title: Control ChIP-seq from middle frontal area 46 (ENCSR394ZWY)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR391SNO)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from uterus (ENCSR839SAN)

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


title: Control ChIP-seq from A549 (ENCSR814XCZ)

summary:
Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR376YUP)


title: long read RNA-seq from HCT116 (ENCSR388RWE)

type: Expression profiling by high throughput sequencing

summary:
HCT 116 cell line

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


title: Histone ChIP-seq from pancreas (ENCSR423OOD)

summary:
H3K36me3 ChIP-seq on pancreas tissue female adult (61 years)

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


title: Control ChIP-seq from K562 (ENCSR387OYT)

summary:
ChIP-seq on human K562

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


title: TF ChIP-seq from adrenal gland (ENCSR408ZEE)


title: TF ChIP-seq from endodermal cell (ENCSR398RET)

summary:
CTCF ChIP-seq on endodermal cell originated from endodermal cell

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


title: Histone ChIP-seq from left lung (ENCSR352BOS)

summary:
H3K4me1 ChIP-seq on left lung tissue female child (16 years)

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR372YQR)

summary:
H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (86 years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCSR384AGH)

summary:
H3K27me3 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

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


title: Histone ChIP-seq from stomach (ENCSR819DOR)


title: Histone ChIP-seq from middle frontal area 46 (ENCSR807TBS)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from stomach (ENCSR361KVZ)


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCSR350KJU)

summary:
H3K4me1 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

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


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCSR351RPE)

summary:
H3K9me3 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR347KLR)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue male adult (86 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from HEK293 (ENCSR348AGV)

summary:
SETDB1 ChIP-seq on human HEK293

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


title: Control ChIP-seq from SK-N-SH (ENCSR358RZO)

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

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


title: long read RNA-seq from MCF-7 (ENCSR810XLL)

summary:
MCF-7 cell line

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


title: Histone ChIP-seq from vagina (ENCSR346FVK)


title: long read RNA-seq from psoas muscle (ENCSR803QWH)

summary:
ENC4_46 W61 psoas #2

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


title: Control ChIP-seq from A549 (ENCSR344CSQ)

summary:
Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.

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


title: long read RNA-seq from heart right ventricle (ENCSR329ZQG)

summary:
ENC4_51 W73 heart right ventricle

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


title: Histone ChIP-seq from left lung (ENCSR800MYV)

summary:
H3K27me3 ChIP-seq on left lung tissue female child (16 years)

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


title: Control ChIP-seq from A549 (ENCSR324VMZ)

summary:
Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.

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


title: Control ChIP-seq from foreskin keratinocyte (ENCSR335GGM)

summary:
ChIP-seq control (input DNA) on primary keratinocytes in day 6 of differentiation

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR787QZE)

summary:
H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR786VUJ)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (86 years) originated from dorsolateral prefrontal cortex

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


title: long read RNA-seq from lower lobe of left lung (ENCSR261GOA)

summary:
ENC4_80 W73 lower lobe of left lung

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


title: Histone ChIP-seq from thyroid gland (ENCSR309UVT)

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


title: long read RNA-seq from excitatory neuron (ENCSR257JBF)

summary:
excitatory cortical neurons

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR799VTP)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from nephron (ENCSR266ZUX)

summary:
CTCF ChIP-seq on nephron female embryo (5 days)

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


title: Histone ChIP-seq from left lung (ENCSR796SRF)

summary:
H3K9me3 ChIP-seq on left lung tissue female child (16 years)

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR291VCJ)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (88 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from nephron progenitor cell (ENCSR799GJD)

summary:
CTCF ChIP-seq on nephron progenitor cell

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


title: long read RNA-seq from osteocyte (ENCSR296PQZ)

summary:
H9-derived osteocytes

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


title: long read RNA-seq from left ventricle myocardium inferior (ENCSR786FLO)

summary:
ENC4_55 W78 left ventricle myocardium inferior

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


title: TF ChIP-seq from left lung (ENCSR255SQR)

summary:
CTCF ChIP-seq on left lung male adult (40 years)

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


title: long read RNA-seq from heart right ventricle (ENCSR782LGT)

summary:
ENC4_50 W72 heart right ventricle

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


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCSR309EQQ)

summary:
H3K36me3 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR335YEH)

summary:
H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from osteocyte (ENCSR300DWM)

summary:
CTCF ChIP-seq on osteocyte originated from osteocyte

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR251PPB)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR258GSA)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from SK-N-SH (ENCSR245JGC)

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

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


title: TF ChIP-seq from pancreas (ENCSR253ALG)

summary:
CTCF ChIP-seq on pancreas female adult (61 years)

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


title: Histone ChIP-seq from left lung (ENCSR793LDG)

summary:
H3K36me3 ChIP-seq on left lung tissue female child (16 years)

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


title: Histone ChIP-seq from Peyer's patch (ENCSR249IKQ)

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


title: long read RNA-seq from left ventricle myocardium superior (ENCSR777CCI)

summary:
ENC4_54 W78 left ventricle myocardium superior

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR776TJT)


title: Control ChIP-seq from K562 (ENCSR766WPH)

summary:
ChIP-seq on human K562

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


title: Control ChIP-seq from WTC11 (ENCSR764ZNN)

summary:
ChIP-seq on human WTC11

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


title: TF ChIP-seq from pancreas (ENCSR774PGN)

summary:
CTCF ChIP-seq on pancreas female adult (41 years)

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR774IHJ)

summary:
H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR739QEI)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR237QNB)

summary:
H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from pancreas (ENCSR751GUM)

summary:
H3K4me3 ChIP-seq on pancreas tissue female child (16 years)

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


title: Histone ChIP-seq from pancreas (ENCSR233EDV)

summary:
H3K4me1 ChIP-seq on pancreas tissue female adult (59 years)

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


title: Control ChIP-seq from A549 (ENCSR204GMP)

summary:
Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.

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


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCSR737WCC)

summary:
H3K4me3 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

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


title: Control ChIP-seq from WERI-Rb-1 (ENCSR723FET)

summary:
ChIP-seq on human WERI-Rb-1

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


title: Control ChIP-seq from A549 (ENCSR212FST)

summary:
Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR198MJK)

summary:
H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from adrenal gland (ENCSR775NSL)

summary:
H3K4me3 ChIP-seq on adrenal gland female adult (41 years)

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR200JVJ)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from brain (ENCSR225KOS)

summary:
CTCF ChIP-seq on brain female embryo (5 days)

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


title: TF ChIP-seq from nephron (ENCSR194WQV)

summary:
CTCF ChIP-seq on nephron female embryo (5 days)

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


title: Control ChIP-seq from SK-N-SH (ENCSR197JBL)

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

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR714GKF)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex

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


title: long read RNA-seq from Panc1 (ENCSR181CES)

summary:
Panc1 cell line

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


title: Histone ChIP-seq from upper lobe of left lung (ENCSR229GEL)

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


title: Histone ChIP-seq from pancreas (ENCSR713YDD)

summary:
H3K4me3 ChIP-seq on pancreas tissue female adult (59 years)

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


title: TF ChIP-seq from lower lobe of left lung (ENCSR195POA)

summary:
CTCF ChIP-seq on lower lobe of left lung male adult (60 years)

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


title: TF ChIP-seq from neural crest cell (ENCSR218MVT)

summary:
CTCF ChIP-seq on neural crest cell originated from neural crest cell

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


title: Histone ChIP-seq from pancreas (ENCSR703XCI)

summary:
H3K9me3 ChIP-seq on pancreas tissue female adult (61 years)

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


title: TF ChIP-seq from heart left ventricle (ENCSR718SDR)


title: Histone ChIP-seq from pancreas (ENCSR703KLE)

summary:
H3K9me3 ChIP-seq on pancreas tissue female adult (41 years)

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


title: TF ChIP-seq from chondrocyte (ENCSR190BZA)

summary:
CTCF ChIP-seq on chondrocyte originated from chondrocyte

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR233RWF)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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


title: long read RNA-seq from heart left ventricle (ENCSR700XDQ)

summary:
ENC4_49 W72 heart left ventricle

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR698YQL)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex

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


title: Histone ChIP-seq from pancreas (ENCSR179GVP)

summary:
H3K27me3 ChIP-seq on pancreas tissue female adult (59 years)

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR668DIS)


title: long read RNA-seq from GM23338 (ENCSR676IWT)

summary:
iPSCs via Sendai-viral Yamanaka factors

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


title: Control ChIP-seq from SK-N-SH (ENCSR684GHA)

summary:
SK-N-SH immortalized cell line (treated with 6 uM all-trans-retinoic acid for 48 hours) stably expressing C-terminal eGFP-TOX2 fusion protein.

