title: ChIP-seq from heart (ENCSR222IHX)

summary:
H3K27ac ChIP-seq on embryonic 11.5 day mouse heart

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


title: microRNA-seq from intestine (ENCSR212RKJ)

status: Public on Jun 22 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Non-coding RNA profiling by high throughput sequencing

summary:
miRNA-seq on embryonic 16.5 day mouse intestine

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


title: microRNA-seq from embryonic facial prominence (ENCSR199LBO)

summary:
miRNA-seq  on embryonic 14.5 day mouse cranioface

For data usage terms and conditions, please refer to http://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 midbrain (ENCSR203KIB)

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
H3K4me3 ChIP-seq on embryonic 14.5 day mouse midbrain

For data usage terms and conditions, please refer to http://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 midbrain (ENCSR205XBQ)

summary:
H3K36me3 ChIP-seq on embryonic 16.5 day mouse midbrain

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


title: WGBS from midbrain (ENCSR215QTA)

type: Methylation profiling by high throughput sequencing

summary:
Whole genome bisulfite-seq on embryonic 15.5 day mouse midbrain

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


title: ChIP-seq from intestine (ENCSR198ACZ)

summary:
H3K4me3 ChIP-seq on postnatal 0 day mouse intestine

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


title: ChIP-seq from limb (ENCSR233LBT)

summary:
H3K36me3 ChIP-seq on embryonic 12.5 day mouse limb

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


title: ChIP-seq from limb (ENCSR229LTY)

summary:
H3K27me3 ChIP-seq on embryonic 12.5 day mouse limb

For data usage terms and conditions, please refer to http://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 embryonic facial prominence (ENCSR193AEW)

summary:
H3K4me2 ChIP-seq on embryonic 15.5 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 embryonic facial prominence (ENCSR195NDO)

summary:
H3K4me2 ChIP-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 hindbrain (ENCSR190RKJ)

summary:
H3K9ac ChIP-seq on embryonic 13.5 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 hindbrain (ENCSR179ITA)

summary:
miRNA-seq on embryonic 13.5 day mouse hindbrain

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


title: ChIP-seq from liver (ENCSR191XHV)

summary:
H3K9me3 ChIP-seq on embryonic 13.5 day mouse liver

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


title: microRNA-seq from lung (ENCSR185XJA)

summary:
miRNA-seq  on embryonic 14.5 day mouse 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: WGBS from lung (ENCSR191UKH)

summary:
Whole genome bisulfite-seq on embryonic 14.5 day mouse 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 hindbrain (ENCSR185JBL)

summary:
H3K4me3 ChIP-seq on embryonic 14.5 day mouse hindbrain

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


title: ChIP-seq from hindbrain (ENCSR186PIV)

summary:
H3K9ac ChIP-seq on embryonic 14.5 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 neural tube (ENCSR207UMX)

summary:
H3K36me3 ChIP-seq on embryonic 15.5 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: WGBS from intestine (ENCSR217TMK)

summary:
Whole genome bisulfite-seq on embryonic 16.5 day mouse intestine

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


title: ChIP-seq from kidney (ENCSR178MLS)

summary:
Input control ChIP-seq on postnatal 0 day mouse kidney

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


title: ChIP-seq from limb (ENCSR176BXC)

summary:
H3K4me3 ChIP-seq on embryonic 14.5 day mouse limb

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


title: ChIP-seq from hindbrain (ENCSR175QZX)

summary:
H3K36me3 ChIP-seq on embryonic 11.5 day mouse hindbrain

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


title: ChIP-seq from liver (ENCSR175KBJ)

summary:
H3K27ac ChIP-seq on embryonic 13.5 day mouse liver

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


title: ChIP-seq from kidney (ENCSR196ENU)

summary:
H3K4me1 ChIP-seq on embryonic 14.5 day mouse kidney

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


title: ChIP-seq from forebrain (ENCSR172XOZ)

summary:
H3K4me3 ChIP-seq on embryonic 14.5 day mouse forebrain

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


title: WGBS from hindbrain (ENCSR168RTO)

summary:
Whole genome bisulfite-seq on postnatal 0 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 lung (ENCSR161PUT)

summary:
miRNA-seq  on postnatal 0 day mouse 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 midbrain (ENCSR167ZGV)

summary:
H3K4me3 ChIP-seq on embryonic 13.5 day mouse midbrain

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


title: ChIP-seq from hindbrain (ENCSR158ONM)

summary:
H3K4me3 ChIP-seq on embryonic 12.5 day mouse hindbrain

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


title: ChIP-seq from hindbrain (ENCSR161DAW)

summary:
H3K4me2 ChIP-seq on embryonic 16.5 day mouse hindbrain

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


title: ChIP-seq from intestine (ENCSR159RVN)

summary:
H3K4me1 ChIP-seq on postnatal 0 day mouse intestine

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


title: ChIP-seq from lung (ENCSR154DTK)

summary:
H3K4me2 ChIP-seq on embryonic 16.5 day mouse 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 midbrain (ENCSR157IVC)

summary:
H3K4me1 ChIP-seq on embryonic 12.5 day mouse midbrain

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


title: ChIP-seq from liver (ENCSR149GYK)

summary:
H3K9me3 ChIP-seq on embryonic 12.5 day mouse liver

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


title: ChIP-seq from lung (ENCSR148IGO)

summary:
H3K27me3 ChIP-seq on embryonic 14.5 day mouse 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: WGBS from heart (ENCSR149GUT)

summary:
Whole genome bisulfite-seq on embryonic 13.5 day mouse heart

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


title: ChIP-seq from embryonic facial prominence (ENCSR147PYG)

summary:
H3K9me3 ChIP-seq on embryonic 13.5 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 neural tube (ENCSR138YZB)

summary:
Input control ChIP-seq on embryonic 11.5 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: WGBS from neural tube (ENCSR144UTF)

summary:
Whole genome bisulfite-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: WGBS from forebrain (ENCSR141ZVB)

summary:
Whole genome bisulfite-seq on embryonic 13.5 day mouse forebrain

For data usage terms and conditions, please refer to http://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 forebrain (ENCSR141ZQF)

summary:
H3K4me1 ChIP-seq on embryonic 16.5 day mouse forebrain

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


title: ChIP-seq from liver (ENCSR135QMP)

summary:
H3K27me3 ChIP-seq on embryonic 16.5 day mouse liver

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


title: ChIP-seq from liver (ENCSR133EGP)

summary:
H3K4me1 ChIP-seq on embryonic 15.5 day mouse liver

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


title: ChIP-seq from forebrain (ENCSR161UUY)

summary:
H3K9ac ChIP-seq on embryonic 12.5 day mouse forebrain

For data usage terms and conditions, please refer to http://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 embryonic facial prominence (ENCSR137NUN)

summary:
H3K9me3 ChIP-seq on embryonic 15.5 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 intestine (ENCSR157LYR)

summary:
H3K4me1 ChIP-seq on embryonic 14.5 day mouse intestine

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


title: total RNA-seq from heart (ENCSR150CUE)

type: Expression profiling by high throughput sequencing

summary:
e12.5 heart

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


title: ChIP-seq from forebrain (ENCSR129DIK)

summary:
H3K4me3 ChIP-seq on embryonic 16.5 day mouse forebrain

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


title: ChIP-seq from hindbrain (ENCSR129LAP)

summary:
H3K27ac ChIP-seq on embryonic 11.5 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 midbrain (ENCSR129OJN)

summary:
H3K27me3 ChIP-seq on embryonic 13.5 day mouse midbrain

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


title: ChIP-seq from liver (ENCSR125VVG)

summary:
H3K9me3 ChIP-seq on embryonic 14.5 day mouse liver

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


title: ChIP-seq from forebrain (ENCSR128ZCB)

summary:
H3K9ac ChIP-seq on embryonic 14.5 day mouse forebrain

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


title: WGBS from kidney (ENCSR128HOP)

summary:
Whole genome bisulfite-seq on postnatal 0 day mouse kidney

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


title: ChIP-seq from heart (ENCSR122HLY)

summary:
H3K27me3 ChIP-seq on embryonic 12.5 day mouse heart

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


title: WGBS from liver (ENCSR129SBE)

