title: ChIP-seq from 22Rv1 (ENCSR246MLJ)

summary:
ZFX ChIP-seq on human 22Rv1

For data usage terms and conditions, please refer to http://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 (ENCSR230PTV)

status: Public on Oct 20 2017

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
ZBTB2 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 sigmoid colon (ENCSR190PGI)

summary:
Chip-Seq on -human (fragmentation date:Mon Sep 19 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 spleen (ENCSR236WEQ)

summary:
ChIP-seq on human spleen

For data usage terms and conditions, please refer to http://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 (ENCSR239POD)

summary:
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 (ENCSR178QVJ)

summary:
eGFP-ZNF274 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 (ENCSR173EEH)

summary:
COPS2 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 suprapubic skin (ENCSR225UUX)

summary:
Chip-Seq on -human (fragmentation date:Mon Sep 12 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 (ENCSR183AXJ)

summary:
HNRNPUL1 ChIP-seq in 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 HepG2 (ENCSR182QWU)

summary:
Chip-Seq on 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 (ENCSR194IJN)

summary:
eGFP-ZNF766 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 spleen (ENCSR234HEM)

summary:
CTCF ChIP-seq on human spleen

For data usage terms and conditions, please refer to http://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 breast epithelium (ENCSR226SNN)

summary:
Chip-Seq on -human (fragmentation date:Fri Nov 11 2016 00:00:00 GMT-0600 (CST)

For data usage terms and conditions, please refer to http://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 transverse colon (ENCSR170BPY)

summary:
Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 (ENCSR178DEG)

summary:
eGFP-NR2C1 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 subcutaneous adipose tissue (ENCSR176BAH)

summary:
Chip-Seq on adipose tissue

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


title: ChIP-seq from K562 (ENCSR178NTX)

summary:
eGFP-CUX1 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 (ENCSR173AIR)

summary:
CTCF ChIP-seq on human stomach

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


title: ChIP-seq from HEK293 (ENCSR229DYF)

summary:
eGFP-ZBTB26 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 stomach (ENCSR228ZPZ)

summary:
Chip-Seq on stomach

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


title: ChIP-seq from GM12878 (ENCSR173ZVL)

summary:
ZNF592 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 K562 (ENCSR159MTA)

summary:
Input control ChIP-seq on human eGFP-CEBPG 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 (ENCSR171CAY)

summary:
E2F7 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 omental fat pad (ENCSR225OKX)

summary:
CTCF ChIP-seq on human omental fat pad

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


title: ChIP-seq from sigmoid colon (ENCSR225KOT)

summary:
ChIP-seq on human sigmoid colon

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


title: ChIP-seq from K562 (ENCSR222MYK)

summary:
SRSF7 ChIP-seq in 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 (ENCSR223MLH)

summary:
BRCA1 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 ovary (ENCSR158TRP)

summary:
Chip-Seq on female gonad

For data usage terms and conditions, please refer to http://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 esophagus squamous epithelium (ENCSR156UQO)

summary:
POLR2A ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from MCF-7 (ENCSR158PLQ)

summary:
Input control ChIP-seq on human eGFP-ELF1 tagged MCF7 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 HEK293T (ENCSR218GSN)

summary:
ZFX 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 transverse colon (ENCSR170NMC)

summary:
Chip-Seq on transverse colon

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


title: ChIP-seq from uterus (ENCSR224COZ)

summary:
ChIP-seq on human uterus

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


title: ChIP-seq from K562 (ENCSR150XYW)

summary:
Input control ChIP-seq on human eGFP-ZNF197 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 HEK293 (ENCSR224NFP)

summary:
eGFP-ZNF426 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 esophagus squamous epithelium (ENCSR147PYL)


title: ChIP-seq from K562 (ENCSR168CEE)

summary:
NCOA6 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 transverse colon (ENCSR147NJH)

summary:
Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 (ENCSR149ZBI)

summary:
eGFP-ZNF584 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 sigmoid colon (ENCSR222SQE)

summary:
CTCF ChIP-seq on human sigmoid colon

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


title: ChIP-seq from MCF-7 (ENCSR167UME)

summary:
Input control ChIP-seq on human eGFP-KLF4 tagged MCF7 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 HepG2 (ENCSR145BHD)

summary:
NFRKB 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 (ENCSR162IEM)

summary:
MYBL2 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 (ENCSR167XFW)

summary:
eGFP-ZNF544 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: microRNA-seq from adrenal gland (ENCSR160XYB)

type: Non-coding RNA profiling by high throughput sequencing

summary:
miRNA-seq on human adrenal gland

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


title: ChIP-seq from tibial nerve (ENCSR154GUK)

summary:
POLR2A ChIP-seq on human tibial nerve

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


title: ChIP-seq from K562 (ENCSR212RMP)

summary:
Input control ChIP-seq on human eGFP-ZNF584 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 esophagus squamous epithelium (ENCSR153OQA)

summary:
ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from subcutaneous adipose tissue (ENCSR147VKD)

summary:
Chip-Seq on adipose tissue

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


title: ChIP-seq from K562 (ENCSR160QYK)

summary:
GATAD2A 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 adrenal gland (ENCSR135FYV)

summary:
ChIP-seq on human adrenal gland

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


title: ChIP-seq from suprapubic skin (ENCSR213GWR)

summary:
Chip-Seq on -human (fragmentation date:Wed Sep 07 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 thyroid gland (ENCSR144QLB)

summary:
ChIP-seq on human thyroid gland

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


title: ChIP-seq from HEK293 (ENCSR217QCK)

summary:
eGFP-ZNF697 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 (ENCSR211GNP)

summary:
eGFP-ZSCAN4 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 transverse colon (ENCSR138QGB)

summary:
Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 (ENCSR143CEO)

summary:
ZC3H8 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 (ENCSR211LTF)

summary:
EGR1 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: Hi-C from DLD1 (ENCSR213DHH)

summary:
HiC experiment done on DLD1

For data usage terms and conditions, please refer to http://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 Panc1 (ENCSR141ITZ)

summary:
ChIP-seq on human Panc1

For data usage terms and conditions, please refer to http://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 uterus (ENCSR142SQX)

summary:
POLR2A ChIP-seq on human uterus

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


title: ChIP-seq from gastroesophageal sphincter (ENCSR211EXK)

summary:
ChIP-seq on human esophagogastric junction

For data usage terms and conditions, please refer to http://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 gastrocnemius medialis (ENCSR126QXT)

summary:
ChIP-seq on human gastrocnemius medialis

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


title: ChIP-seq from prostate gland (ENCSR122LGV)

summary:
POLR2A ChIP-seq on human prostate gland

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


title: ChIP-seq from gastrocnemius medialis (ENCSR139VAY)


title: ChIP-seq from HEK293 (ENCSR138RCE)

summary:
eGFP-ZNF132 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 (ENCSR121MVZ)

summary:
Input control ChIP-seq on human eGFP-ZNF639 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 ovary (ENCSR118WAD)

summary:
ChIP-seq on human ovary

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


title: ChIP-seq from transverse colon (ENCSR132XRW)

summary:
POLR2A ChIP-seq on human transverse colon

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


title: ChIP-seq from epithelial cell of prostate (ENCSR131SEB)

summary:
ChIP-seq on human epithelial cell of prostate

For data usage terms and conditions, please refer to http://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 (ENCSR128IYN)

summary:
SNRNP70 ChIP-seq in 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 MCF-7 (ENCSR126YEB)

summary:
FOXA1 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 stomach (ENCSR122EYE)

summary:
POLR2A ChIP-seq on human stomach

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


title: ChIP-seq from MCF-7 (ENCSR125ZYC)

summary:
eGFP-KLF9 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 HepG2 (ENCSR210ZYL)

summary:
NBN 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 (ENCSR119VCX)

summary:
PHF21A 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 IMR-90 (ENCSR124AIG)

summary:
FOS ChIP-seq on human IMR-90

For data usage terms and conditions, please refer to http://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 suprapubic skin (ENCSR038FOS)

summary:
CTCF ChIP-seq on human suprapubic skin

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


title: ChIP-seq from heart left ventricle (ENCSR035ELI)

summary:
ChIP-seq on human heart left ventricle

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


title: ChIP-seq from stomach (ENCSR033FDW)

summary:
Chip-Seq on stomach

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


title: ChIP-seq from Panc1 (ENCSR203QEB)

summary:
CTCF ChIP-seq on human Panc1

For data usage terms and conditions, please refer to http://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 omental fat pad (ENCSR117KTL)

summary:
ChIP-seq on human omental fat pad

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


title: ChIP-seq from esophagus muscularis mucosa (ENCSR116RGC)

summary:
Chip-Seq on muscle layer of esophagus

For data usage terms and conditions, please refer to http://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 (ENCSR115BLD)

