then transferred into an indicated glucose gradient Vogel's salts for 1 or 2 hours. For Avicel growth, Conidia of WT and indicated mutants were inoculated with 10e6 conidia/mL into 100 mL 1×Vogel’s salts with 2% (w/v) Avicel grown for indicated hours. Two or three biological replicates were designed for each treatment. Mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN). The qualified RNA was prepared with standard protocol from Shenzhen BGI (China) and sequenced on the Illumina HiSeqTM 2000/2500 platform.

first: Chaoguang

last: Tian


title: ChIP-seq from HEK293 (ENCSR098YLE)

first: ENCODE

last: DCC

summary:
eGFP-PRDM1 ChIP-seq on human HEK293 cells.

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


title: Transcriptional profiling of mouse embryonic stem cells without Huntingtin (Htt)

city: New York

first: Man Shan

last: Yu

state: NY

address: 550 First Ave., MSB 258

department: Microbiology

institute: New York University School of Medicine

summary: Mutation in the huntingtin (HTT) gene causes Huntington’s disease. Wild type Htt is essential for development as Htt knockout mice die at day E7.5. Increasing evidence suggests mutant Htt may alter neurogenesis and development of striatal neurons resulting in neuronal loss. Using mouse embryonic stem cells (mESCs), we examined the role of Htt in neural differentiation. We found Htt-null (HN) mESCs inefficient in generating neural stem cells. In contrast differentiation into progenitors of mesoderm and endoderm lineages was not affected. To investigate the basis for the lack of neural differentiation, we carried out gene expression profiling by RNA-seq to examine if genes involved in neural differentiation were dysregulated in HN mESCs.

overall_design: Gene expression profiles of R1 wild type and Htt-null (HN) mESCs were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Man

first: Naoko

last: Tanese

first: Adriana

last: Heguy

first: Igor

last: Dolgalev


title: Evolution of A-to-I RNA Editing in Drosophila

first: Jin Billy

last: Li

summary: We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) and targeted RNA sequencing to quantify RNA editing levels at targeted sites in 6 Drosophila species and 8 strains of D. melanogaster.

platform_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis
Drosophila yakuba

overall_design: We performed two rounds of targeted RNA sequencing. In the first round, we used mmPCR-seq to amplify and sequence all selected editing loci for all samples from six species. For D. ana, D. pse, and D. vir, we designed additional multiplex primers for ~210 loci that could be amplified in D.mel, D.sim and D.yak but not in D.ana, D.pse and D.vir. We used these primers for the second round of targeted RNA sequencing. We amplified these loci using a regular PCR machine. All samples were then barcoded, pooled and sequenced in one Illumina MiSeq run with 150 bp paired-end reads.

first: Rui

last: Zhang

first: Patricia

last: Deng

first: Dionna

last: Jacobson

first: Jin-Billy


title: Cooperative Associations with Sites on Different Nucleosomes Mediate Heterochromatin Spreading

city: Boston

first: Gloria

last: Jih

state: MA

address: 240 Longwood Ave, LHRRB 517

department: Cell Biology

institute: Harvard Medical School

summary: Sir3wH and Sir4CC are required for SIR complex spreading in vivo but play partially redundant roles when Sir3 is overexpressed.

overall_design: ChIP-seq analysis of Sir3 chromatin binding and its dependence on Sir3wH domain deletion and Sir4-I1311N mutation.

first: Chenning

last: Lu

middle: T

first: Danesh

last: Moazed


title: Small RNA transcriptome in distinct cell types of the jejunal intestinal epithelium of germfree and conventionalized mice

first: Bailey

last: Peck

summary: We evaluated miRNA expression profiles by next-generation high-throughput small RNA-sequencing in distinct IEC subtypes of germ-free (GF) and conventionalized (CV) mice. We used the highly characterized Sox9-EGFP transgenic mouse model, which permits the isolation and analysis of four distinct IEC populations using fluorescence-activated cell sorting (FACS) based on differing levels of cellular EGFP intensity. These are Sox9-EGFP Low (actively cycling IESCs), Sox9-EGFP Sublow (progenitor cells), Sox9-EGFP Neg (mostly differentiated enterocytes as well as goblet cells and Paneth cells), and Sox9-EGFP High (primarily EECs).

overall_design: To assess the effect of microbiota on these distinct IEC populations, we used four pairs of female GF Sox9-EGFP littermates. One littermate from each pair was randomly selected at 8-10 weeks of age for conventionalization. Following a two-week conventionalization, the jejunal epithelial tissue from both the CV and GF littermates were harvested and IECs were sorted by FACS. RNA was isolated from the four sorted populations from each animal, as well as from non-sorted (NS) IECs, and subject to small RNA sequencing. Sequencing was performed in two groups, each of which contained small RNA libraries from sorted and unsorted IECs of two GF animals and two CV animals. miRNAs and their isomiRs were aligned and quantified using our previously described method (Baran-Gale, Plos-One, 2013). To avoid noise introduced by lowly expressed transcripts, we analyzed only robustly expressed miRNAs, defined as those with an expression of at least 100 reads per million mapped (RPMM).