summary:
Whole genome bisulfite-seq on embryonic 16.5 day mouse liver

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


title: ChIP-seq from heart (ENCSR119YTR)

summary:
H3K4me3 ChIP-seq on embryonic 16.5 day mouse heart

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


title: ChIP-seq from limb (ENCSR115FTP)

summary:
H3K4me2 ChIP-seq on embryonic 11.5 day mouse limb

For data usage terms and conditions, please refer to http://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 (ENCSR122CJZ)

summary:
H3K9me3 ChIP-seq on embryonic 16.5 day mouse heart

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


title: ChIP-seq from lung (ENCSR140UEX)

summary:
H3K27ac ChIP-seq on embryonic 16.5 day mouse 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 kidney (ENCSR121BWA)

summary:
H3K36me3 ChIP-seq on embryonic 16.5 day mouse kidney

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


title: ChIP-seq from lung (ENCSR108TWE)

summary:
H3K36me3 ChIP-seq on embryonic 14.5 day mouse 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 kidney (ENCSR140YPL)

summary:
H3K27ac ChIP-seq on postnatal 0 day mouse kidney

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


title: ChIP-seq from liver (ENCSR110MSZ)

summary:
H3K4me2 ChIP-seq on embryonic 12.5 day mouse liver

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


title: ChIP-seq from neural tube (ENCSR107SLP)

summary:
H3K36me3 ChIP-seq on embryonic 13.5 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: microRNA-seq from hindbrain (ENCSR110GMH)

summary:
miRNA-seq on embryonic 15.5 day mouse hindbrain

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


title: ChIP-seq from hindbrain (ENCSR110TIW)

summary:
H3K4me3 ChIP-seq on embryonic 16.5 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 embryonic facial prominence (ENCSR106QSU)

summary:
H3K4me3 ChIP-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 embryonic facial prominence (ENCSR105OGF)

summary:
H3K9ac ChIP-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 midbrain (ENCSR104PWP)

summary:
H3K27me3 ChIP-seq on embryonic 12.5 day mouse midbrain

For data usage terms and conditions, please refer to http://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 (ENCSR123MLY)

summary:
H3K27ac ChIP-seq on embryonic 12.5 day mouse heart

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


title: ChIP-seq from intestine (ENCSR100DLL)

summary:
H3K4me2 ChIP-seq on embryonic 16.5 day mouse intestine

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


title: ChIP-seq from neural tube (ENCSR099BYW)

summary:
H3K27me3 ChIP-seq on embryonic 14.5 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 limb (ENCSR098AHF)

summary:
H3K4me2 ChIP-seq on embryonic 15.5 day mouse limb

For data usage terms and conditions, please refer to http://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 (ENCSR098USP)

summary:
H3K9me3 ChIP-seq on embryonic 13.5 day mouse heart

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


title: ChIP-seq from liver (ENCSR095FDG)

summary:
H3K9me3 ChIP-seq on embryonic 16.5 day mouse liver

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


title: ChIP-seq from forebrain (ENCSR094TTT)

summary:
H3K27ac ChIP-seq on postnatal 0 day mouse forebrain

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


title: WGBS from limb (ENCSR099RYD)

summary:
Whole genome bisulfite-seq on embryonic 14.5 day mouse limb

For data usage terms and conditions, please refer to http://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 forebrain (ENCSR093DWU)

summary:
H3K9me3 ChIP-seq on postnatal 0 day mouse forebrain

For data usage terms and conditions, please refer to http://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 (ENCSR091ZTZ)

summary:
miRNA-seq  on embryonic 11.5 day mouse cranioface

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


title: ChIP-seq from kidney (ENCSR091DHJ)

summary:
Input control ChIP-seq on embryonic 14.5 day mouse kidney

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


title: ChIP-seq from embryonic facial prominence (ENCSR091WNX)

summary:
H3K4me1 ChIP-seq on embryonic 15.5 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 neural tube (ENCSR094QZC)

summary:
H3K36me3 ChIP-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: WGBS from midbrain (ENCSR091VFX)

summary:
Whole genome bisulfite-seq on embryonic 11.5 day mouse midbrain

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


title: WGBS from intestine (ENCSR089FFK)

summary:
Whole genome bisulfite-seq on embryonic 14.5 day mouse intestine

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


title: ChIP-seq from neural tube (ENCSR087PLZ)

summary:
H3K9ac ChIP-seq on embryonic 13.5 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 midbrain (ENCSR088UKA)

summary:
H3K27ac ChIP-seq on embryonic 11.5 day mouse midbrain

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


title: ChIP-seq from liver (ENCSR082JEN)

summary:
Input control ChIP-seq on embryonic 16.5 day mouse liver

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


title: ChIP-seq from midbrain (ENCSR081UQY)

summary:
Input control ChIP-seq on embryonic 11.5 day mouse midbrain

For data usage terms and conditions, please refer to http://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 (ENCSR077QRY)

summary:
Control ChIP-seq on embryonic 13.5 day mouse heart

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


title: ChIP-seq from heart (ENCSR080GQM)

summary:
H3K4me1 ChIP-seq on embryonic 14.5 day mouse heart

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


title: ChIP-seq from stomach (ENCSR076MXH)

summary:
H3K4me2 ChIP-seq on embryonic 14.5 day mouse 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: microRNA-seq from limb (ENCSR070GAZ)

summary:
miRNA-seq on embryonic 15.5 day mouse limb

For data usage terms and conditions, please refer to http://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 embryonic facial prominence (ENCSR076FAM)

summary:
H3K9ac ChIP-seq on embryonic 11.5 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 heart (ENCSR069XHI)

summary:
H3K9ac ChIP-seq on embryonic 13.5 day mouse heart

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


title: ChIP-seq from limb (ENCSR070OXL)

summary:
Control ChIP-seq on embryonic 15.5 day mouse limb

For data usage terms and conditions, please refer to http://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 forebrain (ENCSR069TDC)

summary:
H3K36me3 ChIP-seq on postnatal 0 day mouse forebrain

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


title: ChIP-seq from limb (ENCSR085EYQ)

summary:
H3K27me3 ChIP-seq on embryonic 11.5 day mouse limb

For data usage terms and conditions, please refer to http://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 embryonic facial prominence (ENCSR068AQC)

summary:
Input control ChIP-seq on embryonic 11.5 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 forebrain (ENCSR087JEN)

summary:
H3K36me3 ChIP-seq on embryonic 13.5 day mouse forebrain

For data usage terms and conditions, please refer to http://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 forebrain (ENCSR070MOK)

summary:
H3K27me3 ChIP-seq on postnatal 0 day mouse forebrain

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


title: ChIP-seq from hindbrain (ENCSR066SPF)

summary:
Input control ChIP-seq on postnatal 0 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 neural tube (ENCSR093BYV)

summary:
H3K4me3 ChIP-seq on embryonic 14.5 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 midbrain (ENCSR067FKP)

summary:
H3K9ac ChIP-seq on embryonic 14.5 day mouse midbrain

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


title: ChIP-seq from hindbrain (ENCSR066XXZ)

summary:
H3K36me3 ChIP-seq on embryonic 14.5 day mouse hindbrain

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


title: ChIP-seq from hindbrain (ENCSR066XFL)

summary:
H3K27ac ChIP-seq on embryonic 15.5 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 midbrain (ENCSR065LAB)

summary:
H3K9me3 ChIP-seq on postnatal 0 day mouse midbrain

For data usage terms and conditions, please refer to http://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 forebrain (ENCSR067ZDE)

summary:
H3K4me2 ChIP-seq on embryonic 11.5 day mouse forebrain

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


title: ChIP-seq from liver (ENCSR075SNV)

summary:
H3K27ac ChIP-seq on embryonic 14.5 day mouse liver

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


title: ChIP-seq from neural tube (ENCSR065CJC)

summary:
H3K9ac ChIP-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 stomach (ENCSR064DGY)

summary:
H3K27me3 ChIP-seq on embryonic 14.5 day mouse 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 forebrain (ENCSR066LZB)

summary:
H3K36me3 ChIP-seq on embryonic 11.5 day mouse forebrain

For data usage terms and conditions, please refer to http://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 (ENCSR071SQK)