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


title: ChIP-seq from transverse colon (ENCSR107EUS)


title: ChIP-seq from MCF-7 (ENCSR116QUR)

summary:
CSDE1 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 (ENCSR200JYP)

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 testis (ENCSR036LUN)

summary:
ChIP-seq on human testis

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


title: ChIP-seq from MCF-7 (ENCSR038RXU)

summary:
eGFP-GABPA 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 MCF-7 (ENCSR109ODF)

summary:
HES1 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: microRNA-seq from neural tube (ENCSR107JRF)

summary:
miRNA-seq on embryonic 12.5 day mouse neural tube

For data usage terms and conditions, please refer to http://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 (ENCSR201NQZ)

summary:
CTBP1 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 RWPE1 (ENCSR203KEU)

summary:
H3K27ac ChIP-seq on human RWPE1

For data usage terms and conditions, please refer to http://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 prostate gland (ENCSR109IEL)

summary:
ChIP-seq on human prostate gland

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


title: ChIP-seq from upper lobe of left lung (ENCSR033NHF)

summary:
POLR2A ChIP-seq on human upper lobe of left lung

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


title: ChIP-seq from suprapubic skin (ENCSR106JXD)

summary:
Chip-Seq on -human (fragmentation date:Wed Sep 07 2016 00:00:00 GMT-0500 (CDT)

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


title: Hi-C from SK-N-DZ (ENCSR105KFX)

summary:
HiC experiment done on SK-N-DZ

For data usage terms and conditions, please refer to http://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 (ENCSR032EZQ)

summary:
Control ChIP-seq on 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 gastrocnemius medialis (ENCSR103UPR)

summary:
POLR2A ChIP-seq on human gastrocnemius medialis

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


title: ChIP-seq from HEK293 (ENCSR028EGI)

summary:
eGFP-ZNF26 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 transverse colon (ENCSR102CSD)

summary:
CTCF ChIP-seq on human transverse colon

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


title: ChIP-seq from upper lobe of left lung (ENCSR027FSZ)

summary:
CTCF ChIP-seq on human upper lobe of left lung

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


title: ChIP-seq from adrenal gland (ENCSR031KWR)

summary:
POLR2A ChIP-seq on human adrenal gland

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


title: ChIP-seq from adrenal gland (ENCSR091EBM)

summary:
ChIP-seq on human adrenal gland

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


title: ChIP-seq from gastroesophageal sphincter (ENCSR088VUG)

summary:
Chip-Seq on esophagogastric junction

For data usage terms and conditions, please refer to http://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 (ENCSR029LBT)

summary:
FOXP1 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 (ENCSR096LSN)

summary:
eGFP-ZNF311 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 spleen (ENCSR028YEV)

summary:
CTCF ChIP-seq on human spleen

For data usage terms and conditions, please refer to http://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 C4-2B (ENCSR027UFT)

summary:
ZFX ChIP-seq on human C4-2B

For data usage terms and conditions, please refer to http://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 subcutaneous adipose tissue (ENCSR078CBW)

summary:
ChIP-seq on human adipose tissue

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


title: ChIP-seq from K562 (ENCSR084AIG)

summary:
Control ChIP-seq in 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 (ENCSR094ZCF)

summary:
eGFP-CEBPG 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 (ENCSR024CNP)

summary:
EGR1 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 body of pancreas (ENCSR079WBX)

summary:
ChIP-seq on human body of pancreas

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


title: ChIP-seq from stomach (ENCSR081KET)

summary:
ChIP-seq on human stomach

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


title: ChIP-seq from suprapubic skin (ENCSR025ZZA)

summary:
POLR2A ChIP-seq on human suprapubic skin

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


title: ChIP-seq from omental fat pad (ENCSR089DTY)

summary:
CTCF ChIP-seq on human omental fat pad

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


title: ChIP-seq from gastroesophageal sphincter (ENCSR091CSG)

summary:
POLR2A ChIP-seq on human gastroesophageal sphincter

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


title: ChIP-seq from omental fat pad (ENCSR088FBX)

summary:
Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)

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


title: Genome wide mapping of H3K4me3 and H3K27me3 marks in trophoblast progenitors derived from human embryonic stem cells

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Center Munich

summary:
Human embryonic stem cells (hESC) can be differentiated into progenitors resembling trophoblast upon exposure to BMP4. Putative trophpblast progenitors express APA cell surface marker
Using trophoblast progenitors at day 2.5 of BMP4-induced differentiation, here we profile H3K4me3 and H3K27me3 chromatin marks that mark active and inactive genes, respectively. Double occupancy indicates bivalency

overall_design: Undifferentiated hESC and hESC treated with BMP4 for 2.5 days (cell line H9) were FACS-sorted to isolate APA+, APA- and SSEA5+ cell populations. Sorted cells were subjected to ChIP with anti-H3K4me3 and H3K27me3 antibodies followed by next generation sequencing

first: Christian

last: Krendl

first: Tobias

last: Straub


title: ChIP-seq from liver (ENCSR080XEY)

summary:
Chip-Seq on FOXA2-human

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


title: Hi-C from G401 (ENCSR079VIJ)

summary:
HiC experiment done on G401

For data usage terms and conditions, please refer to http://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 (ENCSR076KZW)

summary:
eGFP-ZNF280C 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 (ENCSR074VAI)

summary:
eGFP-ZIK1 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 gastroesophageal sphincter (ENCSR023BPG)

summary:
Chip-Seq on -human (fragmentation date:Tue Sep 20 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 thyroid gland (ENCSR088BOY)

summary:
ChIP-seq on human thyroid gland

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


title: ChIP-seq from K562 (ENCSR021JFW)

summary:
Input control ChIP-seq on human eGFP-GTF2E2 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 GM12878 (ENCSR072PWP)

summary:
ZNF24 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 MCF-7 (ENCSR018MQH)

summary:
ZNF579 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 esophagus muscularis mucosa (ENCSR074SFL)

summary:
CTCF ChIP-seq on human esophagus muscularis mucosa

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


title: ChIP-seq from Peyer's patch (ENCSR067AZA)

summary:
ChIP-seq on human Peyer's patch

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


title: ChIP-seq from HEK293 (ENCSR019WUS)

summary:
eGFP-ZNF10 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: microRNA expression profile of the SVF of visWAT under β3-adrenegic stimulation

city: Stockholm

first: Carina

last: Fischer

address: Nobels väg 16

country: Sweden

institute: Karolinska Institute

summary:
We used microRNA expression analysis to identify which microRNAs are expressed in the stromal vascular fraction (SVF) of visceral white adipose tissue (visWAT) to identify of microRNA expression patterns are changed upon  CL-316,243 treatment
Agilent mouse miRNA microarray (Cat. No. G4872A-046065, Agilent Technologies) was performed on the SVF of visWAT of 8-week-old C57/BL6 mice treated with CL 316243 or Vehicle (PBS) for three days. Isolated miRNA and total RNA was used for array analysis by Shanghai Biotechnology Corporation. Normalization and analysis for differentially expressed genes were performed using robust multi-array analysis and significance analysis of microarrays (SAM) via R statistical software packages “oligo” and “samr”.  Several up- and downregulated microRNAs could be identified and were further varified with qPCR and compared with mRNA expression levels of their main targets.