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


title: long read RNA-seq from mesenteric fat pad (ENCSR648QZP)

summary:
ENC4_93 W73 mesenteric fat pad FLASH

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


title: long read RNA-seq from right lobe of liver (ENCSR657HJW)

summary:
W61 right lobe of liver

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR641QPH)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (86 years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR638CSE)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from mesothelial cell of epicardium (ENCSR647SQF)

summary:
CTCF ChIP-seq on epicardium (mesothelium) cells originated from epicardium (mesothelium) cells

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR153LYY)


title: Histone ChIP-seq from left lung (ENCSR155YWB)

summary:
H3K4me1 ChIP-seq on left lung tissue male adult (40 years)

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


title: long read RNA-seq from posterior vena cava (ENCSR138TAS)

summary:
ENC4_102 W73 posterior vena cava

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR131MFE)

summary:
H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (86 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from HFFc6 (ENCSR163ULN)

summary:
CTCF ChIP-seq on HFFc6

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR151NEZ)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (89 years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from foreskin keratinocyte (ENCSR631ESZ)

summary:
ChIP-seq control (input DNA) on primary keratinocytes in day 0 of differentiation

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


title: Control ChIP-seq from K562 (ENCSR150QOJ)

summary:
ChIP-seq on human K562

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


title: long read RNA-seq from IMR-90 (ENCSR113MEY)

summary:
IMR90 cell line

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


title: Histone ChIP-seq from pancreas (ENCSR637NGB)

summary:
H3K36me3 ChIP-seq on pancreas tissue female adult (59 years)

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


title: Control ChIP-seq from foreskin keratinocyte (ENCSR113CMI)

summary:
ChIP-seq control (input DNA) on primary keratinocytes in day 3 of differentiation

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


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCSR165CDY)

summary:
H3K27ac ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

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


title: TF ChIP-seq from pancreas (ENCSR113COJ)

summary:
CTCF ChIP-seq on pancreas female adult (59 years)

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


title: long read RNA-seq from endothelial cell (ENCSR148IIG)

summary:
PGP1 derived endothelial-cells

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


title: TF ChIP-seq from lower lobe of left lung (ENCSR133AFF)

summary:
CTCF ChIP-seq on lower lobe of left lung female adult (59 years)

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


title: long read RNA-seq from type B pancreatic cell (ENCSR130CIK)

summary:
H9-derived insulin-producing beta-like cells

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


title: TF ChIP-seq from thyroid gland (ENCSR145HBC)

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


title: long read RNA-seq from HepG2 (ENCSR634AKC)

summary:
HepG2 Ljungman

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR141EDV)

summary:
H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex

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


title: long read RNA-seq from adrenal gland (ENCSR081NRO)

summary:
Adrenal Gland 1-2 ENTEX50

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR086BNR)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR096QCF)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from A549 (ENCSR085WWL)

summary:
Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.

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


title: Histone ChIP-seq from adrenal gland (ENCSR086QZD)

summary:
H3K27me3 ChIP-seq on adrenal gland tissue female adult (41 years)

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


title: long read RNA-seq from neural crest cell (ENCSR056MYH)

summary:
H9-derived neural crest cells

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR095NSV)

summary:
H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (86 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from vagina (ENCSR614HHL)


title: Control ChIP-seq from SK-N-SH (ENCSR072QAK)

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

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


title: Control ChIP-seq from SK-N-SH (ENCSR086GBI)


title: Histone ChIP-seq from pancreas (ENCSR029SIG)

summary:
H3K27ac ChIP-seq on pancreas female child (16 years)

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


title: Control ChIP-seq from adrenal gland (ENCSR071ILJ)

summary:
Control ChIP-seq on adrenal gland female adult (41 years)

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR613JAK)


title: Histone ChIP-seq from pancreas (ENCSR571RCH)

summary:
H3K4me1 ChIP-seq on pancreas tissue female adult (61 years)

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


title: TF ChIP-seq from GM23338 (ENCSR611HGB)

summary:
CTCF ChIP-seq on GM23338

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR617ONQ)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex

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


title: long read RNA-seq from H9 (ENCSR044ARQ)

summary:
H9 ESCs

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


title: TF ChIP-seq from GM23338 (ENCSR591DTH)

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


title: Histone ChIP-seq from mucosa of descending colon (ENCSR067VEM)

summary:
H3K9me3 ChIP-seq on mucosa of descending colon tissue male adult (40 years)

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


title: Control ChIP-seq from SK-N-SH (ENCSR042UCB)


title: Control ChIP-seq from SK-N-SH (ENCSR594IZZ)


title: Control ChIP-seq from SK-N-SH (ENCSR618JZG)


title: Histone ChIP-seq from middle frontal area 46 (ENCSR555HJT)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex

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


title: long read RNA-seq from Right ventricle myocardium inferior (ENCSR591OZR)

summary:
ENC4_57 W78 right ventricle myocardium inferior

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


title: Control ChIP-seq from left ventricle myocardium inferior (ENCSR608IVH)

summary:
Control ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR039TGB)

summary:
H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from endothelial cell (ENCSR031PXV)

summary:
CTCF ChIP-seq on endothelial cell

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


title: Histone ChIP-seq from adrenal gland (ENCSR038KST)

summary:
H3K4me1 ChIP-seq on adrenal gland tissue female adult (41 years)

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


title: Histone ChIP-seq from body of pancreas (ENCSR588PZN)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR038ODI)


title: long read RNA-seq from progenitor cell of endocrine pancreas (ENCSR530BOC)

summary:
H9-derived pancreatic progenitors

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


title: long read RNA-seq from heart left ventricle (ENCSR575LWI)

summary:
ENC4_33 W73 heart left ventricle

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


title: long read RNA-seq from K562 (ENCSR526TQU)

summary:
K562 Ljungman

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


title: Histone ChIP-seq from middle frontal area 46 (ENCSR524MPL)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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


title: Control ChIP-seq from SK-N-SH (ENCSR566WAB)

summary:
SK-N-SH immortalized cell line (treated with 6 uM all-trans-retinoic acid for 48 hours) stably expressing C-terminal eGFP-ARNTL fusion protein.