summary:
H3K9me3 ChIP-seq on embryonic 15.5 day mouse heart

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


title: ChIP-seq from embryonic facial prominence (ENCSR059LYY)

summary:
H3K4me3 ChIP-seq on embryonic 14.5 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 embryonic facial prominence (ENCSR061DPP)

summary:
H3K27me3 ChIP-seq on embryonic 15.5 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 kidney (ENCSR057SHA)

summary:
H3K27ac ChIP-seq on embryonic 14.5 day mouse kidney

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


title: ChIP-seq from midbrain (ENCSR066WUD)

summary:
H3K36me3 ChIP-seq on embryonic 13.5 day mouse midbrain

For data usage terms and conditions, please refer to http://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 midbrain (ENCSR068XYW)

summary:
H3K9ac ChIP-seq on embryonic 16.5 day mouse midbrain

For data usage terms and conditions, please refer to http://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 (ENCSR052CDF)

summary:
H3K4me3 ChIP-seq on embryonic 14.5 day mouse heart

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


title: ChIP-seq from embryonic facial prominence (ENCSR057BKH)

summary:
H3K4me3 ChIP-seq on embryonic 13.5 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: microRNA-seq from thymus (ENCSR047EJT)

summary:
miRNA-seq  on postnatal 0 day mouse thymus

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


title: ChIP-seq from hindbrain (ENCSR046SWI)

summary:
H3K27me3 ChIP-seq on embryonic 16.5 day mouse hindbrain.NOTE- Files associated with this experiment are undergoing additional review and analysis

For data usage terms and conditions, please refer to http://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 (ENCSR048IZJ)

summary:
H3K9ac ChIP-seq on postnatal 0 day mouse 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: WGBS from heart (ENCSR050EXR)

summary:
Whole genome bisulfite-seq on embryonic 16.5 day mouse heart

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


title: ChIP-seq from liver (ENCSR045NOD)

summary:
H3K4me1 ChIP-seq on embryonic 13.5 day mouse liver

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


title: ChIP-seq from intestine (ENCSR051CUH)

summary:
H3K4me1 ChIP-seq on embryonic 15.5 day mouse intestine

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


title: ChIP-seq from midbrain (ENCSR037HLB)

summary:
H3K4me1 ChIP-seq on embryonic 14.5 day mouse midbrain

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


title: ChIP-seq from hindbrain (ENCSR054JHZ)

summary:
H3K27ac ChIP-seq on embryonic 14.5 day mouse hindbrain

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


title: WGBS from liver (ENCSR033PGF)

summary:
Whole genome bisulfite-seq on embryonic 11.5 day mouse liver

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


title: ChIP-seq from kidney (ENCSR036YKL)

summary:
H3K4me2 ChIP-seq on embryonic 15.5 day mouse kidney

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


title: ChIP-seq from liver (ENCSR037HCS)

summary:
H3K36me3 ChIP-seq on embryonic 13.5 day mouse liver

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


title: WGBS from hindbrain (ENCSR037RNN)

summary:
Whole genome bisulfite-seq on embryonic 16.5 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 lung (ENCSR025AOC)

summary:
H3K27me3 ChIP-seq on postnatal 0 day mouse 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 limb (ENCSR028ZHS)

summary:
H3K9me3 ChIP-seq on embryonic 15.5 day mouse limb

For data usage terms and conditions, please refer to http://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 embryonic facial prominence (ENCSR027DMG)

summary:
H3K36me3 ChIP-seq on embryonic 11.5 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 stomach (ENCSR023VJO)

summary:
H3K4me3 ChIP-seq on embryonic 14.5 day mouse 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: WGBS from lung (ENCSR027ICI)

summary:
Whole genome bisulfite-seq on embryonic 15.5 day mouse 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 forebrain (ENCSR024JAN)

summary:
Input control ChIP-seq on embryonic 11.5 day mouse forebrain

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


title: ChIP-seq from liver (ENCSR058DOA)

summary:
H3K27ac ChIP-seq on embryonic 11.5 day mouse liver

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


title: ChIP-seq from stomach (ENCSR050VUZ)

summary:
Input control ChIP-seq on postnatal 0 day mouse 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 forebrain (ENCSR044SUW)

summary:
H3K4me2 ChIP-seq on embryonic 13.5 day mouse forebrain

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


title: ChIP-seq from limb (ENCSR022DED)

summary:
H3K9me3 ChIP-seq on embryonic 13.5 day mouse limb

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


title: ChIP-seq from limb (ENCSR021ALF)

summary:
H3K27ac ChIP-seq on embryonic 14.5 day mouse limb

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


title: ChIP-seq from hindbrain (ENCSR014MXQ)

summary:
H3K4me1 ChIP-seq on embryonic 12.5 day mouse hindbrain

For data usage terms and conditions, please refer to http://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 (ENCSR012BVY)

summary:
Input control ChIP-seq on embryonic 16.5 day mouse 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 forebrain (ENCSR014TEJ)

summary:
H3K9ac ChIP-seq on embryonic 16.5 day mouse forebrain

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


title: WGBS from forebrain (ENCSR020GGM)

summary:
Whole genome bisulfite-seq on postnatal 0 day mouse forebrain

For data usage terms and conditions, please refer to http://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 embryonic facial prominence (ENCSR008WOQ)

summary:
H3K27me3 ChIP-seq on embryonic 13.5 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 intestine (ENCSR014YAY)

summary:
H3K27me3 ChIP-seq on embryonic 14.5 day mouse intestine

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


title: WGBS from forebrain (ENCSR019HJV)

summary:
Whole genome bisulfite-seq on embryonic 15.5 day mouse forebrain

For data usage terms and conditions, please refer to http://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 kidney (ENCSR008EQG)

summary:
miRNA-seq on embryonic 15.5 day mouse kidney

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


title: ChIP-seq from forebrain (ENCSR022KDE)

summary:
H3K4me3 ChIP-seq on embryonic 15.5 day mouse forebrain

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


title: WGBS from stomach (ENCSR013VIR)

summary:
Whole genome bisulfite-seq on embryonic 15.5 day mouse 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 heart (ENCSR007XTC)

summary:
H3K9me3 ChIP-seq on embryonic 14.5 day mouse heart

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


title: WGBS from forebrain (ENCSR007JSP)

summary:
Whole genome bisulfite-seq on embryonic 12.5 day mouse forebrain

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


title: The Lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway [PAR-CLIP]

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

summary: The Lupus autoantigen (La) is a single-stranded RNA-binding protein that stabilizes RNA polymerase III (pol III) transcripts and supports RNA folding. In addition, La has been implicated in different steps of the mammalian small RNA pathway. Here, we have analyzed effects of La depletion on the Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago protein complexes and our data suggests that La prevents the production and loading of such tRNA fragments. However, one specific isoleucine tRNA escapes this regulation and produces both a functional tRNA as well as a microRNA (miRNA). We demonstrate that fully complementary 5' leader and 3' trailer of the pre-tRNA-Ile form a double-stranded RNA molecule that has low affinity to La. Instead, Exportin 5 (Xpo5) recognizes it as miRNA precursor and transports it into the cytoplasm for Dicer processing and Ago loading. Thus, La functions as gatekeeper to ensure correct tRNA generation and to protect the miRNA pathway from potentially functional tRNA fragments.

overall_design: Identification by PAR-CLIP analysis of tRNAs differentially associated with FLAG/HA-Dicer under La knockdown or control knockdown.

first: Daniele

last: Hasler

first: Norbert

last: Eichner

first: Yasuhiro

last: Murakawa

first: Filippos

last: Klironomos

first: Nikolaus

last: Rajewsky

first: Markus

last: Landthaler

first: Gunter

last: Meister


title: The Lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway [miRNA-seq]

overall_design: Identification and characterization of miRNAs and small RNAs derived from pol III transcripts interacting with Ago1-4 isolated by Ago-APP or input samples under La knockdown or control knockdown.