overall_design: The microRNA profile of SVFs of 3-day CL-316,243 treated visWAT was compared to buffer treated controls.

first: Yihai

last: Cao


title: ChIP-seq from K562 (ENCSR068GPE)

summary:
Input control ChIP-seq on human eGFP-ZNF507 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 HepG2 (ENCSR015TKV)

summary:
BCLAF1 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 HepG2 (ENCSR066EBK)

summary:
FOXA2 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 upper lobe of left lung (ENCSR062MVC)

summary:
ChIP-seq on human upper lobe of left lung

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


title: ChIP-seq from K562 (ENCSR017GBO)

summary:
eGFP-TFDP1 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 (ENCSR017CYU)

summary:
Input control ChIP-seq on human eGFP-NR2C2 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 upper lobe of left lung (ENCSR061CNP)


title: ChIP-seq from adrenal gland (ENCSR015WSU)

summary:
ChIP-seq on human adrenal gland

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


title: ChIP-seq from A549 (ENCSR064LJN)

summary:
RFX5 ChIP-seq on human A549

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


title: ChIP-seq from body of pancreas (ENCSR055WBT)

summary:
POLR2A ChIP-seq on human body of pancreas

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


title: ChIP-seq from upper lobe of left lung (ENCSR068WNI)

summary:
POLR2A ChIP-seq on human upper lobe of left lung

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


title: ChIP-seq from prostate gland (ENCSR047WFN)

summary:
ChIP-seq on human prostate gland

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


title: ChIP-seq from omental fat pad (ENCSR047DRF)

summary:
Chip-Seq on adipose tissue of omentum

For data usage terms and conditions, please refer to http://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 gastrocnemius medialis (ENCSR071XWO)

summary:
CTCF ChIP-seq on human gastrocnemius medialis

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


title: ChIP-seq from K562 (ENCSR051DXE)

summary:
FUS ChIP-seq in 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 adrenal gland (ENCSR014GSQ)

summary:
CTCF ChIP-seq on human adrenal gland

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


title: ChIP-seq from esophagus muscularis mucosa (ENCSR014XSP)

summary:
Chip-Seq on -human (fragmentation date:Wed Sep 07 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 omental fat pad (ENCSR013JVJ)

summary:
ChIP-seq on human omental fat pad

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


title: ChIP-seq from GM12878 (ENCSR014YCR)

summary:
ATF7 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 RWPE1 (ENCSR061MKW)

summary:
ChIP-seq on human Prostate epithelial

For data usage terms and conditions, please refer to http://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 testis (ENCSR046INL)

summary:
Chip-Seq on testis

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


title: ChIP-seq from HepG2 (ENCSR029IBC)

summary:
ARNT 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 subcutaneous adipose tissue (ENCSR009SHE)

summary:
Chip-Seq on -human (fragmentation date:Tue Aug 30 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://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 (ENCSR011PEI)

summary:
eGFP-ZNF175 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 (ENCSR047LSJ)

summary:
TAF15 ChIP-seq in 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: Hi-C from astrocyte of the cerebellum (ENCSR011GNI)

summary:
HiC experiment done on astrocyte of the cerebellum

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


title: ChIP-seq from HEK293 (ENCSR044FMM)

summary:
eGFP-SALL2 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 transverse colon (ENCSR009MWG)

summary:
ChIP-seq on human transverse colon

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


title: ChIP-seq from K562 (ENCSR176UHI)

summary:
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: microRNA-seq from embryonic facial prominence (ENCSR005FZJ)

summary:
miRNA-seq on embryonic 12.5 day mouse embryonic facial prominence

For data usage terms and conditions, please refer to http://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 (ENCSR039ZBB)

summary:
Input control ChIP-seq on human eGFP-FOSL1 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 esophagus squamous epithelium (ENCSR003SZZ)

summary:
CTCF ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from HepG2 (ENCSR047BUZ)

summary:
ATF2 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: Distinct ‘safe zones’ at the nuclear envelope ensure robust replication of heterochromatic chromosome regions

city: Bethesda

first: Hani

last: Ebrahimi

address: 7170 Woodmont Ave

department: NCI

institute: NIH

summary: Chromosome replication and transcription occur within a complex nuclear milieu whose functional subdomains are only beginning to be mapped out. The nuclear envelope (NE) generally interacts with heterochromatic regions of the genome that are inherently difficult to replicate. Here we delineate compositionally and functionally distict domains of the fission yeast NE, focusing on the NE regions specifically enriched for the inner NE protein, Bqt4, or the conserved lamin interacting domain protein, Lem2. Bqt4 is relatively mobile around the NE and acts in two capacities. First, Bqt4 is required for tethering two key heterochromatic regions, the chromosome termini and the mat locus, to the NE specifically while these regions are undergoing DNA replication. This positioning is required for robust replication and heterochromatin assembly in the wake of the replication fork. Second, Bqt4 mobilizes a subset of Lem2 molecules around the NE, where Lem2/Bqt4 promote pericentric heterochromatin maintenance. Opposing Bqt4-dependent Lem2 mobility are factors that stabilize Lem2 at its most abundant localization site beneath the centrosome, where Lem2 plays a crucial role in kinetochore maintenance. Our data prompt a model in which Bqt4-rich nuclear subdomains are ‘safe zones’ in which collisions between transcription and replication are averted and heterochromatin is reassembled faithfully following replication.

overall_design: Examination of H3K9me histone modifications in 5 strains. Different strain numbers indicates that there could be unknown differences in genotypes of cells that should be otherwise similar. There are two types of replicates. One is by repeating the ChIP-Seq experiment on the same strain (e.g. JCT109 that is the parent). The second type of replicate is 'independent  sister cells'; in this case the strain number is different but "relevant" genotype is the same. For example, JCF14512 and JCF14513  are sisters that come from the same parent with identical genotypes.

first: Hirohisa

last: Masuda

first: Devanshi

last: Jain

first: Julia

last: Promisel Cooper


title: ChIP-seq from stomach (ENCSR038YKU)

summary:
POLR2A ChIP-seq on human stomach

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


title: ChIP-seq from tibial nerve (ENCSR004FGW)

summary:
ChIP-seq on human tibial nerve

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


title: ERRBS dataWT and TET2cKOgp33+ CD8+ T cells isolated on D8 LCMV-Armstrong infection

city: Ann Arbor

first: Shannon

last: Carty

state: MI

address: 109 Zina Pitcher Place

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: The epigenetic modifier TET2 plays a role in cell fate decisions in hematopeotic stem cells and CD4+ Th1 and Th17 differentiation. Here, we demonstrate that loss of TET2 promotes CD8+ memory differentiation following acute viral infection with LCMV-Armstrong.

overall_design: To identify methylation changes in WT versus TET2-deficiency gp33+ CD8+ T cells, we sorted gp33+CD44+CD8+ T cells from WT and TET2fl/flCD4Cre+ mice on day 8 of LCMV-Armstrong infection

middle: A

first: Gary

last: Koretzky

first: Martha

middle: S

last: Jordan


title: Expression data from  CD28+/- resting CD8 T cells

city: San Francisco

first: Philip Ansumana

last: Hull

address: 1650 Owens Street

department: GIVI

institute: Gladstone Insitute of Virology and Immunology

summary:
We used microarrays to detail the global programme of gene expression underlying the loss of CD28 co-receptor on primary human CD8+ T cells.
We identified distinct classes of differentially regulated genes between sorted T cell subsets.

overall_design: Primary human CD8 T cells from blood from HIV- individuals were isolated, and CD28+ and CD28- T cells subsets were sorted for RNA extraction and hybridization on Affymetrix microarrays.