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


title: Control ChIP-seq from left lung (ENCSR519WCC)

summary:
Control ChIP-seq on left lung tissue female child (16 years)

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


title: Control ChIP-seq from middle frontal area 46 (ENCSR557HEX)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex

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


title: TF ChIP-seq from uterus (ENCSR527TPP)


title: TF ChIP-seq from OCI-LY1 (ENCSR520VTO)


title: long read RNA-seq from right cardiac atrium (ENCSR553SVP)

summary:
ENC4_36 W73 cardiac right atrium

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


title: Control ChIP-seq from SK-N-SH (ENCSR540RTZ)

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

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


title: long read RNA-seq from right cardiac atrium (ENCSR514YQN)

summary:
ENC4_59 W72 right cardiac atrium

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


title: Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset1]

city: Long Island City

first: Alyssa

last: Fronk

state: NY

address: 30-02 48th Avenue, Suite 140

institute: Envisagenics

summary: Here, we set out to understand if and how splicing kinetics are coordinated beyond individual intron removal and if this potential coordination could regulate alternative splicing outcomes. By measuring rates of transcription and splicing genome-wide, we found that the rate of splicing is coordinated across introns within individual genes. Furthermore, we found that elongation rates and splicing rates are coordinated within TADs, as are alternative splicing changes that result from cell type differences, differentiation programs, and alterations in splicing factor levels. Overall, our work establishes that the kinetics of transcription and splicing are coordinated within the spatial organization of the genome, which could be a control point for alternative splicing regulation that can modulate the function of a cell.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design:
Nascent RNA-sequencing in two cell lines at 7 time points following 3hr DRB treatment and washout
Please note that the *_steadyState samples represent those treated with DMSO as a vehicle control for 3 hours.

middle: D

last: Casill

first: Matthew

middle: J

last: Gamble


title: TAZ-CAMTA1 vs TAZ4A expressing MS1 cells

city: Dallas

first: Jordan

last: Driskill

state: TX

address: 5323 Harry Hines Blvd

department: Physiology

institute: UT Southwestern

summary: TAZ-CAMTA1 is a defining genetic aberration in the vascular cancer epithelioid hemangioendothelioma. We studied the transcriptome of TAZ-CAMTA1 and compared it to that of control or activated TAZ (TAZ4A)-expressing endothelial cells. We utilized an immortalized, mouse endothelial cell line known as MS1. We present and make available the first RNA-sequencing data of TAZ-CAMTA1's transcriptome in endothelial cells

overall_design: mRNA sequencing of Ctrl, TAZ4A, and TAZ-CAMTA1 stably expressing MS1 cells

first: Duojia

last: Pan


title: Histone ChIP-seq from middle frontal area 46 (ENCSR025KPY)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex

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


title: A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 [ChIP-seq]

city: Melbourne

first: Stephin

last: Vervoort

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Gene expression by RNA Polymerase II (RNAPII) is tightly controlled by Cyclin-dependent kinases (CDKs) at discrete checkpoints during the transcription cycle. The RNAPII pausing checkpoint, engaged after transcription initiation, is controlled by CDK9 to regulate transcription in metazoans.  We discovered that CDK9-mediated RNAPII pause-release is functionally opposed by a protein phosphatase 2A (PP2A) complex. PP2A dynamically competes for key CDK9 substrates, DSIF and RNAPII-CTD, and is recruited to transcription pausing sites by the Integrator complex subunit INTS6. INTS6 depletion confers resistance to CDK9 inhibition in a variety of normal and tumor cell lines. Loss of INTS6 abolishes the Integrator-PP2A association leading to unrestrained CDK9 activity, which amplifies transcriptional responses. Pharmacological PP2A activation synergizes with CDK9 inhibition to kill MLL-rearranged leukemias and solid tumors and provide therapeutic benefit in vivo.  These data demonstrate that f  inely-tuned gene expression relies on the balance of kinase and phosphatase activity at the pausing checkpoint.

overall_design: We performed ChIP-seq on THP-1 or Drosophila S2 cells expressing Cas9 and non-targeting or INTS6 targeting sgRNAs which had been treated with a CDK9 inhibitor (AZ5576) to determine the location of RNAPII, RNAPII CTD phospho-serine2, CDK9, INTS11, INTS6 or BRD4 across the genome. We also performed ChIP-seq on THP-1 cells treated with a CDK9 inhibitor, a PP2A agonist (DBK-1154) or a combination of both to determine the location of RNAPII across the genome.

first: Izabela

last: Todorovski

first: Matteo

last: Costacurta

first: Jennifer

middle: R

last: Devlin

first: Ricky

middle: W

last: Johnstone


title: Genomic profiling of spermatogonial stem cells and embryonic stem cells

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

summary: Through comparing the global expression profiles of SSCs and ESCs using DNA microarrays, the differences between the SSC and ESCs have been revealed , especially these pluripotency-related genes.

overall_design: Total RNA was isolated from cells, including spermatogonial stem cells (SSCs), embryonic stem cells (ESCs), and gene expression signiture was detected by microarray.

first: Huacheng

last: Luo


title: Control ChIP-seq from foreskin keratinocyte (ENCSR528SMB)

summary:
ChIP-seq control (input DNA) on primary keratinocytes in day 6 of differentiation

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


title: scRNAseq of TAZ-CAMTA1 expressing endothelial cells in vivo

summary: TAZ-CAMTA1 is a defining genetic aberration in the vascular cancer epithelioid hemangioendothelioma. We generated a novel transgenic mouse that expresses TAZ-CAMTA1 in endothelial cells. These mice develop vascular tumors in the lung and die by average on day 40. We isolated GFP + endothelial cells from three five-week old TRE-TAZ-CAMTA1;Cdh5-tTA;TRE-GFP mice and subjected these endothelial cells to scRNA-seq via the 10X genomics platform

overall_design: scRNA seq of GFP+ cells from 5 week-old TRE-GFP;TRE-TAZ-CAMTA1;Cdh5-tTA mice


title: A PP2A-Integrator complex regulates transcriptional pause-release by functionally opposing CDK9

city: Philadelphia

first: Sarah

middle: A

last: Welsh

state: PA

address: 3601 Spruce St

institute: Wistar Institute

summary: We investigated the function of the Integrator Complex and PP2A during transcription.

overall_design: Analysis of genome occupancy of PP2A and RNAPII upon gene induction and transcriptome phenotype upon loss of PP2A

first: Elisa

last: Barbieri

first: Alessandro

last: Gardini


title: A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 [3UTR-seq]

overall_design: We performed 3'RNA-seq on RNA isolated from THP-1 cells expressing Cas9 and non-targeting or INTS6 targeting sgRNAs which had been treated with LPS to perform differential gene expression analysis. We also performed 3'RNA-seq on RNA isolated from HT-29 cells treated with a CDK9 inhibitor (AZ5576) or a PP2A agonist (DBK-1154) to perform differential gene expression analysis.


title: A PP2A-Integrator complex fine-tunes transcription by opposing CDK9

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

overall_design: Refer to individual Series


title: A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 [4sU-seq]

overall_design: We performed RNA-seq on nascent RNA isolated from THP-1 cells expressing Cas9 and non-targeting or INTS6 targeting sgRNAs which had been treated with a CDK9 inhibitor (AZ5576) and labelled with 4-thiouridine to measure nascent RNA production across the transcriptome


title: RIOK2 ko RNA Seq

status: Public on May 22 2021

city: Copenhagen N

first: Jan-Erik

last: Messling

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: RNA-Seq  in murine Riok2 MLL-AF9 cells 72 hours after RIOK2 depletion or treatment with RIOK2i

overall_design: RNA-Seq was performed in cells 72 hours after addition of hydroxytamoxifen, ethanol, DMSO or 1µM RIOK2i to the celll culture medium

first: Kristian

last: Helin


title: Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains

last: Fronk


title: Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset2]

summary: In this study, we performed mRNA sequencing on IMR90 and A549 cells in order to understand the differences in gene expression patterns and alternative splicing patterns between the two cell lines.

overall_design: Poly(a) RNA-sequencing in IMR90 and A549 cells

last: Casill


title: Control ChIP-seq from middle frontal area 46 (ENCSR518COE)

first: ENCODE

last: DCC

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex

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


title: Plasma miRNA expression profiling of pancreatic ductal adenocarcinoma patient, chronic pancreatitis patients and healthy population in China

city: Kifeng

first: Yifan

last: Zhu

state: Henan

address: Xi Men Da Jie 115

institute: Henan University Huaihe Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: There is an urgent need for early detection of Pancreatic ductal adenocarcinoma (PDAC). Due to high stability and tight relationship with tumor genesis and development, miRNA has been considered as a type of potential biomarkers for PDAC detection and surveillance. However, up to now, the common miRNA panel for PDAC detection is still undetermined.  In order to reveal the differential miRNA expression profiles between PDAC patients(P group), chronic pancreatitis patients(C group) and healthy persons(H group), plasma samples were collected from threegroups, further the genome wide small RNA expression profiling was performed.