first: Praveen

last: Sethupathy

first: Pauline

last: Lund

first: Amanda

last: Mah


title: RAMPAGE from upper lobe of left lung (ENCSR099FOD)

first: ENCODE

summary:
The library contained in this experiment come from human upper lobe of left lung tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: ChIP-seq from HepG2 (ENCSR101FJT)

summary:
ZNF143 ChIP-seq on human HepG2

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


title: ChIP-seq from K562 (ENCSR099NCH)

summary:
ZNF24 ChIP-seq on human K562

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


title: Whole transcriptome analysis of functionally distinct cell types of the jejunal intestinal epithelium of germfree and conventionalized mice

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


title: ChIP-seq from K562 (ENCSR097PLG)

summary:
Input control ChIP-seq on human eGFP-ATF1 tagged K562 cell line.

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


title: eCLIP from HepG2 (ENCSR095SIV)

summary:
eCLIP control experiment on HepG2 against LARP7

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


title: eCLIP from adrenal gland (ENCSR096YAP)

summary:
eCLIP control experiment on adrenal gland against HNRNPU

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


title: eCLIP from K562 (ENCSR096SZE)

summary:
eCLIP control experiment on K562 against PRPF8

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


title: Nuclear Surveillance of long intervening noncoding RNA

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: Numerous long intervening non-coding RNA (lincRNA) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription.  Although multiple functions have been ascribed to lincRNA, their synthesis and turnover remain poorly characterised. Here we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq). Notably mNET-seq patterns specific for different Pol II CTD phosphorylation states reveal weak co-transcriptional splicing and poly(A) signal independent Pol II termination on lincRNA as compared to pre-mRNA. In addition, lincRNA are mostly restricted to chromatin where they are co-transcriptionally degraded by the RNA exosome. We also show that a lincRNA specific co-transcriptional RNA cleavage mechanism acts to induce premature termination. In effect functional lincRNA must escape from this targeted nuclear surveillance process.

overall_design:
We employed CTD phospho specific mNET-Seq with pla-B splicing inhibitor and RNA processing factors knockdown (DGCR8, Dicer1, EXOSC3 and CPSF73 proteins). mNET-seq experiments with 1% Empigen detergent treatment were performed to separate Pol II-associated complex from Pol II. We also analyzed subcellur RNA and  pA+ and pA- nucleoplasm RNA libraries for RNA processing efficiency and the turnover.
There are 4  raw files come from an illumina experiment (per sample), produced in 2 lanes. They were all mapped together.

first: Margarita

last: Schlackow

first: Takayuki

last: Nojima

first: Tomas

last: Gomes

first: Ashish

last: Dhir

first: Maria

last: Carmo-Fonseca

first: Nick

last: Proudfoot


title: ChIP-seq from K562 (ENCSR085OAX)

last: DCC

summary:
Input control ChIP-seq on human eGFP-PTTG1 tagged K562 cell line.

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


title: ChIP-seq from K562 (ENCSR090JNM)

summary:
HLTF ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR085QEV)

summary:
NBN ChIP-seq on human K562

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


title: ChIP-seq from HEK293T (ENCSR090ZDO)

summary:
SUZ12 ChIP-seq on human HEK293T

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


title: eCLIP from HepG2 (ENCSR090VXV)

summary:
eCLIP control experiment on HepG2 against DDX3X

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


title: ChIP-seq from HepG2 (ENCSR081WLS)

summary:
RAD51 ChIP-seq on human HepG2

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


title: ChIP-seq from K562 (ENCSR091GVJ)

summary:
eGFP-ATF1 ChIP-seq on human K562

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


title: ChIP-seq from HEK293 (ENCSR093HXE)

summary:
eGFP-ZNF16 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from HEK293T (ENCSR094WHO)

summary:
FOXA1 ChIP-seq on human HEK293T

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


title: ChIP-seq from K562 (ENCSR086FZL)

summary:
KAT8 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR093FKD)

summary:
eGFP-CREB3 ChIP-seq on human K562

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


title: RAMPAGE from stomach (ENCSR081NTK)

summary:
The library contained in this experiment come from human stomach tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: eCLIP from HepG2 (ENCSR081WUU)

summary:
eCLIP control experiment on HepG2 against TBRG4

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


title: ChIP-seq from K562 (ENCSR085DDI)

summary:
NFXL1 ChIP-seq on human K562

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


title: eCLIP from HepG2 (ENCSR077KVG)

summary:
eCLIP control experiment on HepG2 against IGF2BP3

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


title: ChIP-seq from K562 (ENCSR091JXL)

summary:
HES1 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR081JYH)

summary:
eCLIP experiment on K562 against NSUN2

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


title: ChIP-seq from K562 (ENCSR080EOT)

summary:
Control ChIP-seq on human K562

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


title: ChIP-seq from HEK293 (ENCSR080CST)

summary:
eGFP-ZNF639 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from MCF-7 (ENCSR096KWU)

summary:
ZNF207 ChIP-seq on human MCF-7

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


title: eCLIP from K562 (ENCSR067UKU)

summary:
eCLIP control experiment on K562 against EWSR1

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


title: ChIP-seq from HEK293 (ENCSR076EZB)

summary:
eGFP-KLF9 ChIP-seq on human HEK293 cells.