title: RNA sequencing analysis of DAF-16 target gene expression when math-33 function is genetically inactivated

city: Freiburg

first: Thomas

last: Heimbucher

state: Baden Württemberg

address: Schaenzlestrasse 1

department: Biologie III

institute: Thomas Heimbucher

summary: In this study we have investigated the effect of loss of math-33 activity on DAF-16-mediated target gene regulation in C. elegans under conditions of reduced Insulin/IGF-1 signaling (IIS). Using whole nematode RNA sequencing experiments we found that the daf-2(e1370)-mediated induction and repression of DAF-16 target genes was decreased in daf-2(e1370); math-33(tm3561) mutant animals. Our data suggest that the downregulation of endogenous DAF-16 isoforms in the absence of a functional MATH-33 severely affects the global expression of DAF-16 targets when IIS activity is reduced. Therefore, MATH-33 is essential for DAF-16-mediated target gene activation and repression in the context of IIS.

overall_design: DAF-16 mediated target gene regulation was analyzed in daf-2(e1370) nematodes and compared to daf-2(e1370); math-33(tm3561) mutant animals. daf-16(mu86); daf-2(e1370); N2 (wild type) and math-33(tm3561) single mutant animals were used as controls.

first: Bogdan

last: Tanasa

first: Andrew

last: Dillin


title: Identification of mRNAs Regulated in Response to Transcriptional Activation of the Arabidopsis ABA INSENSITIVE GROWTH 1 (ABIG1) Transcription Factor cDNA

first: Samuel

last: Hokin

state: California

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science

summary: Liquid grown, seven day old wild type Arabidopsis seedlings and seedlings carrying a cDNA encoding the ABA INSENSITIVE GROWTH 1 (ABIG1) gene under the control of an estrogen inducible promoter were treated with estrogen for 0, 60 and 120 minutes at which point seedlings were flash frozen and mRNA was extracted.

overall_design: Wild-type and ESTAIG1 Col samples were treated with estrogen and flash frozen 0, 60 and 120 minutes later. Each sample type has three biological reps, except ESTAIG1.120, which has two. There are therefore 17 total samples. mRNA samples were sequenced by Otogenetics and then analyzed using the Tuxedo suite of applications. (Note: "AIG1" has since been renamed "ABIG1" in publication.)

first: M

middle: K

last: Barton

first: Tie

last: Liu

first: Franklin

last: Talavera-Rauh


title: NOTCH1 mediates a reciprocal switch between two distinct secretomes during senescence [N1ICD]

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

summary: ER:RAS-G12V expressing IMR90 cells were transduced with N1ICD-containing or control vectors before treatment with either 100nM 4-OHT or vehicle for 6 days leading to Notch-induced senescence (NIS), RAS-induced senescence (RIS) or combined Notch and Ras-induced senescence (RNIS).

overall_design: IMR90 cells expressing a 4-hydroxytamoxifen (4-OHT) inducible estrogen receptor (ER)-coupled RAS-G12V (ER:RAS-G12V) were transduced with N1ICD-FLAG-containing (residues 1758-2556 of human NOTCH1, as per Capobianco et al, Mol Cell Biol, 1997) or control vector before treatment with either 100nM 4-OHT or vehicle for 6 days , leading to RAS-induced senescence (RIS), NOTCH-induced senescence (NIS) or combined Ras & NOTCH-induced senescence (RNIS).  The total RNA was then analysed for transcriptional profiling using mRNA-sequencing. There were 6 (six) biological replicates for each experimental condition. Untreated, vector-transduced ER:RAS IMR90 cells were the control condition

first: Matthew

last: Hoare

first: Masashi

last: Narita

first: Suraj

last: Menon


title: Global re-wiring of p53 transcription regulation by the hepatitis B virus X (HBx) protein [ChIP-Seq]

city: Singapore

last: Thurnherr

address: 11 Hospital Drive

country: Singapore

institute: NCCS

summary: As HBx has been reported to interact with p53 and alter the recruitment of p53 to its binding sites, we obtained a comprehensive genome-wide profile of deregulated p53 transcription complex-DNA binding by the HBx protein using massively parallel deep sequencing coupled to p53 chromatin immunoprecipitation (ChIP-Seq) on HBx-expressing and control HepG2 liver cell culture model system.

overall_design: HepG2 cells were transduced with recombinant HBx and control adenoviruses 24 hours post seeding. HepG2 cells were treated with UVC (254 nm) irradiation 48 hours postransduction and harvested 24 hours after UV irradiation. 30 µg of control and HBx-expressing UV-treated HepG2 cell lysates were immunoprecipitated using 4 µg of p53 FL-393 antibody (Santa Cruz Biotechnology). The subsequent yield and size of the ChIP library generated was quantified, followed by sequencing using HiSeq (Illumina, CA, USA) to read counts of 7.7 M total reads.

first: Cheryl

last: Chan

first: Caroline

last: Lee


title: Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals

city: Bethesda

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

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

overall_design: Refer to individual Series


title: The Lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway

first: Gerhard

last: Lehmann


title: Global re-wiring of p53 transcription regulation by the hepatitis B virus X (HBx) protein


title: JQ1 +/- Vemurafenib in BRAF mutant melanoma (A375)

status: Public on Jun 21 2016

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: The combination of JQ1 and Vemurafenib acted synergistically in BRAF-mutant cell lines, resulting in marked apoptosis in vitro, with up-regulation of pro-apoptotic proteins. In vivo, combination treatment suppressed tumor growth and significantly improved survival compared to either drug alone. RNA sequencing of tumor tissues revealed almost four thousand genes that were uniquely modulated by the combination, with several anti-apoptotic genes significantly down-regulated.

overall_design: 16 samples analyzed from 8 mice (each mouse was bearing two tumors, one on each flank) in 4 treatment groups (control, vemurafenib alone, JQ1 alone, JQ1+vemurafenib)

first: Luca

last: Paoluzzi

first: Eva

last: Hernando


title: Genome-wide analysis of rats' mRNA profile after knocking down PIWIL1 in embryonic cultured neurons.

city: Shanghai

first: Pingping

last: Zhao

address: No. 320, YueYang Road, Shanghai, China

country: China

institute: Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: We have demonstrated that PIWIL1 can regulate neuronal radial migration during corticogenesis. In order to explore the mechanism, we carried out high-throughtput sequencing (mRNA profile) to define downstream target of PIWIL during the process of neuronal migration. And we found the expression level of several microtubule-associated proteins decreased after downregulation of PIWIL1. Therefore, PIWIL1 plays an important role in neuronal migration by regulating the expression microtubule-associated proteins (such as Map1B, Map2, Tau) .

overall_design: Examine mRNA profile in two groups of primary cultured neurons with electroporation of control or RNAi plasmid.

first: Ping-ping

first: Mao-jin

last: Yao

first: Si-yuan

last: Chang

first: Xiao-bing

last: Yuan


title: The effects of cytosine methylation on general transcription factors

city: Beijing

first: Xiao-Dong

last: Su

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Science

institute: Peking University

summary: DNA methylation (mC) on CpG sites is the most common epigenetic modification.  Recently methylation on non-CpG context was found to widely occur on genomic DNA.  However, how non-CpG methylation influences DNA/protein interaction and regulates transcription is unknown.  Using single-molecule assays, we studied the interactions of transcription factors (TFs) GR, ER and BMAL1-CLOCK with methylated or unmethylated cognate DNA binding sequences.  The results demonstrated that these TFs interact with methylated DNA discriminatively.  We then performed BisChIP-seq with GR and BMAL1-CLOCK in HEK-293T cells and showed that they can recognize and bind to the methylated sites within chromatin.  The effects of non-CpG methylation on transcriptional regulation were validated by in vitro transcription assays with correlated RNA level, and further studied mechanistically by crystallographic analyses and molecular dynamics simulations.  We conclude that the non-CpG methylation of DNA provides another general mechanism for regulating gene expression through affecting TFs binding affinity.

overall_design: In order to verify that TFs can bind to and distinguish the methylated and unmethylated DNA in vivo, we performed bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) for two TFs - GR and BMAL1-CLOCK in HEK-293T cells.  The experiment revealed that both GR and BMAL1-CLOCK could distinguish between the methylated and the unmethylated sites in cells.

first: Jianshi

last: Jin

first: Tengfei

last: Lian

first: Chan

last: Gu

first: Kai

last: Yu

first: Yi

middle: Q

last: Gao


title: Novel features of telomeres biology revealed by the absence of telomeric DNA methylation

