title: 6486

description:
HumanMethylation450 BeadChip - standard protocol
6229068071_R02C02

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: monocytes

tag: network life stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 6632

status: Public on Sep 03 2015

type: genomic

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

country: USA

institute: Emory University

description:
HumanMethylation450 BeadChip - standard protocol
6229068071_R04C02

hyb_protocol: Standard Illumina protocol, HumanMethylation450

scan_protocol: Standard Illumina protocol, BeadStudio

data_processing: beta-values (non-normalized, background subtracted), BeadStudio

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole Blood

extract_protocol: Invitrogen Puregene Genomic DNA kit

tag: Sex

value: Male

tag: age

tag: childhood sexual/physical abuse moderate to extreme

value: Yes

tag: treatment for depression

tag: treatment for bipolar disorder

value: No

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: cumulative life stress

tag: personal life stress

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index

tag: tissue

value: whole Blood

tag: race/ethnicity

value: African American


title: 6241

description:
HumanMethylation450 BeadChip - standard protocol
6229068071_R04C01

label_protocol: Standard Illumina protocol, HumanMethylation450

tag: Sex

value: Female

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: monocytes

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 6492

description:
HumanMethylation450 BeadChip - standard protocol
6229068071_R03C02

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: network life stress


title: 6228

description:
HumanMethylation450 BeadChip - standard protocol
6229068071_R02C01

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: posttraumatic stress disorder symptom scale total score


title: 6216

description:
HumanMethylation450 BeadChip - standard protocol
6229068071_R01C01

tag: Sex

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: monocytes

tag: childhood trauma questionnaire total score

tag: tissue

tag: race/ethnicity


title: 9757

description:
HumanMethylation450 BeadChip - standard protocol
6229068071_R01C02

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: beck depression inventory total score

tag: body mass index


title: 6044

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R02C02

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress

tag: posttraumatic stress disorder symptom scale total score


title: 6538

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R05C02

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: monocytes

tag: childhood trauma questionnaire total score

tag: tissue

tag: race/ethnicity


title: 6233

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R03C01

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: network life stress

tag: beck depression inventory total score

tag: body mass index


title: 6267

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R04C02

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: dna methylation-predicted age

tag: cumulative life stress

tag: personal life stress

tag: current stress


title: 7009

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R06C01

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: monocytes

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6220

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R03C02

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: network life stress

tag: beck depression inventory total score

tag: body mass index


title: 6846

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R04C01

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: monocytes

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: childhood trauma questionnaire total score


title: 7005

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R05C01

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 5965

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R02C01

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: monocytes

tag: cumulative life stress

tag: network life stress

tag: beck depression inventory total score

tag: body mass index


title: 5949

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R01C01

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: personal life stress

tag: current stress

tag: childhood trauma questionnaire total score


title: 7082

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R06C02

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6019

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R01C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: monocytes

tag: cumulative life stress

tag: network life stress

tag: beck depression inventory total score

tag: body mass index


title: 6297

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R05C01

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: childhood trauma questionnaire total score


title: 6324

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R06C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6152

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R03C01

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: monocytes

tag: personal life stress

tag: current stress


title: 6290

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R01C02

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: body mass index


title: 6121

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R02C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 6291

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R04C01

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6496

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R02C02

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: personal life stress

tag: current stress

tag: body mass index


title: 7052

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R05C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 6560

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R03C02

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 9603

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R06C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: granulocytes

tag: body mass index


title: 6577

description:
HumanMethylation450 BeadChip - standard protocol
6229068065_R06C02

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 7467

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R03C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: natural killer cells

tag: b cells

tag: monocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 9483

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R04C01

tag: treatment for depression

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: granulocytes

tag: body mass index


title: 6023

description:
HumanMethylation450 BeadChip - standard protocol
6229068064_R01C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for bipolar disorder

tag: treatment for anxiety disorder

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 8521

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R05C02

tag: treatment for depression

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: natural killer cells

tag: b cells

tag: monocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6624

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R01C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for bipolar disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: body mass index


title: 7454

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R02C01

tag: treatment for depression

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: natural killer cells

tag: b cells

tag: monocytes

tag: current stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 7427

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R02C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for bipolar disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: granulocytes

tag: cumulative life stress

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 8586

description:
HumanMethylation450 BeadChip - standard protocol
6164647077_R01C01

tag: treatment for depression

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: natural killer cells

tag: b cells

tag: monocytes

tag: network life stress

tag: personal life stress

tag: body mass index


title: 9501

description:
HumanMethylation450 BeadChip - standard protocol
6164647074_R04C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: granulocytes

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 7536

description:
HumanMethylation450 BeadChip - standard protocol
6164647074_R02C02

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 9350

description:
HumanMethylation450 BeadChip - standard protocol
6164647074_R03C01

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: natural killer cells

tag: b cells

tag: monocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress

tag: body mass index


title: 7795

description:
HumanMethylation450 BeadChip - standard protocol
6164647074_R04C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: granulocytes

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 7417

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R01C01

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: natural killer cells

tag: b cells

tag: monocytes

tag: network life stress

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 7372

description:
HumanMethylation450 BeadChip - standard protocol
6164647074_R01C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: body mass index


title: 7497

description:
HumanMethylation450 BeadChip - standard protocol
6164647074_R02C01

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes

tag: network life stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 7155

description:
HumanMethylation450 BeadChip - standard protocol
6164647074_R01C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 9321