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


title: eCLIP from K562 (ENCSR062NNB)

summary:
eCLIP experiment on K562 against IGF2BP2

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


title: ChIP-seq from HEK293 (ENCSR072LQF)

summary:
eGFP-ZNF76 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from K562 (ENCSR079WHK)

summary:
MCM5 ChIP-seq on human K562

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


title: ChIP-seq from MCF-7 (ENCSR062HDL)

summary:
HSF1 ChIP-seq on human MCF-7

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


title: eCLIP from HepG2 (ENCSR080OLK)

summary:
eCLIP control experiment on HepG2 against ILF3

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


title: eCLIP from HepG2 (ENCSR061EVO)

summary:
eCLIP experiment on HepG2 against SND1

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


title: eCLIP from K562 (ENCSR057DWB)

summary:
eCLIP experiment on K562 against TIA1

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


title: eCLIP from HepG2 (ENCSR056RZV)

summary:
eCLIP control experiment on HepG2 against FUBP3

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


title: eCLIP from K562 (ENCSR051IXX)

summary:
eCLIP control experiment on K562 against RBFOX2

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


title: eCLIP from HepG2 (ENCSR060VZF)

summary:
eCLIP control experiment on HepG2 against SRSF9

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


title: ChIP-seq from MCF-7 (ENCSR066TET)

summary:
RFX1 ChIP-seq on human MCF-7

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


title: ChIP-seq from HEK293 (ENCSR049NDP)

summary:
Input ChIP-seq on eGFP-ZNF572 tagged human HEK293 cells.

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


title: eCLIP from HepG2 (ENCSR049GND)

summary:
eCLIP control experiment on HepG2 against U2AF2

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


title: eCLIP from K562 (ENCSR059CWF)

summary:
eCLIP experiment on K562 against SBDS

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


title: ChIP-seq from K562 (ENCSR075HTM)

summary:
HDAC2 ChIP-seq on human K562

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


title: eCLIP from HepG2 (ENCSR044NGV)

summary:
eCLIP control experiment on HepG2 against XRCC6

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


title: siRNA RNA-seq from K562 (ENCSR047MQO)

summary:
RNA-seq on K562 cells treated with siRNA targeting VEZF1.

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


title: eCLIP from K562 (ENCSR038TMA)

summary:
eCLIP control experiment on K562 against SBDS

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


title: ChIP-seq from liver (ENCSR041SMK)

summary:
CTCF ChIP-seq on postnatal 0 day mouse liver

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


title: RAMPAGE from sigmoid colon (ENCSR035MAJ)

summary:
The library contained in this experiment come from human sigmoid colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: ChIP-seq from K562 (ENCSR065XVO)

summary:
CHAMP1 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR041AXL)

summary:
RFX1 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR038RGL)

summary:
MCM7 ChIP-seq on human K562

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


title: eCLIP from K562 (ENCSR028CRL)

summary:
eCLIP control experiment on K562 against DDX3X

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


title: eCLIP from HepG2 (ENCSR023UHL)

summary:
eCLIP experiment on HepG2 against FASTKD2

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


title: ChIP-seq from MCF-7 (ENCSR028NUR)

summary:
ZNF592 ChIP-seq on human MCF-7

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


title: ChIP-seq from HEK293 (ENCSR065WUF)

summary:
eGFP-KLF17 ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from K562 (ENCSR033VAZ)

summary:
TARDBP ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR031TFS)

summary:
POLR2A ChIP-seq on human K562

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


title: ChIP-seq from HEK293 (ENCSR021DJC)

summary:
eGFP-BCL11A ChIP-seq on human HEK293 cells.

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


title: eCLIP from K562 (ENCSR022BVV)

summary:
eCLIP experiment on K562 against LSM11

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


title: eCLIP from HepG2 (ENCSR041NUV)

summary:
eCLIP experiment on HepG2 against EIF3D

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


title: ChIP-seq from HepG2 (ENCSR019KPC)

summary:
PLRG1 ChIP-seq on human HepG2

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


title: ChIP-seq from HEK293 (ENCSR022IZK)

summary:
eGFP-ZNF623 ChIP-seq on human HEK293 cells.

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


title: eCLIP from K562 (ENCSR006OEQ)

summary:
eCLIP experiment on K562 against FAM120A

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


title: ChIP-seq from HEK293 (ENCSR017QBI)

summary:
eGFP-ZNF600 ChIP-seq on human HEK293 cells.

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


title: RAMPAGE from upper lobe of left lung (ENCSR004UBM)

summary:
The library contained in this experiment come from human upper lobe of left lung tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: ChIP-seq from liver (ENCSR014GMV)

summary:
Reverse Crosslink Control ChIP-seq on postnatal 0 day mouse lung (fragmentation date 08-13-14)

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: ChIP-seq from HEK293 (ENCSR011XCI)

summary:
eGFP-ZNF585B ChIP-seq on human HEK293 cells.