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

summary: Cytosine methylation regulates the length and stability of telomeres, which can affect a wide variety of biological features including cell differentiation, development or illness. Whereas it is well established that subtelomeric regions are methylated, the presence of methylated cytosines at telomeres has remained controversial. Here, we have analyzed multiple bisulfite sequencing studies to address the methylation status of Arabidopsis thaliana telomeres. We found that the levels of telomeric DNA methylation estimated varied among studies. Interestingly, we estimated higher levels of telomeric DNA methylation in studies that produced C-rich telomeric strands with lower efficiency. However, these high methylation estimates arose due to experimental limitations of the bisulfite technique. We found a similar phenomenom for mitochondrial DNA: the levels of mitochondrial DNA methylation detected were higher in experiments with lower mitochondrial read production efficiencies. Based on experiments with high telomeric C-rich strand production efficiencies, we concluded that Arabidopsis telomeres are not methylated, which was confirmed by methylation dependent restriction enzymes analyses. Thus, our studies indicate that telomeres are refractory to de novo DNA methylation by the RNA directed DNA methylation machinery. This result, together with previously reported data, reveals that subtelomeric DNA methylation controls the homeostasis of telomere length.

overall_design: Four different samples, two replicates each

first: Alejandro

last: Vega-Vaquero

first: Giancarlo

last: Bonora

first: Marco

last: Morselli

first: María

middle: I

last: Vaquero-Sedas

first: Liudmilla

last: Rubbi

first: Matteo

last: Pellegrini

first: Miguel

middle: A

last: Vega-Palas


title: Both H4K20 mono-methylation and H3K56 acetylation mark transcription-dependent histone turnover in fission yeast

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

summary: Nucleosome dynamics facilitated by histone turnover is required for transcription as well as DNA replication and repair. Histone turnover is often associated with various histone modifications such as H3K56 acetylation (H3K56Ac), H3K36 methylation (H3K36me), and H4K20 methylation (H4K20me). In order to correlate histone modifications and transcription-dependent histone turnover, we performed genome wide analyses for euchromatic regions in G2/M-arrested fission yeast. The results show that transcription-dependent histone turnover at 5’ promoter and 3’ termination regions is directly correlated with the occurrence of H3K56Ac and H4K20 mono-methylation (H4K20me1) in actively transcribed genes. Furthermore, the increase of H3K56Ac and H4K20me1 and antisense RNA production was observed in the absence of the histone H3K36 methyltransferase Set2 and histone deacetylase complex (HDAC) that are involved in the suppression of histone turnover within the coding regions. These results together indicate that H4K20me1 as well as H3K56Ac are bona fide marks for transcription-dependent histone turnover in fission yeast.

overall_design: For histone turnover experiment : yeast cells ectopically expressing C-terminal Flag-tagged H3.2 (hht+2) under the control of sucrose-inducible promoter (inv1+) were synchronized, and H3-Flag was induced under G2/M arrest conditions to minimize the effect of replication-dependent histone deposition. Chromatin immunoprecipitation (ChIP) against anti-FLAG antibody was performed in wild type cells. For ChIP experiment : ChIP against H3, H3K56Ac, H4K20me1, H4K20me3 was performed for a wild type strain and strains lacking Set2 and Alp13. Each experiment was performed twice in biological replicates. All ChIP experiments were performed at G2/M arrested condition.  For RNA experiment : Total RNA was prepared from cells arrested in G2/M followed by mRNA isolation with the magnetic method.

first: H

last: Yang

first: C

middle: S

last: Kwon

first: Y

first: D

last: Lee


first: Matthew

last: Brooks

summary: Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution.

overall_design: Fixed, GFP positive cells from Nrlp-GFP mouse retinas at post-natal ages P2, P10, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Cells resuspended in shearing buffer were processed for sonication using Covaris S220 focused-ultrasonicator to obtain chromatin fragments with the average size of 150-200 bp. DNA chromatin solution was then incubated with anti-H3K4me3, anti-H3K27me3 or normal IgG. The immunoprecipitated DNA was then purified using Agencourt AMPure XP beads. Sequencing libraries were prepared using TruSeq DNA sample preparation kit (Illumina) with multiple adjustments, which include usage of 1/100 dilution of TruSeq adapters and gel-free DNA size selection using AMPure XP beads. Libraries were PCR-amplified for 18 cycles and each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.

first: Jung-Woong

last: Kim

first: Hyun-Jin

first: A

middle: P

last: Oel

first: Li

last: Jia

first: David

middle: C

last: Plachetzki

first: Wei

last: Li

first: William

middle: T

last: Allison

first: Anand

last: Swaroop


title: microRNAs with an AAGUGC seed motif constitute an integral part of a signaling network driving NSCLC cell proliferation

city: Stockholm

first: Janne

last: Lehtiö

state: Stockholm

address: SciLifeLab

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: miR-372-3p target identification mRNA level

overall_design: Differential expression analysis 30h post transfection with miR-372-3p mimics

first: Yan

last: Zhou

first: Oliver

last: Frings

first: Rui

middle: M

last: Branca

first: Jorrit

last: Boekel

first: Carlos

last: le Sage

first: Erik

last: Fredlund

first: Reuven

last: Agami

first: Lukas

last: Orre


first: Matthew

last: Brooks

overall_design: GFP positive cells from Nrlp-GFP mouse retinas at post-natal ages P2, P10, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). DNA was extracted by Purelink gDNA isolation kit (Life technologies). Reduced Representation Bisulfite Sequencing library construction using 50 ng of DNA as input. Libraries were constructed using a modification of the Illumina TruSeq DNA. Bisulfite modification was performed using Epitech kit (Qiagen). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases. Fastq files were generated from reads passing chastity filter.

first: Jung-Woong

last: Yang

first: Adam


title: Primary cancer cell culture: mammary-optimized versus conditional-reprogramming [RNA-seq]

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

summary: Experiments used RNAseq data to compare transcriptomes of primary cells from different genetic backgrounds cultured under EpiCult and CRC conditions to each other and to allografts grown from these primary cells in nude mice

overall_design: Paired-end mRNA-seq with WT, Esr1 over-expressing (CERM, tetracycline-operator(tet-op)-Esr1MMTV-rtTA), CYP19A1 over-expressing (AROM, tet-op-CYP19A1MMTV-rtTA) and Brca1 KO  (BRCA, Brca1fl11/fl11/MMTV-Cre/p53+/- ) mice

first: Ahmad

last: Alamri

first: Svenja

last: Groeneveld

first: Weisheng

last: Wang

first: Xiaogang

last: Zhong

first: Bhaskar

last: Kallakury

first: Lothar

last: Hennighausen

first: Xuefeng

last: Liu

first: Priscilla

last: Furth


title: Regulation of Th17 cell pathogenic function by miR-183/96/182

city: La Jolla

first: Changchun

last: Xiao

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

summary: Th17 cells are key players in autoimmune diseases. However, the roles of non-coding RNAs in Th17 cells are largely unknown. Here, we show that deletion of the Dicer gene specifically in Th17 cells protects from experimental autoimmune encephalomyelitis (EAE). Th17 cells highly express the miR-183/96/182 cluster (miR-183C), in response to IL-6/STAT3 signaling. Moreover, miR-183C regulates pathogenic cytokine expression during Th17 development. Furthermore, transcription factor Foxo1 is one of functional targets of miR-183C in Th17 cells: Foxo1 negatively regulates the pathogenicity of Th17 cells and miR-183C represses Foxo1 expression. Collectively, our results demonstrate one of crucial roles for miR-183C cluster in regulation of Th17 cell function in autoimmune diseases.

overall_design: Control vector- or miR-96-overexpressing T cells and miR-183C+/+ or miR-183C-/- T cells were cultured under the Th17(23) condition and were harvested on day 4-5. Cell sorting was performed using a FACSAria cell sorter to obtain GFP-positive cells. Total RNA was extracted using the TRIzol reagent, enriched for polyA-containing RNAs and submitted to RNA-Seq.

first: Ichiyama

last: Kenji

first: Gonzalez-Martin

last: Alicia

first: Dong

last: Chen

first: Xiao

last: Changchun


title: Cbx8 acts non-canonically with Wdr5 to promote mammary tumorigenesis [ChIP-Seq]