first: Hye-Sook

last: Kwon

first: Melanie

last: Ott


title: ChIP-seq from upper lobe of left lung (ENCSR000MMZ)

summary:
Chip-Seq on upper lobe of left lung

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


title: ChIP-seq from SK-N-SH (ENCSR009TKN)

summary:
RCOR1 ChIP-seq on human SK-N-SH

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


title: RNA-seq data of intestinal epithelial cells and lamina propria dendritic cells

city: Shinjuku-ku

first: Koji

last: Atarashi

state: TOKYO

address: 35 Shinanomachi

department: Dept of Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

type: Expression profiling by high throughput sequencing

summary: We report that Klebsiella pneumoniae promote Th1 cell induction in colon. To examine the influence of Klebsiella on colonic epithelial cells (ECs) and lamina propria CD11c+ dendritic cells (DCs), we performed RNA seq on them. Germ free mice were orally inoculated with Kp-2H7 or BAA-2552 and total RNA was isolated from colonic ECs and DCs 1 week after inoculation. Furthermore, we examined the involvement of TLRs in induction of Th1 cells using Myd88 KO, Trif KO, Myd88/Trif DKO mice. These deficient germ free mice were orally inoculated with Kp-2H7 and total RNA was isolated from colonic ECs 3 weeks after inoculation.

overall_design: The gene expression of colonic ECs and DCs isolated from germ free mice, and GF mice inoculated with Kp-2H7 or BAA-2552, and colonic ECs isolated from GF Myd88 KO, Trif KO or Myd88/Trif DKO mice inoculated with Kp-2H7.

first: Kenya

last: Honda


title: Gene Expression in the Human Lacrimal Gland

city: Portland

first: James

last: Rosenbaum

state: OR

address: 3181 SW Sam Jackson Park Road

department: Casey Eye Institute

institute: Oregon Health & Science University

summary:
Diagnosis of inflamed human lacrimal gland with standard clinical and histopathology evaluation data is imprecise. A large number of these patients are diagnosed with the catch-all classification of nonspecific orbital inflammation (NSOI).
We utilized gene expression analysis of lacrimal gland biospy/surgical waste tissues to assist in the classification of sarcoidosis, granulomatosis with polyangiitis (GPA), thyroid eye disease (TED), and subdivisions of NSOI. As part of this process, we are investigating correlations between gene expression levels and disease characteristics.

overall_design: Formalin-fixed, paraffin-embedded lacrimal gland tissues were collected for RNA extraction and analysis with Affymetrix microarrays. Biopsy/surgical waste samples were obtained from subjects with inflammatory diseases such as NSOI, sarcoidosis, GPA, and TED as well as from normal controls. In some cases, more than one sample was obtained for a subject.

middle: T

first: Stephen

middle: R

last: Planck

first: Dongseok

last: Choi

first: Christina

last: Harrington


title: Identification of genome-wide targets of Olig2 in the adult mouse spinal cord using ChIP-Seq

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary: Olig2 is a crucial factor in the specification and differentiation of oligodendrocyte precursor cells that give rise to mature, myelin-producing OLs in the developing and postnatal CNS; however, its role in adulthood is less well understood.  To investigate the role Olig2 plays in regulating gene expression in the adult oligodendrocyte lineage in a physiologically-relevant context, we performed chromatin immunoprecipitation followed by next generation sequencing analysis using whole spinal cord tissue harvested from adult mice. We found that many of the Olig2-bound sites were associated with genes with biological processes corresponding to myelination and ensheathment, as well as cell cycle and cytoskeletal regulation, suggesting Olig2 continues to play a critical role in processes related to OL differentiation and myelination well into adulthood.

overall_design: Examination of in vivo genomic loci occupied by Olig2 in adult  whole mouse spinal cord

first: Andrew

middle: J

last: Darr

first: Pantelis

last: Tsoulfas


title: ChIP-seq from GM12878 (ENCSR009MBP)

first: ENCODE

last: DCC

summary:
HSF1 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 MCF-7 (ENCSR042TWZ)

summary:
SNIP1 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 omental fat pad (ENCSR005LPI)

summary:
CTCF ChIP-seq on human omental fat pad

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


title: Ability of SPEN to bind to chromatin in testicular cells

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: Since SPEN co-localizes with transcriptionally active chromatin and it is considered as a nuclear matrix platform that organizes and integrates transcriptional responses, we aimed to find out how it is involved in gene expression regulation in spermatogenic cells. We assumed that SPEN could be directly involved in down-regulation of gene expression during recovery from heat shock, when general repression of the transcription was observed. Nascent SPEN (~400 kDa) is processed to several fragments. We tested antibodies to N-terminal, internal, or C-terminal SPEN sequences in ChIP experiments on mouse testicular cells either untreated or heat shocked. Only antibodies against N-terminal or internal SPEN epitopes were effective while C-terminal SPEN did not bind to chromatin. However sequencing of N-terminal or internal SPEN ChIP samples did not reveal any strong SPEN binding to the chromatin and the enrichment was seen primarily in genomic structural variants. This suggests that SPEN could be loosely associated with DNA via other proteins.

overall_design: We sequenced DNA immunoprecipitated from isolated testicular cells using rabbit polyclonal anti-SPEN antibodies raised against N-terminal or internal part of the protein. Cells were either untreated (control) or heat shocked for 15-30 minutes with subsequent recovery. Five to six ChIP replicates were collected per each sequenced sample; negative control sample with rabbit IgG (performed in parralel to SPEN Ab samples, then pooled for sequencing) and input samples were included.

first: Joanna

last: Korfanty

first: Wieslawa

last: Widlak


title: MNase-seq after CBP inhibition in Drosophila S2 cells

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

institute: Stockholm University

summary: Nucleosome position does not change after 10 min of CBP (also known as nejire) inhibition.

overall_design: Drosophila melanogaster S2 cells were treated with control (C37) or the CBP inhibitor C646 for 10 min, fixed with formaldehyde, and digested with MNase. One percent Saccharomyces cerevisiae chromatin was mixed with this chromatin (spike-in).

first: Ann

last: Boija

first: Per

last: Stenberg


title: Expression data from Hm mutant

city: Mishima

first: Kousuke

last: Mouri

address: Yata 1111

institute: National Institute of Genetics

summary: Mouse Hammer toe (Hm) shows syndactyly. To reveal the molecular mechanisms of Hm phenotype, we performed microarray analysis to search differencially expressed genes in Hm limb.

overall_design: Interdigital region from Wild type and Hm hind limb were dissected and total RNA was isolated. 3 sets of 5 littermates, totally 15 enbryos in each genotypes were hybridized on Affimetrix microarray.


title: Drosophila TFIIB ChIP-seq after CBP inhibition

summary: TFIIB chromatin binding is drastically reduced genome-wide after 10 min of CBP (also known as nejire) inhibition.

overall_design: Drosophila melanogaster S2 cells were treated with control (C37) or the CBP inhibitor C646 for 10 min, fixed with with formaldehyde, and chromatin prepared. One percent Drosophila virilis chromatin was mixed with this chromatin (spike-in). An antibody raised against Drosophila TFIIB (gift from Jim Kadonaga, UCSD) was used for ChIP-seq.