overall_design: Plasma miRNA samples were extracted from three groups respectively, each group 5 samples. miRNA profiles were investigated by second generation small RNA sequencing,  we used CAP-miRSeq algorithm for a comprehensive analysis of small RNA sequencing reads to identify, annotate and quantify miRNAs according to the user guide with some modifications.

first: Xiangqian

last: Guo

first: Jian

last: Wang


title: Single-cell staging of meiotic entry identifies a sequential order in meiotic sex chromosome activation

city: Utrecht

first: Abel

last: Vertesy

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The switch from mitosis to meiosis is a major transition that takes place during germ cell development. The precise sequence and the different gene expression programs activated during this process are only partly known. Here, we applied single-cell mRNA sequencing to interrogate the transcriptional changes that occur during the early steps of male germ cell differentiation. We isolated single cells from testes using a Dazl-GFP reporter mouse, which allowed us to focus on germ cells undergoing the mitotic to meiotic transition. We identified 4 distinct meiotic stages with unique transcriptome profiles and reconstructed the timeline of the meiotic entry in silico, from spermatogonia up to the pachytene stage, identifying transcriptional changes with an unprecedented resolution. This allowed us to characterize 3 major transitions in the meiotic prophase 1 of the male germline: meiotic entry, the meiotic sex chromosome inactivation (MSCI), and concomitant pachytene transcriptional activation. Meiotic entry is initiated following the downregulation of a tightly connected set of pluripotency factors and accompanied by a global transcriptional silencing. In contrast, during subsequent sex chromosome inactivation at the zygotene stage, gene silencing proceeds in a defined order, related to gene function.

overall_design: Single-cell mRNA sequencing on isolated cells from testes from three Dazl-GFP reporter mice.Testes were isolated from Dazl-GFP mice (Chen 2014, PMID: 25418731), and extracted cells were prepared into a single-cell suspension. Live, Dazl-GFP+ cells were sorted intro 384 well plates with either 96 CEL-seq1 or 384 CEL-seq2 barcodes (see "CEL-seq.demultiplexing.barcodes.pdf"). CEL-seq1 plates have 4 libraries, CEL-seq2 plates have 1 library per plate. Sequencing lanes concatenated in fastq-files uploaded here. See Supplementary Methods for details.

first: Ábel

last: Vértesy

first: Javier

middle: F

last: Aldeguer

first: Zeliha

last: Sahin

first: Nicolas

last: Rivron

first: Alexander

last: van Oudenaarden

first: Niels

last: Geijsen


title: Transcriptomic profiling of cultured CD8+ T cells from mice and treated with either IL2,  IL2/SIINFEKL(TCR), IL2/IL4, or IL2/IL4/SIINFEKL(TCR)

city: Denver

first: Brian

middle: Patrick

last: OConnor

state: Colorado

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

summary: The plasticity of CD8 cells lend itself well to understanding underlying molecular mechanism for cell identity and downstream effects of microenvironment exposures. CD8 T cells in the context of memory has been studied at the epigenomic level; however, responses after immunologic microenvironment exposures culminating in a final receptor stimulation readout has not been studies in detail. We use RNA-seq to explore these questions.

overall_design: RNA-sequencing of TCR activated (SIINFEKL) and unactivated CD8+ T cells purified from OT1 Mouse spleens and cultured in the presence of IL-2 or IL-2/IL-4 for 4 Days.

middle: P

last: O'Connor

first: Laura

last: Harmacek

first: Thomas

last: Danhorn

first: Sonia

middle: M

last: Leach

first: Erwin

last: Gelfand

first: Michaela

last: Schedel

first: Yi

last: Jia


title: Molecular profiling of cultured CD8+ T cells from mice and treated with either IL2,  IL2/SIIKFEKL(TCR), IL2/IL4, or IL2/IL4/SIINFEKL(TCR)


title: BRD4 ChIP-Seq of CD8+ T cell subsets during LCMV infection [ChIP-seq_D7]

status: Public on May 21 2021

city: La Jolla

first: Ananda

last: Goldrath

address: 9500 Gilman Dr

institute: UCSD

summary: Brd4 ChIP-seq of TE P14 cells during LCMV.

overall_design: 3 samples, P14 cells Day 7 LCMV infection CD8+ T cell subsets.

first: J

last: Milner

first: A


title: Whole genome bisulfite sequencing for bud, catkin and leaf of California Valley Oak, Quercus lobata (SW786)

city: Los Angeles

first: Sorel

middle: Tanya

last: Fitz-Gibbon

state: CALIFORNIA

address: 961 Wellesley Ave

department: Ecology & Evolutionary Biology

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: WGBS sequencing of Valley Oak  bud, catkin and leaf tissues

overall_design: WGBS sequencing using Qiagen EpiTect kit and Illumina HiSeq 4000.

first: Victoria

middle: L

last: Sork

middle: T

first: Shawn

last: Cokus

first: Matteo

last: Pellegrini


title: ChIP-Seq of three H3 Acetylation epitopes in cultured CD8+ T cells from mice and treated with either IL2,  IL2/SIINFEKL(TCR), IL2/IL4, or IL2/IL4/SIINFEKL(TCR)

overall_design: ChIP-Sequencing for Acetylation of Histone H3 of activated (SIINFEKL) and unactivated CD8+ T cells purified from OT1 Mouse spleens and cultured in the presence of IL-2 or IL-2/IL-4 for several days.


title: PacBio Iso-Seq transcriptome for California Valley Oak, Quercus lobata (SW786)

summary: Iso-Seq "full length" transcript sequences were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

overall_design:
Iso-Seq long reads prepared from bud, leaf & stem tissues
Please note that the processed (extra-filtered wig files) data were lost and are unavailable.


title: Illumina RNA-seq for bud, leaf and stem of California Valley Oak, Quercus lobata (SW786)

summary: STAR aligned RNA-seq reads were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

overall_design: Iillumina RNA-seq 101+101 nt paired end from bud, leaf & stem tissues


title: Next Generation Sequencing of T6PNE human pancreatic cell with  DMSO vs NCT (HNF4a agonist) in palmitate

city: San Diego

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: T6PNE human pancreatic cells  were treated by DMSO or N-trans caffeoyltyramine (NCT) for 2 days with palmitate, followed by harvesting for RNA isolation.

overall_design: T6PNE cells treated with DMSO or NCT compound in palmitate

first: Fred

last: Levine


title: Effects of FNR, Arca and oxygen on the synthesis of bacterial cellulose

city: Tianjin

first: Lixuejing

middle: huanglonghui

last: zhongcheng

address: 13th Street, Binhai New Area, Tianjin City

institute: Tianjin University of Science and Technology

summary:
Purpose:The oxygen-regulated genes FNR and ARCA were combined with Komagataeibacter xylinus CGMCC 2955 to provide a new perspective for the study of the mechanism of oxygen environment on BC synthesis.
Methods:The FNR and Arca overexpressing strains and the control strains were fermented under different partial oxygen pressures. The bacterial cellulose membrane in the logarithmic period of fermentation was enzymolyzed, and the bacteria were collected for transcriptome analysis.Sequencing was performed with Illumina and transcriptome analysis was performed on the bacteria under different conditions.
Results:Transcriptome sequencing was performed using Illumina high-throughput sequencing technology on K. xylinus cultured under different oxygen tensions. The differentially expressed genes in the arcA overexpressing strains were mainly in the sulfur metabolism, two-component system, purine metabolism, and amino acid metabolism pathways compared to the control strains. Analysis showed that the arcA overexpression strain activated the sulfur metabolic pathway in K. xylinus. Due to the insufficient oxygen electron acceptors in the hypoxia, sulfate acted as the final electron acceptor and enhanced the growth ability of the strain. Through global regulation of the pathways of bacterial growth and metabolism as well as BC synthesis under low oxygen conditions, the arcA gene has enabled the strain to reach new levels of BC production. This study lays the foundation for further investigation of the mechanism of the effect of oxygen on BC synthesis in K. xylinus.