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


title: ChIP-seq from MCF-7 (ENCSR017CEO)

summary:
CUX1 ChIP-seq on human MCF-7

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


title: ChIP-seq from HEK293 (ENCSR011CKE)

summary:
eGFP-ZNF2 ChIP-seq on human HEK293 cells.

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


title: eCLIP from HepG2 (ENCSR018ZUE)

summary:
eCLIP experiment on HepG2 against FKBP4

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


title: ChIP-seq from K562 (ENCSR005NMT)

summary:
eGFP-ID3 ChIP-seq on human K562

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


title: ChIP-seq from K562 (ENCSR011NOZ)

summary:
ZNF407 ChIP-seq on human K562

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


title: ChIP-seq from HEK293 (ENCSR007GUS)

summary:
Input ChIP-seq on eGFP-CTCF tagged human HEK293 cells.

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


title: eCLIP from K562 (ENCSR000SSH)

summary:
eCLIP experiment on K562 against SLTM

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


title: ChIP-seq from intestine (ENCSR002ZAG)

summary:
CTCF ChIP-seq on postnatal 0 day mouse intestine

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


title: ChIP-seq from IMR-90 (ENCSR000HPG)

summary:
SMC3 ChIP-seq on human IMR90

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


title: RNA-Sequencing to identify the transcriptional targets of Rai1

first: Liqun

last: Luo

address: Herrin Labs, Rooms 152 and 154

department: Department of Biological Sciences

summary:
The goals of this study are to harvest Rai1-deficient mouse brains from multiple tissues and timepoints and compare the transcriptome with their wild-type littermates.
Methods:  mRNA profiles from Rai1 conditional knockouts and wild-type mice were generated by deep sequencing, in duplicate using Illumina system.
Conclusions: Our study suggests that Rai1 preferentially regulate genes involved in cell adhesion and neural projection.

overall_design: Cortical, striatal, and hypothalamic mRNA profiles of wild-type and Rai1 conditional knockout mice were generated by deep sequencing, in duplicates.

first: Wei-Hsiang

last: Huang

first: Jin

last: Xu


title: Genome-wide maps of Rai1 binding sites in mouse cortex

summary: By generating knockin mice with an epitope tag on the C terminus of endogenous Rai1, we were able to perform in vivo ChIP-seq. Rai1 peaks co-localize with H3K4me3, Pol2, and Zfx peaks. Our data suggest that Rai1 is a transcription factor that interacts with chromatin, specifically in the promoter and enhancer regions.

overall_design: Examination of Rai1 binding sites in cortex


title: TRIM28 controls a gene regulatory network based on endogenous retroviruses in human neural progenitor cells

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: Endogenous retroviruses (ERVs), which make up 8% of the human genome, have been proposed to participate in the control of gene regulatory networks. In this study, we find a region- and developmental stage-specific expression pattern of ERVs in the developing human brain, which is linked to a transcriptional network based on ERVs. We demonstrate that almost ten thousand, primarily primate-specific ERVs, act as docking platforms for the epigenetic co-repressor protein TRIM28 in human neural progenitor cells, which results in the establishment of local heterochromatin. Thereby, TRIM28 represses ERVs and consequently regulates the expression of neighboring genes. These results uncover a gene regulatory network based on ERVs that participates in control of gene expression of protein-coding transcripts important for brain development.

overall_design: ChIP-seq; TRIM28 and H3K9me3 in hNPCs, normalized to total input. RNA-seq; WT and TRIM28-KD two hNPCs cell lines. One fetal derived (Sai2) and one iPS-derived (AF22) , three replicates each treatment and each cell line. RNA-seq of the fetal brain.

last: Brattås

first: Marie

last: Jönsson

first: Liana

last: Fasching

first: Jenny

last: Nelander Wahlestedt

first: Mansoureh

last: Shahsavani

first: Ronny

last: Falk

first: Anna

first: Patric

last: Jern

first: Malin

last: Parmar

first: Johan

last: Jakobsson


title: Integrating Molecular and Organismal Analyses of Rai1, The Causal Gene for Smith-Magenis Syndrome

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

overall_design: Refer to individual Series


title: eCLIP from HepG2 (ENCSR018RVZ)

first: ENCODE

summary:
eCLIP experiment on HepG2 against NCBP2

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


title: Piwi negatively regulates Polycomb Group proteins in maintaining germline stem cells  and oogenesis

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

institute: Yale University

summary: Piwi regulates niche and intrinsic mechanisms to maintain germline stem cells in Drosophila, yet how this regulation occurs remains elusive. Here, we show that Piwi interacts with the Polycomb Group Complexes PRC1 and PRC2 to maintain ovarian germline stem cells and oogenesis, as well as to repress retrotransposons. Piwi binds to PRC2 subunits Su(z)12 and Esc in vitro and forms a complex with PRC2 in vivo. Whole-genome analyses of PRC2-mediated histone 3 lysine 27 trimethylation (H3K27m3) in wild type and piwi mutant ovarian nuclei indicate that Piwi inhibits H3K27m3 at PRC2 target genes that are mostly regulators of development and transcription.