title: ChIP-seq from HEK293 (ENCSR041ZIQ)

summary:
eGFP-SALL1 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: Identification of the networks that regulate human monocytic myeloid-derived suppressor cell differentiation into inflammatory macrophages

status: Public on Oct 19 2017

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

institute: National Institutes of Health

summary:
Background: Monocytic myeloid-derived suppressor cells (mMDSC) support immune evasion of tumors by blocking tumoricidal T and NK cell response. Efforts to reverse mMDSC-mediated immunosuppression identified that the TLR7/8 agonist R848 induces their maturation into tumoricidal macrophages
Purpose: The factors that determine whether human mMDSC differentiate into MACinflam or MACsuppress are unclear. To investigate this issue, the role of cytokines and genes activated following R848 treatment was examined.
Methods: After 4 hour stimulation, cells from stimulated mMDSC were stored in RNA protect (Qiagen, Frederick, MD).  Total RNA was isolated using the RNeasy micro kit (Qiagen) and RNA quality was assessed using an Agilent 2200 TapeStation. mRNA libraries were generated using the Smart-Seq ultra-low input kit (Clontech) and sequenced using a HiSeq2500 sequencer using IlluminaTruSeq v4 chemistry with 125bp paired-end reads. Sequences were aligned to the human (hg19) reference genome. Genes that were differentially expressed compared to untreated samples were identified using CLC genomics workbench (version 10).
Results: TNFa combined with IL-6 effectively supports the differentiation of mMDSC into tumoricidal macrophage by activating expression of conserved set of genes. Mechanistically, transcription factors NF-KB and STAT4 emerge as important regulators and potential targets to modify mMDSC behavior.

overall_design: Blood was received from human donors, FACS sorted for MDSC cells and then cultured with IFNg,  R848 or Il6-TNFa for 4 hours.  Rna was collected and mRNA libraries were generated using the Smart-Seq ultra-low input kit (Clontech) and sequenced using a HiSeq2500 sequencer using IlluminaTruSeq v4 chemistry with 125bp paired-end reads. Sequences were aligned to the human (hg19) reference genome. Genes that were differentially expressed compared to untreated samples were identified using CLC genomics workbench (version 10)

first: Defne

last: Bayik

first: Debra

last: Tross


title: Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Post-weaning epiphysiolysis causes distal femur dysplasia and foreshortened hindlimbs in fetuin-A-deficient mice

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary: Fetuin-A / α2-Heremans-Schmid-glycoprotein (gene name Ahsg) is a systemic inhibitor of ectopic calcification. Due to its high affinity for calcium phosphate, fetuin-A is highly abundant in mineralized bone matrix. Foreshortened femora in fetuin-A-deficient Ahsg-/- mice indicated a role for fetuin-A in bone formation. We studied early postnatal bone development in fetuin-A-deficient mice and discovered that femora from Ahsg-/- mice exhibited severely displaced distal epiphyses and deformed growth plates, similar to the human disease slipped capital femoral epiphysis (SCFE). The growth plate slippage occurred in 70 % of Ahsg-/- mice of both sexes around three weeks postnatal. At this time point, mice weaned and rapidly gained weight and mobility. Epiphysis slippage never occurred in wildtype and heterozygous Ahsg+/- mice. Homozygous fetuin-A-deficient Ahsg-/- mice and, to a lesser degree, heterozygous Ahsg+/- mice showed lesions separating the proliferative zone from the hypertrophic zone of the growth plate. The hypertrophic growth plate cartilage in long bones from Ahsg-/- mice was significantly elongated and V-shaped until three weeks of age and thus prior to the slippage. Genome-wide transcriptome analysis of laser-dissected distal femoral growth plates from 13-day-old Ahsg-/- mice revealed a Jak-Stat-mediated inflammatory response including a 550-fold induction of the chemokine Cxcl9. At this stage, vascularization of the elongated growth plates was impaired, which was visualized by immunofluorescence staining. Thus, fetuin-A-deficient mice may serve as a rodent model of growth plate pathologies including SCFE and inflammatory cartilage degradation.

overall_design: 9 samples were analysed: We analyzed distal femoral growth plates from male, 13-day-old Ahsg+/+, Ahsg+/- and Ahsg-/- mice, n=3 per genotype.

first: Laura

last: Brylka

first: Sina

last: Köppert

first: Anne

last: Babler

first: Beate

last: Kratz

first: Timur

last: Yorgan

first: Julia

last: Etich

first: Ivan

middle: G

last: Costa

first: Bent

last: Brachvogel

first: Peter

last: Boor

first: Thorsten

last: Schinke

first: Willi

last: Jahnen-Dechent


title: CBP regulates recruitment and release of promoter-proximal  RNA polymerase II

first: Mattias

last: Mannervik

summary:
Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here we identify a novel activity of the histone acetyltransferase p300/CBP in regulating promoter-proximal paused Pol II. We find that Drosophila CBP (nejire) inhibition impedes transcription through the +1 nucleosome leading to accumulation of Pol II at this position on all expressed genes. Promoters strongly occupied by CBP and GAGA-factor have high levels of paused Pol II, a unique chromatin signature and strong expression regardless of cell type. Interestingly, CBP activity is rate-limiting for Pol II recruitment to these highly-paused promoters through an interaction with TFIIB, but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Drosophila melanogaster S2 cells were treated with control (C37) or the CBP inhibitor C646 for 10 min, fixed with with formaldehyde, and either digested with MNase or used in ChIP-seq with a TFIIB antibody. One percent Saccharomyces cerevisiae chromatin was mixed with MNase-digested chromatin, and one percent Drosophila virilis chromatin mixed with the chromatin used for ChIP-seq (spike-in).


title: Transcriptome analysis of naive and Listeria monocytogenes-specific CD8+ T cells

city: Paris

first: Luigia

last: Pace

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary:
The histone methyltransferase Suv39h1 silences transcriptional programs during CD8+-T cell differentiation
The study explores the role of gene silencing by Suv39h1, a histone methyltransferase, that plays a critical role in heterochromatin dynamics.

overall_design: Naïve littermate and Suv39h1-KO CD8+ T cells, and day 7 p.i. Kb-OVA+ CD8+ T cells (from Listeria m.-OVA infected mice), were isolated by FACS. RNA was isolated and analyzed using Affymetrix microarrays. microarrays (three mice per condition were analyzed).

first: Christel

last: Goudot

first: David

last: Gentien

first: Audrey

last: Rapinat


title: Expression data from mouse tissue Angiotensin II treated for 0, 1, 3, 7 days

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Angiotensin II (Ang II) mediated signaling plays a key role in the development of hypertension associated target organ damages. However, the gene expression changes regulated by Ang II in the early stage of acute cerebral, cardiac, renal, vascular injury remain unclear.
we investigated Ang II–mediated gene expression alteration associated with the development of early cerebral, cardiac, renal, vascular injury by microarray assay in a mouse model.

overall_design: All mice were euthanized by an overdose of pentobarbital on days 1, 3 and 7 of Angiotensin II treatment. Total RNA was isolated with TRIzol (Invitrogen) fromvessels (n=3 per group) at each time point according to manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). On the GeneChip Mouse Genome 430 2.0 Array, over 45,000 probe sets analyze the expression level of over 39,000 transcripts and variants from over 34,000 well characterized mouse genes.

first: Hui-Hua

last: Li

first: Yun-Long

last: Zhang


title: AltitudeOmics

city: Denver

first: Daniel

last: Dvorkin

state: CO

address: 1528 Rosemary St

department: Emergency Medicine

institute: University of Colorado

type:
Expression profiling by array
Methylation profiling by array
Non-coding RNA profiling by array

platform_organism:
Homo sapiens
synthetic construct


title: AltitudeOmics methylation data

city: Aurora

first: Robert

last: Roach

address: Campus Box F-524, 12469 E. 17th Place

department: Department of Pulmonology

summary: Acclimatization to high altitude over 21 days, and upon re-ascent 7 and 21 days post-descent. See Subudhi et al. (2014) PLOS ONE 9(3):e92191, PMCID PMC3962396 for experiment details.

overall_design: 107 total samples representing 21 subjects at 7 time points (not all subjects represented at all time points) were taken, plus one sample not used for quality control reasons.  Significance was determined by change vs. baseline (sea level).


title: ChIP-seq from HEK293 (ENCSR004PLU)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
eGFP-ZBTB10 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: Early-life gene expression in neurons modulates lasting epigenetic states. [Mnase-seq]