overall_design: K. xylinus/ pseva331-FNR, K. xylinus/ pseva331-Arca and K. xylinus/pSEVA331 were cultured in static culture at 15%, 21% and 40% oxygen partial pressures and sequenced by Illumina high-throughput sequencing technology

first: Li

middle: x

last: jing

first: Huang

middle: l

last: hui

first: zhong

last: cheng


title: High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.


title: Role of Cop1 on chromatin accessibility in 4T1 mouse triple negative breast cancer cells

city: Boston

first: Xiaoqing

last: Wang

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Cop1 regulates stability of transcription factors. We determined the role of Cop1 in the regulation of Cebpd transciptional output. We generated 4T1breast cancer cells with CRISPR/Cas9 mediated Cop1 (gene symbol RFWD2) knockout. We treated control sgRosa26 and sgCop1 cells with vehicle or IFNgamma (20ng/ml) for 24 hours and did ATAC-seq.

overall_design: ATAC-seq on Cop1-replete or -deficient 4T1 cells that were treated with vehicle or 20ng/ml IFNγ.

first: Binbin

first: Shengqing

last: Gu

first: X

middle: S

last: Liu


title: Differences in vaginal microbiota, host transcriptome and proteins in women with bacterial vaginosis are associated with metronidazole treatment response

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Bacterial vaginosis (BV) treatment failures or recurrences are common. To identify features associated with treatment response, we compared vaginal microbiota and host ectocervical transcriptome before and after oral metronidazole therapy. Response to metronidazole is characterized by significant changes in chemokines and related transcripts suggesting that strategies to promote these pathways may prove beneficial.

overall_design: Women (Bronx, NY (n=20) and Thika, Kenya (n=17)) with BV underwent genital tract sampling of transcriptome (RNAseq) at enrollment (Visit 1) and one month (Visit 3) after completing 7 days of oral metronidazole.

first: Joyce

last: Sultan

first: Tao

first: Richard

last: Hunte

first: Sujatha

last: Srinivasan

first: Jessica

last: McWalters

first: Steven

middle: E

last: Bosinger

first: Tina

last: Fiedler

last: Atrio

first: Kerry

last: Murphy

first: Rebecca

last: Barnett

first: Laurie

last: Ray

first: Meighan

last: Krows

first: David

middle: N

last: Fredricks

first: Elizabeth

last: Irungu

first: Kenneth

last: Ngure

first: Nelly

last: Mugo

first: Jeanne

last: Marrazzo

first: Marla

last: Keller

first: Betsy

middle: C

last: Herold


title: RNA sequencing for the paired TNF-free and -treated intestinal enteroids

city: Seoul

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

summary: RNA sequencing was performed for the TNF-free and -treated enteroids derived from control (n=8 pairs) and Crohn's disease patients (n=8 pairs).

overall_design:
Examination of 32 RNA samples of human small intestinal organids (enteroids); TNF-free control enteroid: n=8, TNF-treated control enteroid: n=8, TNF-free enteroid derived from CD patients: n=8, TNF-treated enteroid derived from CD patients: n=8.
-------------------------------------------------
Authors state the following:
Our data were derived from material obtained from patients at Samsung Medical Center. Therefore, based on the hospital policy and Korean raw, it is difficult to upload law data because they contained the patient information.

first: Sung

first: Chansu

last: Lee


title: Involvement of SIRT1-regulated transcription profiles in prostate cancer

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: In order to understand the mechanism associated with SIRT1-mediated development of prostate cancer progression, we conducted RNA-sequencing analysis in SIRT1 suppressed hormone sensitive prostate cancer cells (LNCaP) under conditions of androgen sufficiency, deprivation, androgen stimulation or AR suppression.

overall_design: Hormone-sensitive LNCaP cells transduced with MOI of 10 lentiviral particles carrying shRNA against non-targeted control (NTC) or SIRT1 (shSIRT1 or 10) were selected with 1 μg/ml puromycin. Stable knockdown (KD) clones were cultured and maintained in culture medium in the presence of 0.5 μg/ml puromycin. To identify SIRT1 target genes in LNCaP cells, LNCaP-NTC and SIRT1 KD (shSIRT1) cells were cultured in androgen supplemented conditions (FBS-supplemented medium). To identify SIRT1 target genes involved in cancer progression, LNCaP-NTC and SIRT1 KD (10) cells were subjected to androgen deprived condition (charcol-stripped serum (CSS)-supplemented medium for 24 hours following 48 hours in FBS-supplemented medium. Cells were then cultured in CSS-supplemented medium with vehicle control (VC), 1 nM Dihydrotestosterone stimulation (D) in the absence or presence of 10 µM Enzalutamide treatment (DE) for 24 hours. Total RNA prepared from cells follwoing treatment was used in RNA-Seq analysis using Illumina Illumina HiSeq 3000Sequencing System.

first: Shih-Bo

last: Huang

first: Diesh

last: Thapa

first: Zhao

last: Lai

first: Hung-I

middle: H

first: Addanki

last: Kumar


title: Gene profiling for B cells and B cells from pDC coculture system in response to R848 stimulation

city: Taipei

first: Ya-Ju

last: Yu

address: 5F ,No 1, Sec 1, Jen-Ai Rd

country: Taiwan

institute: National Taiwan University College of Medicine Graduate Institute of Immunology

summary: Transcriptomic analysis revealed that IFN-I and Mapk pp38 signaing were found to be critical for the pDC-enhanced TLR-mediated B cell responses.

overall_design: Examination of 2 biological duplicated samples from BR (with R848) and BPR (B cells from pDC R848 coculture system).

first: Hsin-Hsiang

first: Ya-Ru

first: Chien-Kuo


title: H3K4 trimethylation is required for postnatal pancreatic endocrine cell functional maturation

city: Vancouver

first: Brad

last: Hoffman

state: BC

country: Canada

institute: University of British Columbia

summary: During pancreas development, endocrine progenitors differentiate into the islet-cell subtypes, which undergo further functional maturation in postnatal islet development. In islet b-cells, genes involved in glucose-stimulated insulin secretion are activated and glucose exposure increases the insulin response as b-cells mature. Here, we investigated the role of H3K4 trimethylation in endocrine cell differentiation and functional maturation by disrupting TrxG complex histone methyltransferase activity in mouse endocrine progenitors. In the embryo, genetic inactivation of TrxG component Dpy30 in NEUROG3+ cells did not affect the number of endocrine progenitors or endocrine cell differentiation. H3K4 trimethylation was progressively lost in postnatal islets and the mice displayed elevated non-fasting and fasting glycemia, as well as impaired glucose tolerance by postnatal day 24. Although postnatal endocrine cell proportions were equivalent to controls, islet RNA-sequencing revealed a downregulation of genes involved in glucose-stimulated insulin secretion and an upregulation of immature b-cell genes. Comparison of histone modification enrichment profiles in NEUROG3+ endocrine progenitors and mature islets suggested that genes downregulated by loss of H3K4 trimethylation more frequently acquire active histone modifications during maturation. Taken together, these findings suggest that H3K4 trimethylation is required for the activation of genes involved in the functional maturation of pancreatic islet endocrine cells.

overall_design: RNA-sequencing of postnatal day 24 control and Dpy30 knockout islets, including 3 biological replicates

first: Stephanie

middle: A

last: Campbell

first: Jocelyn

last: Bégin

first: Cassandra

last: McDonald

first: Ben

last: Vanderkruk

first: Tabea

last: Stephan

middle: G


title: Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: We describe the role of the cellular transcription factor DUX4 in the regulation of herpesviral gene expression.

overall_design: RNA-sequencing was performed from HSV-1 infected 293T cells with and without DUX4 knockout and ChIP-seq. from primary human foreskin fibroblasts infected with HSV-1 and controls,

last: Walter

first: Vedran

last: Franke

first: Nir

last: Drayman

first: Savaş

last: Tay

first: Markus

last: Landthaler

first: Altuna

last: Akalin

first: Armin

last: Ensser

first: Florian

last: Full


title: Bariatric surgery reduces obesity associated breast cancer and enhances response to immunotherapy [Mammary Fat Pad RNA-seq]