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: Here we found that Cbx8 knockdown in MMTV-Myc and MDA-MB-231-Luc cells reduces H3K4me3 mark on Notch-network genes

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mononucleosomes from MMTV-Myc and MDA-MB-231-Luc cells were isolated and ChIP with H3K4me3, H3K27me3 and H3K27ac antibodies. DNA from Input and ChIP samples was purified and sequenced on Illumina Hiseq.

first: Chi-Yeh

last: Chung

first: Zhen

last: Sun

first: Gavriel

last: Mullokandov

first: Almudena

last: Bosch

first: Zulekha

last: Qadeer

first: Esma

last: Cihan

first: Zachary

last: Rapp

first: Ramon

last: Parsons

first: Julio

last: Aguirre-Ghiso

first: Eduardo

middle: F

last: Farias

first: Brian

middle: D

last: Brown

first: Alexandre

last: Gaspar-Maia


title: Cbx8 acts non-canonically with Wdr5 to promote mammary tumorigenesis


title: Cbx8 acts non-canonically with Wdr5 to promote mammary tumorigenesis [RNA-Seq]

summary: Here we show that in MMTV-Myc cells (1) MS culture enriches for aggressive breast cancer cells compared to the bulk cells, (2) Cbx8 knockdown reduces Notch-network gene expression.

overall_design: Gene expression of (1) bulk vs MS MMTV-Myc cells, (2) control vs Cbx8 knockdown MMTV-Myc cells


first: Matthew

last: Brooks

overall_design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.

first: Jung-Woong

last: Kim

first: Hyun-Jin

last: Yang

first: Adam

last: Oel

first: Li

last: Jia

first: David

last: Plachetzki

first: Wei

last: Li

first: William

last: Allison

first: Anand

last: Swaroop


status: Public on Jun 20 2016

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Central to the molecular pathogenesis of MLL leukaemia is the abnormal co-optation of members of transcription complexes including disrupter of telomeric silencing 1-like (DOT1L) and bromodomain containing protein 4 (BRD4). Consequently, targeted therapies against DOT1L and BRD4 are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukaemogenic transcription programs remain unclear. Using quantitative proteomics, chemoproteomics and biochemical fractionation we find that native BRD4 and DOT1L exist in largely separate protein complexes. Genetic disruption or small molecule inhibition of BRD4 and DOT1L shows marked synergistic activity against MLL-FP leukaemia cell lines, primary human leukaemia cells and murine leukaemia models. Mechanistically, we find a previously unrecognised functional collaboration between DOT1L and BRD4 that is especially important at highly transcribed genes in close proximity to superenhancers. DOT1L via H3K79me2 facilitates the deposition of histone H4 acetylation, which in turn regulates the binding of BRD4 to chromatin. These data provide novel insights into the regulation of transcription and specify a molecular framework for therapeutic intervention in this poor prognostic disease.

overall_design: RNASeq of 4SU labelled nascent RNA in MV4;11 cell treated with DMSO, I-BET, SGC0946 and combination of I-BET and SGC0946 in duplicate

first: Omer

last: Gilan

first: Enid

last: Lam


overall_design: RNASeq of MLL-AF9 cells transduced with scramle shRNA or BRD4 shRNA in combination with DMSO or SGC0946 in triplicate


title: The insect prothoracic gland as a model for steroid hormone biosynthesis and regulation

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 11455 saskatchewan driver

department: Biological Sciences

country: Canada

institute: University of Alberta

sample_organism:
Bombyx mori
Drosophila melanogaster

platform_organism:
Bombyx mori
Drosophila melanogaster


title: RNA-seq of poly(A)+, poly(A)- and poly(A)-/RNaseR RNAs from human PA1 cells

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: We have used RNA-seq to examine circular RNAs from poly(A)- and poly(A)-/RNaseR RNAs in human PA1 cells

overall_design: In order to identify novel circular RNAs from PA1 cells

first: Ling-Ling

last: Chen

first: Yang

last: Zhang

last: Xue

first: Xiao-Ou


title: Transcriptome analysis of RANK-positive and RANK-negative luminal progenitor subpopulations in the human breast

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: RANK-positive and RANK-negative luminal progenitor cells were isolated by FACS from histologically normal human breast tissue from wild-type human donors. RNA-seq gene expression profiling was used to find differentially expressed genes between the RANK-positive and RANK-negative cell populations.

overall_design: Cells were isolated from 4 human patients. A paired analysis was used to compare RANK-positive and RANK-negative cells within patients.

first: Emma

last: Nolan

first: Bhupinder

last: Pal

first: Goknur

last: Giner

first: Geoffrey

last: Lindeman

first: Jane

middle: E

last: Visvader


title: ChIP-seq from midbrain (ENCSR028VCU)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
H3K9ac ChIP-seq on postnatal 0 day mouse midbrain

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


title: Time-ChIP in ESCs and NSCs

first: Aimee

last: Deaton

state: MA

address: 360 Binney St

institute: Amgen Inc

summary: Histone H3.3 turnover in ESCs and NSCs was determined using time-ChIP. This was performed by biotin-labeling H3.3_SNAP and following the loss of labeled histones over time. H3.1 time-ChIP was also performed although the resolution of these data is limited due to the depth of sequencing required.

overall_design: ESCs and NSCs carrying a H3.3_SNAP (or H3.1_SNAP) transgene were labeled with CP-biotin. Cells were harvested at 0h, 3h, 6h and 12h post-labeling and biotinylated histones recoved by streptavidin affinity pulldown. The resulting DNA, along with input DNA, was made into libraries and sequenced on an Illumina HiSeq 2500.

first: Mariluz

last: Gomez-Rodriguez

first: Jakub

last: Mieczkowski

first: Michael

middle: Y

last: Tolstorukov

first: Sharmistha

last: Kundu

first: Ruslan

last: Sadreyev

first: Lars

last: Jansen

first: Robert

last: Kingston


title: Enhancer regions show high histone H3.3 turnover that changes during differentiation

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

overall_design: Refer to individual Series


title: Tumor-derived circulating endothelial cell clusters in colorectal cancer

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

summary: Circulating tumor cells (CTCs) are the subject of several translational studies and clinical trials because their examination could offer an insight into tumor progression and clinical outcomes. Circulating tumor microemboli (CTM) are clusters of CTCs that have been described as malignant entities for over 50 years, although a comprehensive characterization of these cells is still lacking. Contrary to current consensus, we demonstrate that CTM isolated from colorectal cancer patients are not cancerous, but represent a discrete population of tumor-derived endothelial cells. CTM express epithelial and mesenchymal markers that are consistent with previous reports on circulating tumor cell phenotyping. However, they do not mirror the genetic variations of matching tumors. Transcriptome analysis of single-CTM reveals that these structures exhibit an endothelial phenotype, with further results supporting a tumor-derived endothelial lineage. CTM are widespread in blood sampled from preoperative cancer patients but not in healthy donors, suggesting CTM count as a potential biomarker of interest for colorectal cancer. CTM should not be confused with bona fide circulating epithelial tumor cells. The characterization of tumor derived endothelial cell clusters (TECCs) is likely of high diagnostic value, and may provide direct information about the underlying tumor vasculature at the time of diagnosis, during treatment and the course of the disease.

overall_design: Profiling of 18 TECCs/CTM from 8 colorectal cancer patients. In addition profiling of  matched 7 normal colonic mucosa, 9 primary colorectal tumor samples (of which three from the same patient), one colorectal cancer metastatis. Additionally,  14 laser-capture-dissected endothelia from the same patients and tissues, and 3 commercially available  normal endothelial cell lines

first: Igor

last: Cima


title: Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula

city: Los Angeles

first: Edward

last: De Robertis

address: 615 Charles E. Young Drive South

department: Biological chemistry

institute: HHMI/UCLA

summary: RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and BAMBI. Complete transcriptome-wide Excel files of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-seq in combination with the Xenopus laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.

overall_design: One stage 10.5 wild type whole embryo and triplicates of stage 10.5 dorsal lips and ventral lips are sequenced.