overall_design: Genome-wide H3K27m3 sites in piwi mutant were explored and compared to those in wild type, via Chromatin immunoprecipitation followed by DNA sequencing technology.

first: Jamy

last: Peng

first: Haifan

last: Lin


title: Producing enteroendocrine cells from Lgr5+ intestinal stem cells by manipulating quiescence

city: Utrecht

first: Kay

last: Wiebrands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Lgr5+ adult intestinal stem cells are highly proliferative throughout life. Single Lgr5+ stem cells can be cultured into 3D epithelial organoids containing all cell types at nearnormal ratios. Culture conditions to generate the main cell types have been established previously, but signals inducing the various types of enteroendocrine cells (EECs) have remained elusive. Here we generate quiescent Lgr5+ stem cells in vitro by inhibition of the EGF-receptor (EGFR) and mitogen-associated protein kinase (MAPK) signaling pathways in organoids, a state that can be readily reversed. Quiescent Lgr5+ stem cells gain a distinct molecular signature, biased towards EEC differentiation. Indeed, combined inhibition of Wnt, Notch and MAPK pathways efficiently generates a diversity of EEC subtypes in vitro. Our observations uncouple Wnt-dependent stem cell maintenance from EGF-dependent proliferation and cell fate choice, and provide an in vitro approach for the study of the elusive EECs.

overall_design: We established a stable culture of quiescent Lgr5+ intestinal stem cells in culture. These highly resemble quiescent secretory precursors, which has high EEC differentiation potential. Following on this lead, we elucidated what signals are required to generate EEC cells of all varieties, and provide a method to produce these EEC cells in large numbers.

first: Onur

last: Basak

first: Joep

last: Beumer

first: Hiroshi

last: Seno

first: Alexander

last: van Oudenaarden

first: Hans

last: Clevers


title: Inactivation of KLF4 in T cell acute lymphoblastic leukemia promotes the expansion of leukemia cells by activating the Map2k7/Jnk pathway. [ChIP-Seq]

first: Toni-Ann

last: Mistretta

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

summary: Chip-Seq analysis of bone marrow cells from control and Klf4 deficient T-ALL mice

overall_design: GFP+CD4+CD8+bone marrow cells were sorted from control and Klf4 deficient T-ALL mice induced by NOTCH1 at 4 weeks after transplantation.

first: Ye

last: Shen

first: Koramit

last: Suppipat

first: Chun

last: Park

first: Terzah

last: Horton

first: Karen

last: Rabin

first: Daniel

last: Lacorazza


title: nactivation of KLF4 in T cell acute lymphoblastic leukemia promotes the expansion of leukemia cells by activating the Map2k7/Jnk pathway.


title: Transfer RNA (tRNA) processing profiles of mouse embryonic frontal lobes at E13.5/E18.5

status: Public on Jan 02 2017

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology and development. The goal of this study is to establish how tRNA-derived small RNAs can affect stem cell function. Methods: four replicates of tRNAs sequencing of wild-type (WT) and NSun2 -/- mouse embryonic frontal lobes at E18.5 were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that deletion of the cytosine-5 tRNA methylase NSUN2 increases tRNA cleaveage of NSUN2 tRNA substrates.

overall_design: Transfer RNA (tRNA) sequencing of wild-type (WT) and NSun2 -/- mouse embryonic frontal lobes

first: Sandra

last: Blanco


title: Exogenous miRNA expression profiling in serum of pig and rat fed with different diets

status: Public on Jan 01 2017

city: Solna

first: Wenjing

last: Kang

address: SciLifeLab, Tomtebodavägen 23

institute: SciLifeLab

summary: We performed carefully designed and controlled animal feeding studies. We devided 9 adult rats in three group and each group fed with one type of diets in 28 days: rice, potatoes and chow. We fed piglets in triplicate either with cow milk or let them feed from sows milk for 4 weeks followed by 7 weeks of maize diet. Based on the small RNA sequencing data from 9 rat and 6 pig serum samples, we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood.

sample_organism:
Sus scrofa
Rattus norvegicus

platform_organism:
Sus scrofa
Rattus norvegicus

overall_design: The miRNA profiles in serum of chow-fed, potato-fed and rice-fed rats in 28 days and the miRNA profiles in serum of cow milk and sows milk fed pigs were generated by sequencing, in triplicate, Illumina TruSeq small RNA.

first: Claus

last: Bang-Bertelsen

first: Anja

last: Holm

first: Anna

last: Houben

first: Anne

last: Holt Müller

first: Thomas

last: Thymann

first: Flemming

last: Pociot

first: Xavier

last: Estivill

first: Marc

last: Friedländer


title: ChIP-seq from K562 (ENCSR004GKA)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ZEB2 ChIP-seq on human K562