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

summary: Patients undergoing bariatric surgery are protected from subsequent breast cancer risk. It is unknown whether weight loss alone or surgery-specific alterations mediate risk reduction. We examined breast cancer in a pre-clinical model of diet induced obesity (DIO) followed by vertical sleeve gastrectomy (VSG) or dietary weight loss. DIO exacerbated tumor progression compared to lean controls, while VSG-induced weight loss reversed this exacerbation. However, dietary interventions were more effective than VSG despite similar reductions in weight and adiposity, potentially due to elevated immunosuppression after VSG. In tumor bearing mice, anti-PD-L1 immunotherapy after VSG improved anti-tumor immunity and potently impaired tumor progression. Thus, weight loss before tumor onset was protective regardless of intervention. Importantly, immunotherapy specifically improved outcomes in VSG.

overall_design: RNA-seq data from contralateral uninjected 4th mammary fat pad in orthotopically injected E0771 breast cancer bearing mice. Female C57BL/6J mice were weaned onto low fat diet (LFD) to remain lean or onto obesogenic high fat diet (HFD) to become obese. After 16 weeks on diet, HFD fed mice displayed marked obesity (Diet Induced Obesity, DIO). DIO mice then underwent surgical or dietary weight loss interventions. 5 Mouse cohorts: 1) Mice were that were lean mice fed low fat diet (LFD), 2) DIO mice fed obesogenic high fat diet (HFD), or mice that lost weight in 3 ways: 4) formerly obese mice receiving bariatric surgery (Vertical sleeve gastrectomy), 5) formerly obese mice with diet switch (DS) from HFD to LFD, or 6) formerly obese mice with caloric restriction (CR) to match weight loss in VSG cohort. All mice not receiving VSG had a sham surgery as a control.  E0771 syngeneic breast cancer cells were orthotopically implanted into the 4th mammary fat pad two weeks following surgical or dietary weight loss interventions, when weight loss was stabilized.

first: Joseph

middle: F

last: Pierre

first: David

last: Hayes

first: Laura

last: Sipe


title: RNA-Seq of CD8+ T cell subsets during LCMV infection [RNA-seq_D8_Brd4_KO]

first: Ananda

last: Goldrath

summary: Brd4 deficient and WT GP33-tetramer+ cells were sorted from spleens on D8 of LCMV infection. Tamoxifen was administered on days 5-7 of infection to induce to deletion of Brd4. KLRG1hiCD127lo TE, KLRG1loCD127lo EEC, and KLRG1loCD127hi MP cells were sorted for RNAseq analysis.

overall_design: 18 samples, 2 replicates. P14 cells Day 8 LCMV infection CD8+ T cell subsets.

first: J

middle: J

last: Milner

first: A

middle: W


title: RNA-Seq of CD8+ T cell subsets during LCMV infection [RNA-seq_D8_JQ1]

summary: LCMV infected mice were treated with JQ1 or vehicle on days 5-7 of infection. On day 8 of infection, KLRG1hiCD127lo TE, KLRG1loCD127lo EEC, and KLRG1loCD127hi MP cells were sorted for RNAseq analysis.

overall_design: 30 samples, 2 replicates. P14 cells Day 8 LCMV infection CD8+ T cell subsets.


title: RNA-Seq of CD8+ T cell subsets during LCMV infection [RNA-seq_D5_JQ1]

summary: P14 cells were transferred to naïve mice subsequently infected with LCMV. Mice were treated with JQ1 or vehicle on days 1-4 of infection. On day 5 of infection KLRG1loCD127lo EEC were sorted for RNAseq analysis. In a separate experiment, P14 cells were transduced with shBrd4a or shBrd4b and mixed with shCtrl transduced P14 cells, and then transferred into naïve mice subsequently infected with LCMV. On day 5 post-infection, transduced EEC were sorted for RNAseq.

overall_design: 12 samples, 2 replicates. P14 cells Day 5 LCMV infection CD8+ T cell subsets.


title: Genome-wide maps of chromatin state in gastric cancer with malignant ascites [ChIP-seq]

city: Tokyo

first: Yosuke

last: Tanaka

address: 5-1-1, tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

summary: Gastric cancer is one of the leading causes of cancer mortality worldwide, and peritoneal metastasis is a hallmark of incurable advanced gastric cancer. The identification of molecular vulnerability for such conditions is imperative to improve the prognosis of gastric cancer. Here, we comprehensively analysed cancer cells purified from malignant ascitic fluid samples and their corresponding cell lines from 98 patients, through whole-genome sequencing, whole transcriptome sequencing, methylation analyses, and genome-wide enhancer analyses.

overall_design: Examination of histone modifications in 44 gastric cancer cell lines.


title: Bromodomain protein BRD4 directs and sustains CD8 T cell differentiation during infection

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

overall_design: Refer to individual Series


title: RNA sequence of gastric cancer with malignant ascites [RNA-seq]

overall_design: Transcript analyses of purified tumour cells and cell lines of gastric cancer with malignant ascites.


title: Bulk RNA-sequencing in Ldlr-/- peritoneal macrophages treated with LPS

city: New Haven

first: Alberto

last: Canfrán-Duque

state: CT

address: 10 Amistad

department: Comparative Medicine

institute: Yale University

summary: Here we study the effect of LPS in the transcriptome of thioglycollate-elicited peritoneal macrophages isolated from Ldlr knock out mice

overall_design: mRNA profiles from thioglycollated-elicited peritoneal macrophages isoaltes from LDLR KO mice

first: Yajaira

last: Suárez

first: Carlos

last: Fernandez-Hernando


title: Bariatric surgery reduces obesity associated breast cancer and enhances response to immunotherapy [Tumor - breast cancer RNA-seq]

overall_design: RNA-seq data from bulk tumors (orthotopically injected E0771 breast cancer). Female C57BL/6J mice were weaned onto low fat diet (LFD) to remain lean or onto obesogenic high fat diet (HFD) to become obese. After 16 weeks on diet, HFD fed mice displayed marked obesity (Diet Induced Obesity, DIO). DIO mice then underwent surgical or dietary weight loss interventions. 5 Mouse cohorts: 1) Mice were that were lean mice fed low fat diet (LFD), 2) DIO mice fed obesogenic high fat diet (HFD), or mice that lost weight in 3 ways: 4) formerly obese mice receiving bariatric surgery (Vertical sleeve gastrectomy), 5) formerly obese mice with diet switch (DS) from HFD to LFD, or 6) formerly obese mice with caloric restriction (CR) to match weight loss in VSG cohort. All mice not receiving VSG had a sham surgery as a control.  E0771 syngeneic breast cancer cells were orthotopically implanted into the 4th mammary fat pad two weeks following surgical or dietary weight loss interventions, when weight loss was stabilized.

middle: M


title: Methylation profiling in gastric cancer with malignant ascites.

overall_design: Examination of DNA methylation patterns in 44 gastric cancer cell lines.


title: Study on Salt Tolerance Mechanism via  Illumina-based RNA-seq in Chrysanthemum Roots

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: The samples were respectively from three replicates of the salt stress treatment and the control, then we obtained six cDNA libraries. In total, 983,827 transcripts and 469,059 unigenes were constructed. We got a total of 75,070 differentially expressed genes (DEGs), of which 48,965 were up-regulated and the other 26,105 were down regulated under the salt treatment.

overall_design: We used the chrysanthemum “jinba” as the main material and the young seedling was breed for 30 days under the circumstance of 23±2℃, photoperiod of 16 hours, respectively moisty of 75%. During the period, the sample was watering controlled for 2 days and mildly salt stressed by salt water with a concentration of 100mM while the controlling sample is watered by purified water. The samples were collected from the root of white seedlings after 24 hours from processing. roots mRNA profiles of the development were generated by deep sequencing, in  triplicate, using Illumina HiSeq.