first: Yi

last: Ding

first: Gabriele

last: Colozza

first: Kelvin

last: Zhang

first: Yuki

last: Moriyama

first: Diego

last: Ploper

first: Eric

last: Sosa

first: Maria

last: Benitez


first: Mark

last: Dawson

overall_design: RNASeq of MV4;11 cells transduced with scramble shRNA or BRD4 shRNA in combination with DMSO or SGC0946 in triplicate

first: Omer

last: Gilan

first: Enid

last: Lam


title: Chromatin-enriched lncRNAs are cell type specifc enhancers for proximal genes

city: Chicago

first: Alex

last: Ruthenburg

address: 920 E. 58th Street

institute: University of Chicago

summary: comparison of chromatin enriched RNA in different human cell lines

overall_design: Biochemically fractionate nuclei to isolate chromatin-attached and soluble RNA populations

first: Michael

last: Werner


title: ChIP-seq for Polycomb group proteins and H3K27me3 in ESCs and NSCs

city: Cambridge

first: Aimee

last: Deaton

summary: ChIP-seq was performed for Ring1b, Ezh2, Cbx2 and H3K27me3 in ESCs and Ring1b and H3K27me3 in NSCs. This was used to define Polycomb-bound regions and to assess their H3.3 enrichment and turnover using time-ChIP.

overall_design: Cells were crosslinked and ChIP performed using the antibodies indicated. The resulting DNA, along with input DNA samples was made into libraries and sequenced on an Illumina HiSeq 2500.

first: Mariluz

last: Gomez-Rodriguez

first: Jakub

last: Mieczkowski

last: Tolstorukov

first: Sharmistha

last: Kundu

first: Ruslan

last: Sadreyev

first: Lars

last: Jansen


title: YY1 plays an essential role at all stages of B cell differentiation [ChIP-seq]

first: Salvatore

last: Loguercio

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

summary: YY1 is a ubiquitously expressed transcription factor that has been demonstrated to be essential for pro-B cell development.  However, the role of YY1 in other B cell populations has never been investigated.  It has been proposed that YY1 is a key regulator for the germinal center B cell program since the YY1 motif was present in much higher frequency in germinal center B cell signature genes than signature genes of other B cell subsets. Indeed, in accord with this prediction, we demonstrated that deletion of YY1 by Cg1-Cre completely prevented differentiation of naïve B cells into germinal center B cells and plasma cells after antigen stimulation.  To determine if YY1 was also required for the differentiation of other B cell populations, we deleted YY1 with CD19-Cre and found that all peripheral B cell subsets including B1 B cells require YY1 for their differentiation.  By deleting YY1 acutely with ER-Cre, we demonstrated that all B cell subsets require YY1 for their maintenance.  ChIP-seq shows that YY1 predominantly binds to promoters, and pathway analysis of the genes which bind YY1 show that they are enriched in ribosomal functions, mitochondrial functions such as bioenergetics, and functions related to transcription, such as mRNA splicing, metabolism of RNA. By RNA-seq analysis of differentially expressed genes, we demonstrated that YY1 normally activates genes involved in mitochondrial bioenergetics, while it normally downregulates genes involved in transcription, mRNA splicing, NF-kB signaling pathways, AP-1 transcription factor network, chromatin remodeling, cytokine signaling pathways, cell adhesion, cell proliferation and c-Myc targets.

overall_design: For the ChIP-seq, input and immunoprecipitated DNA was given to the Next Generation Sequencing Core, where it was prepared for massively parallel sequencing on Illumina HiSeq2000.

first: Haiqun

last: Jia

first: Andrew

last: Su

first: Ann

last: Feeney


title: YY1 plays an essential role at all stages of B cell differentiation [RNA-seq]

overall_design: Total RNA was prepared from RAG-/-pro-B cells, RAG-/-YY1f/f x mb1-Cre pro-B cells, RAG-/- µ+ pre-B cells, C57BL/6 follicular B cells, and C57BL/6 GC B cells. RNA was extracted using TRIzol (Life Technologies) and genomic DNA was eliminated using the genomic DNA wipeout buffer in the QuantiTect Reverse transcription kit (Qiagen). A final purification of the RNA was performed with the RNeasy kit (Qiagen). Ribosomal RNA was eliminated using Ribo-Zero Magnetic Gold Kit (Illumina).RNA samples were submitted to the Next Generation Sequencing Core, where they were processed with the NEBNext Ultra Directional RNA Library Prep Kit  for Illumina and sequenced on the Illumina HiSeq. Three independent RNA-seq samples were used for RAG-/- pro-B and RAG-/- YY1f/f x mb1-Cre pro-B cells, and two samples for the other cell types.


title: Small RNA Deep Sequencing Analysis of Mouse T Helper Cell (Th)  Subsets

first: Changchun

last: Xiao

summary: Small non-coding RNAs, esp. microRNAs (miRNAs), play critical roles in a large diversity of biological processes. The goal of this study is to perform small RNA deep sequencing analysis of mouse Th subsets and to identify miRNAs that are highy and specifically expressed in each subset.

overall_design: Naive T cells from several transcriptional reporter mice (Ifngyfp, Il17frfp and Foxp3gfp) were differentiated into appropriate Th subsets in vitro and harvested on day 4-5. Cell sorting was performed using a FACSAria cell sorter to obtain reporter gene-positive cells. Total RNA was extracted using the TRIzol reagent and subjected to standard small RNA deep sequencing analysis.

first: Ichiyama

last: Kenji

first: Dong

last: Chen

first: Sabouri‐Ghomi

last: Mohsen

first: Xiao

last: Changchun


title: Transcriptome response of Chlamydomonas reinhardtii exposed to methylmercury (MeHg)

city: Versoix

first: Rebecca

last: Beauvais-Flueck

address: 10 route de Suisse - CP 416

department: Institut F.-A. Forel

country: Switzerland

institute: University of Geneva

summary:
This study aims at investigating the effects of methylmercury on a microalga using a transcriptomic approach.
Algal cells were exposed two hours in a simplified artificial medium spiked with 0.05 or 0.5 nM MeHg.
Total RNA was extracted using TRI Reagent®.
Libraries were prepared with the Illumina TruSeq Stranded mRNA kit and sequenced on an Illumina HiSeq 2500 System.

overall_design: Three biological replicates were assessed for each of the 3 tested conditions: Control, 0.05 nM MeHg and 0.5 nM MeHg.

first: Claudia

last: Cosio

first: Vera

last: Slaveykova


title: Human glioblastoma-associated microglia/monocytes express a distinct RNA profile compared to human control and murine samples

status: Public on Jun 19 2016

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: We used RNA sequencing to compare the expression profile of 8 CD11b+ human glioblastoma-associated microglia/monocytes (hGAMs) samples to 8 human non-tumor CD11b+ microglia samples. Hierarchical clustering and principal component analysis showed a clear separation of the two sample groups and we identified 334 significantly regulated genes in hGAMs. In comparison to human control microglia hGAMs up-regulate genes associated with mitotic cell cycle, cell migration, cell adhesion, and extracellular matrix organization.

overall_design: Comparison of the mRNA expression profile of 8 CD11b+ human glioblastoma-associated microglia/monocytes samples and 8 human non-tumor CD11b+ microglia samples (isolated form postmortem and epilepsy tissues).

first: Frank

last: Szulzewsky


title: RNA-seq expression profiling of murine inner-ear hair cells

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: Sensorineural hearing loss affects the majority of the elderly population.  Mammalian hair cells (HC) do not regenerate and current stem cell and gene delivery protocols result only in immature hair cells like-cells.  For this reason, characterization of the transcriptional cascades that lead to development and survival of inner ear HC is essential for designing molecular-based treatments for deafness.  We employed a cell type-specific approach to analyze the transcriptomes of the mouse early postnatal auditory and vestibular sensory epithelia and of hair cells derived from zebrafish model.

overall_design: Murine auditory and vestibular epithelia were separated into hair-cells (HCs)  and epithelial non-sensory cells (ENSCs) by flow cytometry. Gene expression levels were recorded in independent triplicates from the sorted cells using RNA-seq

first: R

last: Hertzano


title: CD4+ T Cells Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis (JIA)

status: Public on Jun 18 2016

city: BUFFALO

first: JAMES

last: JARVIS

address: 875 ELLICOTT STREET 8026

department: PEDIATRIC

institute: UNIVERSITY AT BUFFALO

summary:
Aim: To discovery biomarkers in JIA base on gene expression from RNA sequencing on CD4+ T Cells
Method: Paired-end Ilumina sequencing to capture gene expression of CD4+ T cells from JIA individuals with active disease and patients in clinical remission on medication.