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


title: Systematic in vitro and in vivo characterization of Leukemia-inhibiting factor (LIF)- and Fibroblast growth factor (FGF) -derived porcine induced pluripotent stem cells (piPSC) vs. embryonic stages

city: Frederiksberg

first: Kristine

middle: Karla

last: Freude

address: Groennegardsvej

country: Denmark

institute: University Copenhagen

summary:
Systematic in vitro and in vivo characterization of Leukemia-inhibiting factor (LIF)- and Fibroblast growth factor (FGF) -derived porcine induced pluripotent stem cells (Cell reprogramming -basic developmental studies in the pig) vs Porcine embryonic stages (Plurisys)
Global gene expression analyses and comparisons  of LIF piPSC, FGF piPSC, Parental fibroblast line day 7-8 porcine embryo, day 10-11 porcine embryo, day 12-13 porcine embryo.  Gene network analyses of piPSC lines, pNF and ICM from day 7-8 porcine embryos.

overall_design: RNA-Seq profiles of three embryonic stages with a minimum of 2 replicates. RNA-Seq profiles of piPSC and pNFs performed with 3 biological replicates for each line.

first: Jan

middle: O

last: Secher

first: Gianluca

last: Mazzoni

first: Hendrik

last: Marks

first: Andreia

last: Bernardo

first: Philip

last: Kensche

first: Alice

last: Jouneau

first: Y

last: Tan

first: Julianna

last: Kobolak

first: Anita

last: Feher

first: Zsofi

last: Polgar

first: C

last: Sartori

first: I

last: Bock

last: Louet

first: Vanessa

last: Hall

first: Kaveh

last: Maseyakhi

first: Martin

last: Huynen

first: Giovanna

last: Lazzari

first: Roger

last: Pedersen

first: Henk

last: Stunnenberg

first: Haja

last: Kadarmideen

first: Poul

last: Hyttel

first: Andras

last: Dinnyes


title: Locus-specific isolation of transcription elongation complexes from Saccharomyces cerevisiae

first: Stirling

last: Churchman

address: NRB Rm 356, 77 Ave Loius Pasteur

summary: Transcription of mRNA products by RNA polymerase II (Pol II) is a multi-stage event subject to a multitude of regulatory processes. Transcription, RNA processing, and chromatin related factors all interact with Pol II to ensure proper timing and coordination of transcription and co-transcriptional processes. Many regulators must function simultaneously to coordinate these processes, yet few strategies exist to explore the full complement of factors regulating specific stages of transcription. To this end we developed a strategy to purify Pol II elongation complexes from specific loci of a single gene, namely the 5′ and 3′ regions, using sequences in the nascent RNA. Applying this strategy to Saccharomyces cerevisiae we determined the specific set of factors that interact with Pol II at precise stages during transcription. We identify many known region-specific factors as well as determine a role for the transcription termination factor Rai1 in regulating the early stages of transcription genome-wide. We also demonstrate a role for the ubiquitin ligase Bre1 in regulating Pol II dynamics during the latter stages of transcription. This strategy for gene and loci-specific isolation of transcription complexes will provide a useful tool to explore the host of factors that regulate the different stages of transcription and coordinate co-transcriptional processes.

overall_design: NET-seq of bre1, bye1, paf1, and rtf1 deltion mutants

first: Kevin

last: Harlen

first: L


title: Efficient generation of pancreatic β-like cells from the mouse gallbladder

city: Ashburn

first: Yuhan

last: Wang

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: We report here an improved protocol to reprogram mouse gallbladder cells (GBCs) into pancreatic beta cells. To fully understand the extent of reprogramming, mRNA was extracted from FACS-purified MIP-GFP positive insulin-producing cells (namely rGBC2) for RNA-seq after 10-days of in vitro reprogramming. The global gene expression profile of rGBC2 was compared with that of primary gallbladder cells, GBC reprogrammed with the rGBC1 protocol (Hickey et al., 2013) and mouse pancreatic β cells (Benner et al., 2014). We show that rGBC2 from four independent cell batches showed a unique gene expression phenotype. Compared with the rGBC1 protocol, rGBC2 expressed many additional pancreatic β cell genes,  suppressed many gallbladder genes and resulted in an expression profile closer to pancreatic β cells.

overall_design: Gene expression profiling of galbladder reprogrammed, insulin positive cells using the improved reprogramming protocol

first: Markus

last: Grompe


title: mRNA Sequencing of Ideopathic Pulmonary Fibrosis (IPF) and Control Samples from the Lung Tissue Research Consortium (LTRC)

city: Rochester

first: Nathan

last: LeBrasseur

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: IPF (n=20) and control (n=19) samples were obtained through the LTRC and were sequenced on an Illumina HiSeq 2000 following TruSeq RNA Sample Prep Kit v2 library preparation.

overall_design: Cross-sectional samples were analyzed. IPF diagnosis was based on American Thoracic Society and European Respiratory Society criteria, and all IPF samples displayed typical patterns of usual interstitial pneumonia. RNA libraries were prepared from 200 ng of high quality total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). The concentration and size distribution of TruSeq libraries was determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA), and a final quantification, using Qubit fluorometry (Invitrogen, Carlsbad, CA), was conducted to confirm sample concentration. Libraries were loaded onto paired end flow cells at concentrations of 8-10 pM to generate cluster densities of 700,000/mm2 following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3. The flow cells were sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and SCS version 1.4.8 data collection software. Base-calling was performed using Illumina’s RTA version 1.12.4.2.