first: Qian

last: Zhao


title: ATAC-seq of mESC treated with doxorubicin

city: Salt Lake City

first: Edward

middle: John

last: Grow

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

institute: University of Utah

summary: E14 mESC were treated with doxorubicin

overall_design: mESC were treated with 1uM doxorubicin or vehicle control for 6 or 12 hours


title: ChIP seq of mESC treated with doxorubicin

summary: mESC were treated with doxorubicin and then histone modifications or p53 binding sites were analyzed

overall_design: mESC were treated with doxorubicin 1uM or vehicle for 6 hours, washed out for 6 hours, then crosslinked with 1% formaldehyde at RT for 10 min, quenched with 0.125M glycine for 10 min, then snap frozen in liq N2. ChIP was performed as described in Rada-Iglesias, et al. Nature 2010.


title: scRNAseq of embryoid bodies derived from control mESC or mESC pulsed with DUX expression

summary: scRNAseq identifies extra-embryonic cell type preference for DUX-pulsed mESC differentiating into embryoid bodies.

overall_design: two biological replicates each of day 9 EBs derived from control mESC or DUX-pulsed mESC

first: Jingtao

last: Guo

first: Bradley

last: Cairns


title: miR-148a controls metabolic programming and survival of mature CD19-negative plasma cells

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

institute: Universitätsklinikum Erlangen

summary: Long-lived antibody-secreting plasma cells are essential to establish humoral memory against pathogens. While a plasma cell gene signature has been established, elaborate key regulators remain enigmatic.The plasma cell signature microRNA miR-148a favors in vitro differentiation of plasmablasts by repressing the germinal center transcription factor Bach2 and pro-apoptotic BIM and PTEN. To determine whether miR-148a fine-tunescontrols the in vivo development of B cells into long-lived plasma cells, we established mice with a genomic, conditional and inducible deletion of miR-148a. The analysis of miR-148a-deficient mice revealed reduced serum Ig, decreased numbers of newly formed plasmablasts and a reduced CD19-negative, CD93-positive long-lived plasma cells compartment. RNASeq  and metabolic analysis showed an impaired glucose uptake and oxidative phosphorylation-based energy metabolism, altered abundance of homing receptors CXCR3 (increase) and CXCR4 (reduction) in miR-148a-deficient plasma cells. These findings establish the importance of miR-148a as a regulator of the differentiation and maintenance of late CD19-negative mature plasma cells by controlling their metabolism and retention in the bone marrow niche. clearly  undermine our model of miR-148a as a regulator of the maintenance of long-lived plasma cells.

overall_design: RNASeq of WT and miR148a(-/-) bone marrow plasma cells (TACI+ CD138+)

first: Sebastian

middle: R

last: Schulz

first: Katharina

last: Pracht


title: polyA-RNA-seq from mESC treated with doxorubicin

summary: control vs doxorubicin treated mESC WT, p53 KO mESC, and Dux KO mESC

overall_design: biological duplicate for WT, p53 KO, and Dux KO mESC, either treated with 1uM doxorubicin or vehicle control


title: ATACseq of FHSD iPSC control vs doxorubicin

summary: FSHD iPSC and TP53 KO FSHD iPSC were treated with vehicle or doxorubicin and then harvested for ATACseq

overall_design: two biological replicates of FSHD iPSC or TP53 KO iPSC treated with doxorubicin or vehicle control


title: A role for condensin in mediating transcriptional adaptation to environmental stimuli. [RNA-Seq]

city: London

first: Lucy

last: Lancaster

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

summary: The relationship between chromatin and transcription was investigated through condensin, a key regulator of higher order chromatin structure. We use rapid conditional condensin depletion in cell cycle-staged budding yeast S. cerevisiae cells to study condensin’s role in transcriptional regulation. We observe a large number of small gene expression changes close to condensin binding sites

overall_design: RNA-Seq analysis of Saccharomyces cerevisiae W303-1A strains transformed with promoter exchange of the YCG1 promoter with the MET3 promoter and auxin-inducible degron (IAA7) tagged YCG1, OsTIR1 ligase or control strains . 3 biological replicates for each sample type and condition are analysed. For each biological replicate, cells were grown overnight in YNB + CSM -methioninie media, synchronised from an OD600 of 0.2 in G1 for 1.5 hours, and transitioned into YPD medium (containting methionine) to shut off the MET3 promoter and indole-acetic acid (IAA, auxin) at a final concentration of 88μg/ml to degrade Ycg1. The control and degron strains were treated indentically. Cells was collected in a G1 arrest 2 hours after condensin depletion. The cells were released into fresh YPD medium containing auxin and nocodozole, and after 2 hours the metaphase arrested cells were collected. RNA was either retained as TOTAL RNA or polyA RNA purification to generate TOTAL and POLYA RNA-Seq libraries, respectively.

first: Harshil

last: Patel

first: Gavin

last: Kelly

first: Frank

last: Uhlmann


title: A role for condensin in mediating transcriptional adaptation to environmental stimuli.


title: SMRT-seq of WT vs Trp53 MZ-KO eggs and embryos

summary: Transcriptome of eggs and embryos from wt vs Trp53 KO

overall_design: 3 biological replicates of eggs, 6 biological replicates of early 2-cell and 6 biological replicates of late 2-cell


title: An Auts2-Containing RNA-Binding Complex Regulates Transcript Expression in Developing Cerebral Cortex

city: Seattle

first: Anthony

middle: Scott

last: Castanza

state: Washington

address: 1959 NE Pacific St Box 357470

department: Pathology

institute: University of Washington

summary: Molecular functions of the intellectual disability syndrome gene AUTS2 remain uncertain. Two mechanisms of Auts2 function have been proposed. One study found that Auts2 modifies Polycomb repressive complex 1 (PRC1) to activate transcription of target neurodevelopmental genes by recruiting EP300, a histone acetyltransferase. A second study found that cytoplasmic AUTS2 regulates cytoskeletal assembly through PREX1 to promote neurite outgrowth and migration. To further investigate Auts2 functions, we screened for AUTS2 interactors in cerebral cortex, and profiled changes of transcript expression in the developing cortex of Auts2 conditional mutant mice. AUTS2 immunoprecipitation experiments identified interactions with proteins involved in pre-mRNA processing, and mRNAs, including those encoding EP300 and PREX1, both bound by AUTS2-containing complexes and dysregulated in Auts2 mutant cortex. We propose that AUTS2 interacts with an RNA-binding complex that directly targets transcripts encoding Auts2 effectors. This mechanism provides a unifying model that accounts for previously disparate hypotheses of AUTS2 functions.

overall_design: 4 Biological replicates of P0.5 C57Bl6/J Frontal Cortex, 4 Bioloigical Replicates of Auts2 Exon 15 Flx/Flx Emx1-cre conditional knockout. 2 Biological Replicates of P0.5 C57BL6/J Cortex split into Auts2 C-terminal Antibody RIP-Seq, IgG IP and 10% Input (6 samples total in matched trios)

first: Robert

last: Hevner


title: A role for condensin in mediating transcriptional adaptation to environmental stimuli. [TT-Seq]

summary: The relationship between chromatin and transcription was investigated through condensin, a key regulator of higher order chromatin structure. We use rapid conditional condensin depletion in nocodozole arrested cells in budding yeast S. cerevisiae cells to study condensin’s role in transcriptional regulation. We use TT-Chemseq to assess global RNA levels through a S. pombe spike-in, and found that condensin depletion leads to upregulation of global transcription. We also found transcriptional changes in response to environmental stimuli are subdued by condensin depletion.