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: In mammals during the early postnatal period the environment plays a critical role in promoting the final steps in neuronal development. While epigenetic factors are thought to contribute to this process, the underlying molecular mechanisms remain poorly understood. Here we show that in the brain during early life the DNA methyltransferase DNMT3A transiently binds across transcribed regions of lowly expressed genes, and its binding specifies the pattern of DNA methylation at CA sequences (mCA) within these genes. We find that DNMT3A occupancy and mCA deposition within the transcribed regions of genes is negatively regulated by gene transcription and may be modified by early-life experience. Once deposited, mCA is bound by the methyl-DNA-binding protein MECP2 and functions in a rheostat-like manner to fine-tune the cell type-specific transcription of genes that are critical for brain function.

overall_design: MNase-seq from mouse brain tissue

first: Michael

middle: E

last: Greenberg


title: Early-life gene expression in neurons modulates lasting epigenetic states [ChIP-Seq]

overall_design: ChIP-seq from mouse brain tissue and neurons


title: Whole-Genome Methylation Profile of Fibroblast-Derived Isogenic Induced Pluripotent Stem Cells

city: Moscow

first: Rinat

middle: I

last: Sultanov

address: Malaya Pirogovskaya, 1a

country: Russia

institute: FRCC of Physical Chemical Medicine of the FMBA of the Russian Federation

type: Methylation profiling by genome tiling array

summary: The paper reports data on measuring whole-genome DNA methylation using an Illumina 450K Methylation BeadChip platform for isogenic induced pluripotent stem cells (iPSCs) derived from fibroblasts of a healthy donor and a PARK-associated Parkinson's disease patient via integrating (lentiviral transfection) and non-integrating (Sendai virus infection) reprogramming. Data on whole-genome methylation of neurons generated by differentiation of the iPSCs were also presented. The iPSCs were reprogrammed using the four Yamanaka’s factors: OCT4 (POU5F1), SOX2, KLF4, and cMYC. The data evidence that there are no significant differences in whole-genome methylation of iPSCs produced by various methods.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina HumanMethylation450 BeadChip

first: Maria

last: Lagarkova

first: Olga

last: Lebedeva

first: Sergei

last: Kiselev


title: Early-life gene expression in neurons modulates lasting epigenetic states. [RNA-seq 2]

overall_design: RNA-seq from mouse brain tissue and neurons


title: Early-life gene expression in neurons modulates lasting epigenetic states. [Bisulfite-seq]

sample_organism:
Mus musculus
Lambdavirus lambda

platform_organism:
Mus musculus
Lambdavirus lambda

overall_design: Bisulfite-seq from mouse brain tissue and neurons


title: Control of microRNA expression by mitochondrial function

city: Birmingham

first: Keshav

last: Singh

state: AL

address: 720 20th Street South Kaul 630

department: Genetics

institute: University of Alabama at Birmingham

summary: Normal cellular function requires communication between mitochondria and the nucleus, termed mitochondria-to-nucleus retrograde signaling. Interruption of this mechanism has been implicated in the dysregulation of many cancer-related pathways, including cell death programs and tumor suppressor networks. Many proteins are known modulators of retrograde signaling, but whether microRNAs (miRNAs) are also involved is unknown. We conducted a miRNA microarray analysis using RNA from a parental cell line, a Rho0 line lacking mitochondrial DNA (mtDNA) and a Rho0 line with restored mtDNA. We found that miR-663 was down-regulated in the mtDNA-depleted Rho0 line. mtDNA restoration reversed this miRNA to parental levels, suggesting that it is an epigenetically-regulated mediator of retrograde signaling. We further demonstrated by methylation specific PCR and bisulfite sequencing that miR-663 is epigenetically regulated by pharmacological disruption of oxidative phosphorylation (OXPHOS). Restoration of rotenone-suppressed miR-663 expression by N-acetylcysteine suggested that mitochondrial dysfunction–induced reactive oxygen species play a role in epigenetic miR-663 regulation. We noted that miR-663 regulates the expression of nuclear-encoded respiratory chain subunits, e.g. NDUFB8, SDHB, UQCRFS1, and COX4L1. miR-663 also regulated the OXPHOS assembly factors NDUFAF1, SDHAF2, UQCC2, and SCO1 and was required for respiratory supercomplex stability. Furthermore, using luciferase assays, we found that miR-663 directly regulates UQCC2. The miR-663 sponge reduced OXPHOS complex activity and increased in vitro cellular proliferation and promoted tumor development in mice. We also found that increased miR-663 expression in breast tumors consistently correlates with increased patient survival. We provide first evidence for miRNA mediating retrograde signaling, demonstrating its epigenetic regulation and its role in breast tumorigenesis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: RNA from four cell lines was used in this array: A 143B parental cell line, a Rho0 cell line in which mitochondrial DNA was depleted and two cybrid cell lines in which platelets were fused with the Rho0 lines. One RNA sample per treatment group was used.

first: Trevor

last: Carden


title: Common and differential transcriptional actions of LXRalpha and LXRbeta in murine macrophages

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

summary: The LXR proteins, LXRα and LXRβ, are transcription factors that belong to the nuclear receptor superfamily. LXRs are activated by oxysterols and control the transcription of genes involved in the regulation of cholesterol and fatty acid metabolism. They also mediate several aspects of macrophage biology, including inflammatory responses, cell survival in response to infection and phagocytosis of apoptotic cells. LXRs share a high degree of sequence homology and most of their functions are believed to be performed similarly by LXRα and LXRβ. However, the individual, transcriptional roles of each LXR isoform have not been characterized in detail, in part due to the lack of specific experimental tools that can discriminate between LXRα and LXRβ actions. To identify common and differential transcriptional functions of LXR nuclear receptors in macrophages, we developed a cellular model of stable expression of FLAG-tagged LXRα or LXRβ in LXR-null immortalized murine bone marrow-derived macrophages (parental line published  Elife. 2015 Jul 14;4:e08009. doi: 10.7554/eLife.08009). To take a deeper insight into the epigenomic features of LXR nuclear receptors, we performed chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-seq) to identify genome-wide binding locations of LXRα and LXRβ in the presence of a synthetic agonist (GW3965, 1uM). Additionally, we identified genome-wide DNA locations of acetylation mark on lysine 27 of histone H3 (H3K27ac), upon LXR agonist (GW3965, 1uM) and antagonist (GW2033, 1uM) treatment. Collectively, these studies will increase our understanding of common and differential genomic actions of LXRα and LXRβ in cultured murine macrophages.

overall_design: Examination of genome-wide locations of  LXRα and LXRβ in 3xFLAG-LXRα and 3xFLAG-LXRβ expressing cells using FLAG antibody. Also examination of H3K27ac acetylation mark on the same cells in response to pharmacological treatment with agonist versus antagonist.

first: Antonio

last: Castrillo


title: Artificial acceleration of mammalian cell reprogramming by bacterial proteins

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

institute: Kyoto Univ.

summary: Mammalian cell reprogramming to pluripotency can be achieved by overexpression of a set of defined transcription factors (Yamanaka factors).  Various gene products regulate progression of this process.  Some small molecule compounds have been identified to influence it through interacting cellular proteins by library screenings.  Although such compounds are useful to reveal mechanisms underlying reprogramming as well as enhancing reprogramming efficiency, the screening usually requires huge amount of compounds to be tested to identify an effective one (ex., one effective molecule in several tens of thousands).  Here, we show a case report that there are gene products that can affect efficiency of mammalian cell reprogramming in a xeno-species.  Thirty genes specific for a bacterium Wolbachia pipientis, as a pilot trial, were forcedly expressed along with Yamanaka factors in mammalian cells.  As a result, we found that 8 Wolbachia genes affected the reprogramming efficiency either positively or negatively.  This is a surprisingly high probability compared with small molecule compounds reported.  Although this study is just a case report, it shows that screenings using genes from a xenospecies can be so effective.  In principle, use of genes from a xenospecies could be useful for controls of various cellular states such as induction or maintenance of a cell type of interest and development novel drugs.  Our findings suggest that systems using genes from xeno-species can be novel strategies for a wide variety of cellular events possibly with a high hit rate.