overall_design: RNA sequencing on CD4+T cells consist of JIA patients

first: Lai

last: Wong

first: Kaiyu

last: Jiang

first: Yanmin

first: James

last: Jarvis


title: Establishment of tissue-specific genome organisation by muscle-specific nuclear envelope transmembrane proteins (NETs) during mouse C2C12 myoblast differentiation

status: Public on Jun 17 2016

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

institute: University of Edinburgh


title: LaminB1 DamID in undifferentiated mouse C2C12 myoblasts (ATCC, Lot 59501261) and differentiated C2C12 myotubes

summary: Maps of genomic regions in proximity to the nuclear lamina were determined in undifferentiated C2C12 myoblasts (MBs) and 6 day differentiated C2C12 myotubes (MTs) using DamID with a Dam-Lamin B1-encoding lentivirus.

overall_design: Examination of Lamin B1-chromatin contacts in one cell line in undifferentiated myoblast and differentiated myotube conditions.

first: Michael

last: Robson

first: Eric

last: Schirmer


title: YY1 plays an essential role at all stages of B cell differentiation

first: Salvatore

last: Loguercio


title: Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus [RNA-Seq]

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

summary:
Background:
Preeclampsia, traditionally characterized by high blood pressure and proteinuria, is a common pregnancy complication, which affects 2-8% of all pregnancies.  Although children born to women with preeclampsia have a higher risk of hypertension in later life, the mechanism of this increased risk is unknown.  DNA methylation is an epigenetic modification that has been studied as a mediator of cellular memory of adverse exposures in utero.  Since each cell type in the body has a unique DNA profile, cell subtype composition is a major confounding factor in studies of tissues with heterogeneous cell types.  The best way to avoid this confounding effect is by using purified cell types.  However, the use purified cell types in large cohort translational studies is difficult.  The amnion, the inner layer of the fetal membranes of placenta, is derived from the epiblast and consists of two cell types, which are easy to isolate from the delivered placenta.  In this study, we demonstrate the value of using amnion samples for DNA methylation studies, revealing distinctive patterns between fetuses exposed to preeclampsia or hypertension and fetuses from normal pregnancies.
Results:
We performed a genome-wide DNA methylation analysis, HELP-tagging, on 62 amnion samples from placentas of uncomplicated, normal pregnancies, and those with complications of preeclampsia or hypertension.  Using a regression model approach, we found 123, 85 and 99 loci with high confidence hypertension-associated, proteinuria-associated and hypertension and proteinuria-associated DNA methylation changes, respectively. We also found that these differentially methylated regions overlap loci previously reported as differentially methylated regions in preeclampsia.
Conclusions:
Our findings support prior observations that preeclampsia is associated with changes of DNA methylation near genes that have previously been found to be dysregulated in preeclampsia.  We propose that amnionic membranes represent a valuable surrogate fetal tissue on which to perform epigenome-wide association studies of adverse intrauterine conditions.

overall_design: Directional RNA profiles of amnion membranes were generated by deep sequencing using Illumina HiSeq2500. Twenty-nine human amnion specimens were used: 12 control and 17 preeclampsia exposed.

first: John

last: Greally


title: Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus [Help-tagging]

overall_design: Genome-wide DNA methylation profile was assessed in aminion membrane. Sixty-two human amnion specimens were used: 15 control, 11 hypertension exposed, and 36 preeclampsia exposed.


title: Histone arginine methyltransferase CARM1 Is Crucial for Epigenetic Regulation of Starvation-induced Autophagy

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

summary: Autophagy is a highly conserved self-digestion process, essential to maintain homeostasis and viability in response to nutrient starvation. Although the components of autophagy in the cytoplasm have been well-studied, molecular basis for the epigenetic regulation of autophagy is poorly understood. Here, we identify histone arginine methyltransferase CARM1 as a critical component of autophagy.  We found that nutrient starvation increased CARM1 protein level and subsequently histone H3R17 dimethylation. Genome-wide analyses reveal that CARM1 exerts transcriptional coactivator function on autophagy-related genes and lysosomal genes through TFEB. Our findings demonstrate a previously unrecognized role of CARM1-dependent histone arginine methylation as a critical nuclear event of autophagy.

overall_design: 1) Gene expression profiling of WT and Carm1 KO MEFs  under nutrient rich condition or glucose starvation. 2) Examination of histone H3R17 dimethylation in WT MEFs upon glucose starvation

first: Hi-Jai

middle: R

last: Shin

first: Kyoung-Jae

first: Sung-Hee

last: Baek


title: Demonstration of novel piRNA production in chromosome-fusion containing Oxytricha

city: Washington

middle: Russell

last: Bracht

state: DC

address: 4400 Massachusetts Ave NW

department: Biology

institute: American University

summary: Oxytricha cells containing a chromosome fusion were backcrossed to wild-type, and the production of novel piRNAs spanning the fusion boundary was demonstrated by PIWI-protein (Otiwi-1) immunoprecipitation - seq

sample_organism:
Sterkiella histriomuscorum
Oxytricha trifallax

overall_design: RNA-IP of piRNAs from backcrossing Oxytricha cells, WT control was obtained from GSM860690.

first: J

first: X

last: Wang


title: A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development

status: Public on Jun 16 2016

city: Vancouver

first: Juergen

last: Ehlting

state: BC

address: 321 - 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

summary: We developed a transcriptome resource for Douglas-fir covering key developmental stages of megagametophytes over time: prefertilization, fertilization, embryogenesis, and early, unfertilized abortion. Extracted RNA was sequenced using large-scale sequencing and reads were assembled to generate a de novo reference transcriptome of 105,505 predicted high-confidence transcripts. Expression levels were estimated based on alignment of the original reads to the reference.

overall_design: 200–400 megagametophytes were dissected and pooled per sample on four dates from either pollinated or unpollinated cones: June 10, June 22, June 30, and July 6 2011. These dates coincided with key events in seed development: corrosion cavity formation, fertilization, embryogenesis, or the early stages of abortion in the unpollinated treatment. Sporophytic tissue (i.e. cone bracts and cone scales) were added for comparison. PolyA RNA was used for Illumina sequencing.

first: Stefan

last: Little

first: Ian

middle: G

last: Boyes

first: Kate

last: Donaleshen

first: Patrick

last: von Aderkas


title: TBR1 Regulates Autism Risk Genes in the Developing Neocortex

first: Gill

last: Bejerano

address: 279 Campus Drive West (MC 5329)

department: Developmental Biology

institute: Stanford University

summary: Exome sequencing studies have identified multiple genes harboring de novo loss-of-function (LoF) variants in individuals with autism spectrum disorders (ASD), including TBR1, a master regulator of cortical development. We performed ChIP-seq for TBR1 during mouse cortical neurogenesis and show that TBR1-bound regions are enriched adjacent to ASD genes. ASD genes were also enriched among genes that are differentially expressed in Tbr1 knockouts, which together with the ChIP-seq data, suggests direct transcriptional regulation. Of the 9 ASD genes examined, 7 were misexpressed in the cortices of Tbr1 knockout mice, including 6 with increased expression in the deep cortical layers. ASD genes with adjacent cortical TBR1 ChIP-seq peaks also showed unusually low levels of LoF mutations in a reference human population and among Icelanders. We then leveraged TBR1 binding to identify an appealing subset of candidate ASD genes. Our findings highlight a TBR1-regulated network of ASD genes in the developing neocortex that are relatively intolerant to LoF mutations, indicating that these genes may play critical roles in normal cortical development.

overall_design: ChIP-seq for Tbr1 on mouse whole cortex dissected from embryonic day 15.5 (E15.5) embryos

first: Bin

last: Chen

first: James

middle: H

last: Notwell


title: Pol II and CTD Phosphorylation of ATP-analog sensitive Kin28 budding yeast

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by genome tiling array

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

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae BY4741

overall_design: Refer to individual Series