overall_design: RNA-Seq analysis of Saccharomyces cerevisiae W303-1A strains transformed with promoter exchange of the YCG1 promoter with the MET3 promoter, auxin-inducible degron (IAA7) tagged YCG1 with OsTIR1 ligase, or control strains . 3 biological replicates for each sample type and condition are analysed. For each biological replicate, cells were grown overnight in YNB + CSM -methioninie medium, synchronised from an OD600 of 0.2 in G1 for 2 hours then released into fresh YNB + CSM -methionine medium containing nocodozole for 1.5 hours to achieve a metaphase arrest. Methionine was added at a final concentration of 133μg/ml to shut off the MET3 promoter and indole-acetic acid (IAA, auxin) at a final concentration of 88μg/ml to degrade Ycg1. 4-TU was added to the samples at a final concentration of 5mM for 5 minutes before collection from the control and degron strains with and without methionine and auxin treatment. A sample from each strain which had undergone auxin and methionine treatment  was then heat shocked for 15minutes at 37°C for 15 minutes, followed by a 5 minute 4-TU pulse before collection. Total RNA was collected for nascent RNA isolation. RNA was also obtained from 4-TU pulsed S. pombe for the spike-in.


title: Developmental partitioning of SYK and ZAP70 prevents autoimmunity and cancer

city: POITIERS

first: Mickaël

last: MARTIN

address: 2 rue de la Milétrie

department: Internal Medicine

country: France

institute: Poitiers University Hospital

summary: Even though SYK and ZAP70 kinases share high sequence homology and serve analogous functions, their expression in B and T cells is strictly segregated throughout evolution. Here, we identified aberrant ZAP70 expression as a common feature in a broad range of B cell malignancies. We validated SYK as the kinase that sets the thresholds for negative selection of autoreactive and premalignant clones. When aberrantly expressed in B cells, ZAP70 competes with SYK at the BCR signalosome and redirects SYK from negative selection to tonic PI3K signaling, thereby promoting B cell survival. In genetic mouse models for B-ALL and B-CLL, conditional expression of Zap70 accelerated disease onset, while genetic deletion impaired malignant transformation. Inducible activation of Zap70 during B cell development compromised negative selection of autoreactive B cells, resulting in pervasive autoantibody production. Strict segregation of the two kinases is critical for normal B cell selection and represents a central safeguard against the development of autoimmune disease and B cell malignancies.

overall_design:
Serum of 10-month-old Zap70Mb1-Cre mice (overexpressing ZAP70) and littermate controls was harvested for comparison of IgM and IgG autoreactivity scores against a panel of 94 autoantigens.
Please note that each gpr file contains raw data for multiple samples as indicated in the corresponding sample description field and is linked to the Series records.
2nd antibody 1-532 = IgG
2nd antibody 2-635 = IgM

first: Quan-Zhen

last: Li

first: Chandra

last: Mohan

first: Ignacio

last: Sanz

first: Asiya

last: Chida

first: Christopher

last: Richardson


title: jaw-D;pTCP4::mTCP4:GR_Cycloheximide + Dexamethasone microarray

status: Public on May 20 2021

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: 9-day-old jaw-D;pTCP4::mTCP4:GR treated with Cycloheximide (CHX, control) and the combination of Cycloheximide and Dexamethasone (CHX DEX, treated).

overall_design: Agilent Microarray Gene Expression 8X60K-Arabidopsis thaliana (AMADID: 376611).

first: Krishna

last: Reddy Challa

first: Utpal

last: Nath


title: Targeted RNA sequencing of archived giant cell arteritis temporal artery biopsies reveals viral signatures

city: Burlington

first: Seth

last: Frietze

state: Vermont

address: 106 Carrigan Drive

department: Biomedical and Health Sciences

institute: University of Vermont

summary: Formalin-fixed, paraffin-embedded (FFPE) temporal artery sections from GCA subjects were stained for VZV antigen. Samples testing positive (VZV+) and negative (VZV-) from both GCA and control subjects without GCA were analyzed by targeted RNA sequencing of the whole-human transcriptome (BioSpyder TempO-Seq™).

overall_design: Transcriptomic analysis of temporal arteries from GCA subjects stained positively for VZV antigen (VZV+; n = 20),  stained negatively for VZV antigen (VZV-, n = 20), normal non-GCA subjects that stained positive for VZV antigen (GCA-, VZV+; n = 11) and normal non-GCA subjects that stained negative for VZV antigen (GCA-,  VZV- n = 20) were analyzed.

first: Andrew

last: Buback

first: Michael

last: Mariani


title: Epigenomic analysis of human neural cells

city: München

first: Daniel

last: Lam

address: Ismaninger Straße 22

institute: Technical University Munich

summary: To understand regulatory function in human neural differentiation, we performed ATAC-seq in human induced pluripotent stem cells (iPSC), in vitro-differentiated neural progenitor cells (NPC) and ganglionic eminence-like (GE) cells, as well as commercially available neural stem cells, GABAergic neurons, and glutamatergic neurons. We also performed circular chromosome conformation capture (4C)-seq on these cells.

overall_design: 1-2 replicates per cell type.

middle: D

first: Ana

last: Nikolic

first: Chen

last: Zhao

first: Nazanin

last: Mirza-Schreiber

first: Wojciech

last: Krężel

first: Juliane

last: Winkelmann


title: A follicular regulatory innate lymphoid cell population impairs interactions between germinal center Tfh and B cells

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Here we show a newly identified human Innate Lymphoid Cell population present in the follicles of tonsils and lymph nodes termed follicular regulatory ILCs (ILCFR). ILCFR have a distinct phenotype and transcriptional program when compared to other defined ILCs. Surprisingly, ILCFR inhibit the ability of follicular helper T (Tfh) cells to provide B cell help. The localization of ILCFR to the germinal centers suggests these cells may interfere with germinal center B cell (GC-B) and germinal center Tfh cell (GC-Tfh) interactions through the production of transforming growth factor beta (TGF-b). Intriguingly, under conditions of impaired GC-Tfh-GC-B cell interactions, such as human immunodeficiency virus (HIV) infection, the frequency of these cells is increased. Overall, we predict a role for ILCFR in regulating GC-Tfh-GC-B cell interactions and propose they expand in chronic inflammatory conditions.

overall_design: 7 individual human tonsil samples of 7 different cell poulations were collected for each tonsil

first: Margaret

last: O'Connor

first: Roshell

last: Muir

first: Marita

last: Chakhtoura

last: Fang

first: Eirini

last: Moysi

first: Susan

last: Moir

first: Alison

last: Carey

first: Alyssa

last: Terk

first: Carmen

last: Nichols

first: Talibah

last: Metcalf

first: Costas

last: Petrovas

first: Virginie

last: Tardif

first: Elias

last: Haddad


title: General Anesthetics Induce Epigenetic Alterations in Germ Cells that Result in Autism-like Behaviors

city: Atlanta

first: Hsiao-Lin

middle: V.

last: Wang

address: 615 Michael Street,, Whitehead Biomedical Research Building, Room 355,

department: School of Medicine, Department of Human Genetics

institute: Emory University

summary: One in 54 children in the U.S. is diagnosed with Autism Spectrum Disorder (ASD). However, no one genetic mutation can fully explain the neuropathogenesis of ASD. Given the highly heritable nature of ASD, epigenetic alterations may be the missing link in understanding ASD. Human and animal studies have shown that exposure of the developing brain to anesthetic agents can trigger neurodegeneration and neurobehavioral abnormalities but the effect of general anesthetics on the germ line have not been explored in detail. The gametes carry inherited epigenetic information and they are extremely vulnerable to environmental factors when they undergo epigenetic reprogramming in utero. To understand the inheritable impact of general anesthetics, we exposed pregnant mice to sevoflurane when the germ cells of the embryo undergo epigenetic reprogramming and examined the exposed males and their offspring. We found that 30-40% of the F2 and F3 animals, which were not directly exposed to sevoflurane, exhibit ASD-like behaviors. We performed ATAC-seq in the sperm of F1 animals that give rise to the autistic F2 animals and in sperm of the autistic F2 animals, and found more than 2,000 differential accessible sites. Some of these sites are maintained in the sperm of F2 and F3 animals and are located in the regulatory regions of ASD-associated genes, including Cacna1e and Arid1b. These observations suggest that epimutations caused by exposing germ cells to general anesthetics can lead to ASD in the offspring, and this effect can be transmitted through the male germline inter and trans-generationally.

overall_design: Identifying sevoflurance induced alteration of transcription factors in sperm

middle: V

first: Victor

last: Corces