overall_design: Total RNAs of N31 cells ectopically expressing EGFP and W20 were used to analyze effects of forced expressions of W20 on changes of gene expressions.

first: Shinji

last: Masui


title: Early-life gene expression in neurons modulates lasting epigenetic states.


title: Genome wide mapping of chromatin binding sites of GATA2, GATA3, TFAP2A, TFAP2C transcription factors in trophoblast progenitors derived from human embryonic stem cells

status: Public on Oct 18 2017

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

institute: Helmholtz Center Munich

summary:
Human embryonic stem cells (hESC) can be differentiated into progenitors resembling trophoblast upon exposure to BMP4. Among the earliest transcription factors that are activated after the BMP4 stimulation are GATA2, GATA3, TFAP2A and TFAP2C.
Using trophoblast progenitors at day 3 of BMP4-induced differentiation, here we profile the chromatin binding landscape of these 4 early transcription factors to analyse their putative targets and cross-connectivity in regualtion of trophoblast commitment.

overall_design: hESC cell line H9 was differentiated towards trophoblast lineage using treatment with BMP4 for 3 days. The cells were used to perform ChIP using anti-GATA2, anti-GATA3, anti-TFAP2A and anti-TFAP2C antibodies followed by next generation sequencing.

first: Tobias

last: Straub

first: Christian

last: Krendl


title: Gene expression in sexually differentiating gonads of Xenopus laevis

city: Krakow

first: Rafal

middle: P.

last: Piprek

address: Gronostajowa 9

department: Department of Comparative Anatomy

country: Poland

institute: Jagiellonian University

summary: The aim of this study was to study the gene expression profile in developing female and male gonads of Xenopus laevis at four stages: at the Nieuwkoop-Faber stage 50 (genital ridge), at NF53 (sex-determining period), NF56 (the onset of sexual differentiation), NF62 (gonads sexually differentiated).

overall_design: The tadpoles were genotyped to identify their genetic sex and then dissected at given stages and the gonads were isolated. RNA was extracted from the gonads and gene expression was analyzed using microarray.

middle: P


title: Gene expression of Desulfovibrio vulgaris Hildenborough (DvH) strain ES10-5 evolved under salt stress for 5000 generations

city: Norman

first: Aifen

last: Zhou

state: OK

address: 101 David L. Boren Blvd

department: Microbiology & Plant Biology

institute: University of Oklahoma

summary:
Investigation of gene expression changes in a DvH genotype ES10-5, a strain isolated from population ES10 which has been evolved under salt stress for 5000 generations. The gene expression was compared to a gentype ES9-11 isolated from ES9 evolved under the same condition for 1200 generations and the ancestral strain.
The genotype ES10-5 was characterized in this study. ES9-11 was isolated and characterized in Zhou A et al., 2013. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME J, 7(9), 1790-1802

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Basal gene expression changes in salt-stressed evolved genotype 5000g-ES10-5 was examined and compared with salt-stress evolved genotype 1200g-ES9-11 and ancestor at mid-logarithmic phase in standard growth medium LS4D. The transcriptional responses to high salinity in evolved genotypes ES10-5 and ES9-11 and ancestor were characterized by comparing the gene expressions at mid-logarithmic phase under high salinity (LS4D+300 mM NaCl) to standard growth condition LS4D. Total RNA isolated from three replicates of salt-stress evolved 5000g-ES10-5,1200g-ES9-11, or ancestral DvH was labeled with Cy3 and co-hybridized with Cy5-labeled DvH gDNA to the individual array on a custom 12-plex NimbleGen oligonucleotide array.

first: Zhou

last: Aifen

last: Jizhong


title: Expression analysis of microRNA  by expression microarrays  of breast cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

institute: Japanese Foundation For Cancer Research

summary: We performed the expression microarray experiments for miRNA of breast cancer tissue.

overall_design: microRNA were extracted from primary tumor of 50 breast cancer patients, hybridized and scanned with Agilent miRNA Complete Hybri kit Arrays.

first: Yoshio

last: Miki


title: Gene expression profile of small intestinal mucosa in dog repeatedly infected with the cestode Echinococcus multilocularis

city: Sapporo

first: Hirokazu

last: Kouguchi

address: N19, W12, Kita-ku

institute: Hokkaido Institute of Public Health

summary: Previously, we found that the exclusion of adult worm occurred early stage of reinfection in dog repeatedly infected with E. multilocularis. In this study, we compared gene expression profile in small intestinal mucosa between control (normal dogs), first-infection group (dogs infected with E. multilocularis for the first time) and repeated-infection group (dogs repeatedly infected with this parasite 4 times). A total of 1916 genes for first-infection group and a total of 2950 genes for repeated-infection group were found to be up-regulated >2 fold when compared to control group. The data analysis revealed that genes related to tissue repair were largely upregulated in repeated-infection group compared to controls and first-infection group which indicated that hyperfunction of mucosal response occurred in repeatedly infected dogs. Expression of eight genes was quantified in the same RNA samples by real-time PCR. These microarray results may present new horizons for development of mucosal vaccine for the final hosts.

overall_design: Twelve dogs was divided into three groups (n=4) as followed: control (normal dogs), first-infection group (dogs infected with E. multilocularis for the first time) and repeated-infection group (dogs repeatedly infected with this parasite 4 times). For the first-infection group, 100,000 protoscoleces were orally administrated. For the repeated-infection group, 500,000 protoscoleces was administrated at 1st, 2nd and 3rd infection. At the final infection, 100,000 protoscoleces was administrated by identical method. Small intestine from dogs after 6 days infection (early stage of infection) was used for total RNA extraction. In each group, equal amount of purified total RNAs from four dogs were pooled and then used for microarray analysis.

first: Takao

last: Irie

first: Jun

last: Matsumoto

first: Hidefumi

last: Furuoka

first: Kenji

last: Ishiwata

first: Ryo

last: Nakao

first: Kinpei

last: Yagi


title: The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing [RNA-seq]

city: Ilsan

first: Jinyeong

last: Lim

address: Ilsan

country: South Korea

institute: National Cancer Center

summary: While transcription as regulated by histones and their post-translational modifications have been well described, the connection between histone variants and changes to transcription remains poorly characterized. Potentially important insight into this process is provided by the frequently occurring mutations of H3.3, leading to G34 substitutions in childhood glioblastoma and giant cell tumor of the bone (GCTB). In this study, we have established primary cell lines from GCTB patients and used them to uncover the influence on cellular growth behavior, gene expression, and chromatin compaction. The primary cells with G34W show increased colony formation, infiltration and proliferation, hallmarks in aggressive tumor development. Isogenic cell lines with G34W recapitulated the increased proliferation observed in primary cells. Transcriptomic analysis of primary cells and biopsies suggest that most genes are downregulated, which is also reflected in increased chromatin compaction. We identified components of the spliceosome complex specifically interacting with G34W in established isogenic cell lines with a GFP-tagged H3.3. RNA-sequencing analysis and hybridization-based validations further enforced splicing aberrations. Our data uncover a role in RNA processing and chromatin modulation that is blocked by G34W, potentially driving the tumorigenic process in GCTB.