first: Robert

last: Vassallo

first: Marissa

last: Schafer

first: Elizabeth

last: Atkinson

first: Brian

last: Kabat

first: Diane

last: Grill


title: Molecular distinctions between motor neurons supplying Tibialis anterior (TA), Extensor digitorum longus (EDL), Peroneus longus (PL), Gastrocnemius (GS) and Intrinsic foot (IF) muscles [RNA-seq]

first: Alana

last: Mendelsohn

address: 3227 Broadway

institute: Columbia University

summary: To probe molecular distinctions in the specification of motor neurons innervating digit muscles we performed a screen for genetic markers that distinguish digit innervating motor neurons from other motor pools. Here, we compare the gene expression profiles of motor neurons that supply muscles with defined biomechanical functions.

overall_design: TA, EDL, PL, GS and IF muscles were separately injected at p4 with CTB-555. Pool specific motor neurons were isolated by laser capture from spinal cord sections of p6 wild-type mice.  Each pool was profiled by three biological replicates, with each biological replicate containing 30-40 cells from 2-5 animals

middle: I

first: Thomas

last: Jessell


title: Whole genome epigenetic sequencing on DNA from infarcted non-infarcted left ventricle of WT and NEIL3-deficient mice subjected to myocardial infarction

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

summary: Myocardial  infarction  (MI)  triggers  a  reparative  response  involving  fibroblast  proliferation   and  differentiation  driving  extracellular  matrix  modulation  necessary  to  form  a  stabilizing   scar.  Recently,  it  was  shown  that  a  genetic  variant  of  the  base  excision  repair  enzyme   endonuclease VIII-like 3  (NEIL3)  was associated  with increased risk of MI in humans. Here,   we  report  elevated  myocardial  NEIL3  expression  in  heart  failure  patients  and  marked   myocardial  upregulation  of  Neil3  following  MI  in  mice,  especially  in  a  fibroblast-enriched   cell fraction.  Neil3-/-mice showed increased  mortality after MI compared to WT, caused by   myocardial rupture.  Epigenomic  analysis  suggested  dysregulated  myofibroblast proliferation   and  differentiation  in  Neil3-/-hearts  and  several  differentially  expressed  genes  were   downstream targets of  differentially  methylated/hydroxymethylated transcriptional regulators.  Furthermore, proliferation of Vimentin+ and SMA+ (myo)fibroblasts was increased in Neil3  -/-hearts  following  MI.  We  propose  that  NEIL3-dependent  modulation  of  epigenetic  DNA   methylation regulates cardiac fibroblast proliferation and thereby controls extracellular matrix  modulation after MI.

overall_design: Genomic DNA from infarcted and non-infarcted LV of WT and Neil3-/- C57BL/6 mice obtained three days after induced myocardial infarction were subjected to 5mC and 5hmC sequencing using Illumina Hiseq 2000

first: Maria

middle: B

last: Olsen

first: Gunn

middle: A

last: Hildrestrand

first: Leif

last: Vinge

first: Katrine

last: Alfsnes

first: Vuk

last: Palibrk

first: Junbai

first: Christine

middle: G

last: Neurauter

first: Luisa

last: Luna

first: Jostein

last: Johansen

first: Jonas

last: Øgaard

first: Ingrid

last: Ohm

first: Geir

last: Slupphaug

first: Anna

last: Kuśnierczyk

first: Arnt

last: Fiane

first: Sverre

last: Brorson

first: Lili

last: Zhang

first: Lars

last: Gullestad

first: William

last: Louch

first: Per

last: Iversen

first: Ingunn

last: Østli

first: Arne

last: Klungland

last: Christensen

first: Ivar

last: Sjaastad

first: Pål

last: Sætrom

last: Yndestad

last: Aukrust

first: Magnar

last: Bjørås

first: Alexandra

middle: V

last: Finsen


title: Epigenome-wide association in the METSIM cohort identifies 22 novel loci for diabetes and metabolic syndrome traits

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

institute: University of Washington

summary: In this study, we examined the association of DNA methylation with metabolic traits in humans using adipose tissue samples from the Metabolic Syndrome in Men (METSIM) cohort. The METSIM cohort has been thoroughly characterized for longitudinal clinical data of metabolic traits including a 3-point oral glucose tolerance test, cardiovascular disorders, diabetes complications, drug and diet questionnaire, as well as high density genotyping, and genome-wide expression in adipose. We performed epigenome-wide association studies on clinical traits using reduced representation bisulfite sequencing data and identified 61 signifiant associations for metabolic syndrome traits, corresponding to 25 unique loci. These associations include previously known genes, FASN, RXRA, MSH2, and MSH6, as well as 22 loci harboring 18 new candidate genes for diabetes and obesity in humans.