overall_design: We performed RNAseq on 7 samples, of which 3 were of the GCTB-H3.3_WT primary cell lines (GCTB08, 09, 11) and 3 were of the GCTB-H3.3_G34W primary cell lines (GCTB07,10,12). Control cell lines were the mesenchymal stem cell line KM1234. Collectively,


title: Mechanical shear stress alters NOS3 interacted chromosome conformation [4C-seq]

city: La Jolla

first: Shu

last: Chien

address: 9500 Gilman Drive

department: Institute of Engineering In Medicine

institute: University of California, San Diego

summary: The optimal expression of endothelial nitric oxide synthase (eNOS), the hallmark of endothelial homeostasis, is vital to vascular function. Dynamically regulated by various stimuli, eNOS expression is modulated at transcriptional, post-transcriptional, and post-translational levels. However, epigenetic modulations of eNOS, particularly through long non-coding RNAs (lncRNAs) and chromatin remodeling, remain to be explored. Here we identified an enhancer-associated lncRNA that enhances eNOS expression” (LEENE). Combining RNA-sequencing and chromatin conformation capture methods, we demonstrated that LEENE is co-regulated with eNOS and that its enhancer resides in proximity to eNOS promoter in endothelial cells (ECs). Deletion of LEENE enhancer locus decreases the LEEN-eNOS proximal association and eNOS mRNA level. Inhibition of LEENE using locked nucleic acids (LNA) decreases eNOS expression and monocyte adhesion to ECs, whereas overexpression of LEENE increases eNOS expression and eNOS-derived NO in ECs. Mechanistically, LEENE facilitates the recruitment of RNA Pol II to the eNOS promoter to enhance eNOS nascent RNA transcription. Our findings unravel a new layer in eNOS regulation and provide novel insights into cardiovascular regulation involving endothelial function.

overall_design: 4C-seq for the Endothelial Nitric oxide synthase (NOS3) in endothelial cells under mechanical wall shear stress.

first: Yifei

last: Miao

first: Nassim

last: Ajami

first: Tse-Shun

last: Huang

first: Feng-Mao

last: Lin

first: Chih-Hong

last: Lou

first: Shuai

last: Li

first: Jian

last: Kang

first: Hannah

last: Munkacsi

first: Yun-Ting

last: Wang

first: Mano

last: Maurya

first: Shakti

last: Gupta

first: Shankar

last: Subramaniam

first: Zhen

last: Chen


title: Hsp90 RNAi in C. elegans

status: Public on Oct 17 2017

city: Garching bei München

first: Klaus

last: Richter

address: Lichtenbergstr. 4

department: Chemie

institute: Technische Universität münchen

summary:
Hsp90 is a molecular chaperone involved in the regulation and maturation of kinases and transcription factors. In Caenorhabditis elegans, it contributes to the development of fertility, maintenance of muscle structure, the regulation of heat-shock response and dauer state. To understand the consequences of Hsp90-depletion, we studied Hsp90 RNAi-treated nematodes by DNA microarrays and mass spectrometry. We find that upon development of phenotypes the levels of chaperones and Hsp90 cofactors are increased, while specific proteins related to the innate immune response are depleted. In microarrays, we further find many differentially expressed genes related to gonad and larval development. These genes form an expression cluster that is regulated independently from the immune response implying separate pathways of Hsp90-involvement. Using fluorescent reporter strains for the differentially expressed immune response genes skr-5, dod-24 and clec-60 we observe that their activity in intestinal tissues is influenced by Hsp90-depletion. Instead, effects on the development are evident in both gonad arms. After Hsp90-depletion, changes can be observed in early embryos and adults containing fluorescence-tagged versions of SEPA-1, CAV-1 or PUD-1, all of which are downregulated after Hsp90-depletion. Our observations identify molecular events for Hsp90-RNAi induced phenotypes during development and immune responses, which may help to separately investigate independent Hsp90-influenced processes that are relevant during the nematode’s life and development.
We used microarrays to detail the global programme of gene expression after RNAi-mediated Hsp90 knock-down.

overall_design: 6 samples, three controls and three samples with DAF-21 RNAi

first: Julia

last: Eckl

first: Siyuan

last: Sima

first: Katrin

last: Marcus

first: Claudia

last: Lindemann


title: Comparison of collection strategies for germline analysis

city: Boston

first: Brian

last: Crompton

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Peripheral blood was collected from 3 patients in two types of tubes, EDTA and Streck. After removing plasma, DNA was extracted from the remaining blood and subjected to array profiling

overall_design: Three patients, each patient with an EDTA sample and a Streck sample

first: Julie

last: Gastier-Foster


title: Circulating microRNA signature as novel biomarkers for osteoarthritis development

city: Athens

first: George

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

summary: Introduction: MicroRNAs (miRNAs) in circulation have emerged as promising biomarkers. In this study we aimed to identify a circulating miRNA signature for osteoarthritis (OA) patients. Methods: Serum samples were collected from 12 primary OA patients and 12 healthy individuals and were screened using the Agilent Human miRNA Microarray. Receiver Operating Characteristic (ROC) curves were constructed to evaluate the diagnostic performance of the deregulated miRNAs.  Expression levels of selected miRNAs were validated by quantitative Real-time PCR (qRT-PCR) in all serum samples and in articular cartilage samples from OA patients (n=12) and healthy individuals (n=7). Bioinformatics analysis was used to investigate the involved pathways and target genes of the above miRNAs. Results: We identified 279 differentially expressed miRNAs in the serum of OA patients compared to healthy controls. 205 (73.5%) were up-regulated and 74 (26.5%) down-regulated. ROC analysis revealed that 77 miRNAs had area under the curve (AUC)> 0.8 and p<0.05. Bioinformatics analysis in 7 out of the 77 selected miRNAs (hsa-miR-33b-3p, hsa-miR-4284, hsa-miR-671-3p, hsa-miR-663a, hsa-miR-140-3p, hsa-miR-150-5p and hsa-miR-1233-3p) revealed that their target genes were involved in multiple signaling pathways, among which FOXO, mTOR, pI3K/akt, lipid metabolism and TGF-β. A serum miRNA signature including three down-regulated miRNAs (hsa-miR-33b-3p, hsa-miR-671-3p and hsa-miR-140-3p) were also verified by qRT-PCR in OA patients. Furthermore, we found that hsa-miR-140-3p, hsa-miR-671-3p and potentially hsa-miR-33b-3p expression levels were consistently down-regulated in articular cartilage of OA patients compared to healthy individuals. Conclusions: A global miRNA serum signature was revealed in OA patients. We identified a three- miRNA signature in peripheral serum which could be potential osteoarthritis biomarkers.

overall_design: Serum samples were collected from 12 patients with primary OA (9 females, 3 males, ages: 69.83 ± 4.83 years) undergoing total knee replacement surgery at the Orthopaedics Department of the University Hospital of Larissa. Radiographs were obtained before surgery and graded using the Kellgren-Lawrence system according to the following criteria: grade 1 (doubtful narrowing of joint space and possible osteophytes), grade 2 (definite osteophytes and possible narrowing of joint space), grade 3 (moderate multiple osteophytes, definite narrowing of joint space and some sclerosis and possible deformity of bone ends) and grade 4 (large osteophytes, marked narrowing of joint space, severe sclerosis and definite deformity of bone ends). All OA patients had a Kellgren-Lawrence grade ≥3. The assessment of the radiographs by two independent expert observers was blinded. Patients with rheumatoid arthritis and other autoimmune disease as well as chondrodysplasias, infection-induced OA and post-traumatic OA were excluded from the study. As controls, serum samples were obtained from 12 healthy individuals (6 females, 6 males, ages: 64,25± 5,04 years) undergoing knee fracture repair surgery, with no history of joint disease, who did not show clinical manifestations compatible with OA when specifically explored by radiography. Consent was obtained from each participant. The study protocol conformed to the ethical guidelines of the 1975 Declaration of Helsinki as reflected in a priori approval by the local ethical committee of the University Hospital of Larissa. Articular cartilage samples (n=12) were collected from femoral condyles and tibial plateaus of the same OA patients, while normal articular cartilage was obtained from 7 out of the 12 healthy individuals.

first: Eleni

last: Ntoumou

first: Maria

last: Braoudaki

last: Tzetis

first: Aspasia

last: Tsezou