overall_design: Genomic DNA human adipose tissue samples was analyzed with respect to cytosine methylation levels using reduced-representation bisulfite sequencing. The raw and processed data submitted here represents all 205 samples used in the analysis.

first: Colin

last: Farrell


title: RNA-SEQ analysis of bdf1-Y187F-Y354F mutant strain during yeast sporulation

city: Grenoble

first: Encar

middle: García

last: Oliver

address: 17, avenue des Martyrs

country: France

institute: INSERM

summary: The aim of this study is to compare NGS-derived yeast transcriptome profiling (RNA-seq) of wild-type and bdf1-Y187F-Y354F mutant strains after sporulation induction (time points: 0h 4h and 8h).

overall_design: S. cerevisiae wild-type and bdf1-Y187F-Y354F mutant strains were collected 0h, 4h and 8h after sporulation induction in triplicates. mRNA were purifired, prepared and sequencedusing Illumina HiSeq 2000 sequencer.

first: Jerome

last: Govin

last: Garcia-Oliver

first: Christophe

last: Battail

first: Anne

last: Boland

first: Jean-François

last: Deleuze


title: Layer-specific ATAC-seq of the neurons of adult mouse visual cortex defined by Cre-driver lines

first: Lucas

last: Gray

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

summary: Mammalian cortex is a laminar structure, with each layer composed of a characteristic set of cell types with different morphological, electrophysiological, and connectional properties. Here, we define chromatin accessibility landscapes of major, layer-specific excitatory classes of neurons, and compare them to each other and to inhibitory cortical neurons using the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We surveyed five Cre-reporter-labeled mouse cell lines using ATAC-Seq of 500-cell populations.

overall_design: ATAC-Seq of 500-cell populations

first: Zizhen

last: Yao

first: Thuc

last: Nguyen

first: Tae

last: Kim

first: Hongkui

last: Zeng

first: Bosiljka

last: Tasic


title: Lamin-B1 contributes to the proper timing of epicardial cell migration and function during heart development

city: Baltimore

first: Joseph

last: Tran

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

summary: Gene expression analysis of wid type and Lmnb1-/- epicardial cells

overall_design: Total RNA was isolated from wild type and Lmnb1-/-  epicardial explants and subject ot sequencing on the Illumina platform

first: Yixian

last: Zheng

first: Xiaobin


title: Analysis of germline modifiers of aggressive prostate cancer using cross-species variation and systems genetics

city: Bethesda

first: Jean

last: Winter

address: 50 South Driver

department: NHGRI

institute: NIH

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Functional and spatial segregation of embryo-larval and adult globin genes in Danio rerio major globin gene locus shows possible way of generation of structural-functional genomic domains in eukaryotic genome

city: Moscow

first: Evgeny

middle: Sergeevich

last: Gerasimov

address: Leninskie gori, 1, 12

department: Biological

country: Russia

institute: Lomonosov Moscow State University

summary: To get insights into domain organization and functioning of the Danio rerio major α/β-globin locus (Mα/βGL), we have characterized profiles of histone H3 panacetylation across this locus in erythrocytes of adult fish and 18 dpf larvas. To identify enriched domains in our ChipSeq data we used our original protocol and peak caller MACS2. Histone acetylation profiles of Mα/βGL for adult and embryo cells reveal a breaking point in upstream region of the first embryo-larval gene βe1.There are two sub-segments of acetylation: sub-segment to the left of βe1 harbors adult-specific globin genes and is acetylated only in adult cells. Embryo sub-segment contains embryo-larval globin genes and is located to the right of βe1 gene.  Acetylation in this subsegment was detected only in 18 dpf larva. Acetylation profile in adult subs-egment possess largest acetylation domain which covers two pairs of adult-stage globins: αa1, and βa1. High acetylation level in this domain well correlates with high expression level observed for these 4 genes in adult erythrocyte.  Pattern of H3 panacetylation in 18 dpf larval erythrocytes differs strikingly from that for adult cells. Embryo-larval segment is fragmented in small domains co-located with gene bodies with gaps in intergenic regions. Adult subsegment in adult cells contains strong acetylation domain that cover 4 globin genes along with a part of intergenic regions and few smaller domains. Alternative stage-specific acetylation of subdomains and different pattern of embryonic-larval and adult domain acetylation strongly support the hypothesis of deep structural and functional segregation of stage-specific subdomains within Mα/βGL locus in zebrafish.

overall_design: Examination of histone H3panac in adult and larval erythrocyte of Danio rerio.

first: E

middle: S

first: S

last: Raziv


title: Candidate Gene Identification Through RNA-Seq Analysis of (TRAMP x J:DO) F1 Primary Tumors

summary: RNA-seq analysis of 195 randomly selected (TRAMP x J:DO) F1 prostates that had been harvested at experimental termination (210 days or humane endpoints) was performed to identify metastasis associated transcriptomic changes

overall_design: Total RNA expression profile of TRAMP x DO F1 prostate tumors

first: Derek

middle: E

last: Gildea

first: Nigel

middle: P

last: Crawford