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R05C01

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: body mass index


title: 9304

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R04C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes

tag: network life stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 9372

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R04C02

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cumulative life stress

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 7367

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R01C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes

tag: personal life stress

tag: body mass index


title: 7465

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R03C02

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: network life stress

tag: current stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 9589

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R05C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 7361

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R02C02

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: granulocytes

tag: cumulative life stress

tag: personal life stress

tag: body mass index


title: 7858

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R02C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: network life stress

tag: current stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score


title: 8962

description:
HumanMethylation450 BeadChip - standard protocol
6229068056_R03C01

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: granulocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 8993

description:
HumanMethylation450 BeadChip - standard protocol
6164647065_R02C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress


title: 9692

description:
HumanMethylation450 BeadChip - standard protocol
6164647065_R03C01

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score

tag: body mass index


title: 9489

description:
HumanMethylation450 BeadChip - standard protocol
6164647065_R03C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: cd8 t cells

tag: cd4 t cells

tag: granulocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 9762

description:
HumanMethylation450 BeadChip - standard protocol
6164647065_R05C02

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: natural killer cells

tag: b cells

tag: monocytes


title: 8497

description:
HumanMethylation450 BeadChip - standard protocol
6164647065_R01C01

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score

tag: body mass index


title: 7144

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R05C02

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for posttraumatic stress disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: cd8 t cells

tag: cd4 t cells

tag: granulocytes

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 7275

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R06C02

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: natural killer cells

tag: b cells

tag: monocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress


title: 6633

description:
HumanMethylation450 BeadChip - standard protocol
6164647062_R04C01

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: cd8 t cells

tag: childhood trauma questionnaire total score

tag: body mass index


title: 6202

description:
HumanMethylation450 BeadChip - standard protocol
6164647062_R01C01

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: granulocytes

tag: beck depression inventory total score

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6283

description:
HumanMethylation450 BeadChip - standard protocol
6164647062_R03C01

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: monocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress


title: 7528

description:
HumanMethylation450 BeadChip - standard protocol
6164647062_R06C01

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: childhood trauma questionnaire total score

tag: body mass index


title: 6791

description:
HumanMethylation450 BeadChip - standard protocol
6164647062_R05C01

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes

tag: beck depression inventory total score

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6413

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R04C02

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress


title: 6114

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R04C01

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: childhood trauma questionnaire total score

tag: body mass index


title: 6302

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R03C02

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes

tag: beck depression inventory total score

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6054

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R02C02

tag: Sex

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress


title: 5996

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R02C01

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: childhood trauma questionnaire total score

tag: body mass index


title: 6564

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R05C02

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes

tag: beck depression inventory total score

tag: posttraumatic stress disorder symptom scale total score

tag: tissue

tag: race/ethnicity


title: 6801

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R06C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: current stress


title: 7262

description:
HumanMethylation450 BeadChip - standard protocol
6164647065_R01C02

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score

tag: body mass index


title: 5915

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R01C02

tag: Sex

tag: age

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cumulative life stress

tag: tissue

tag: race/ethnicity


title: 5881

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R01C01

tag: childhood sexual/physical abuse moderate to extreme

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: network life stress

tag: personal life stress

tag: current stress

tag: posttraumatic stress disorder symptom scale total score


title: 9403

description:
HumanMethylation450 BeadChip - standard protocol
6164647065_R02C02

tag: Sex

tag: age

tag: treatment for depression

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: monocytes

tag: granulocytes

tag: childhood trauma questionnaire total score

tag: beck depression inventory total score

tag: body mass index


title: 6569

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R05C01

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: network life stress

tag: tissue

tag: race/ethnicity


title: 6517

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R04C01

tag: Sex

tag: age

tag: treatment for depression

tag: monocytes

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: posttraumatic stress disorder symptom scale total score


title: 6327

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R01C02

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: granulocytes

tag: childhood trauma questionnaire total score

tag: body mass index


title: 6183

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R02C01

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: network life stress

tag: beck depression inventory total score

tag: tissue


title: 6394

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R02C02

tag: Sex

tag: age

tag: treatment for depression

tag: monocytes

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: race/ethnicity


title: 6264

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R03C01

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: granulocytes

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index


title: 6534

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R03C02

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: network life stress

tag: beck depression inventory total score

tag: tissue


title: 7055

description:
HumanMethylation450 BeadChip - standard protocol
6164647067_R01C02

tag: Sex

tag: age

tag: treatment for depression

tag: monocytes

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: race/ethnicity


title: 6053

description:
HumanMethylation450 BeadChip - standard protocol
6164647051_R01C01

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: granulocytes

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index


title: 7422

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R06C01

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: network life stress

tag: beck depression inventory total score

tag: tissue


title: 6676

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R04C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: monocytes

tag: granulocytes

tag: cumulative life stress

tag: personal life stress

tag: current stress

tag: race/ethnicity


title: 6731

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R05C02

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index


title: 7108

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R05C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: monocytes

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: tissue


title: 6631

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R03C02

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: personal life stress

tag: current stress

tag: beck depression inventory total score

tag: race/ethnicity


title: 6707

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R04C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: b cells

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index


title: 6798

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R06C02

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: monocytes

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: tissue


title: 6285

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R03C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: b cells

tag: beck depression inventory total score

tag: race/ethnicity


title: 6402

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R02C02

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: dna methylation-predicted age

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index


title: 6163

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R02C01

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: monocytes

tag: granulocytes

tag: network life stress


title: 6094

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R01C02

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: tissue


title: 6088

description:
HumanMethylation450 BeadChip - standard protocol
6164647041_R01C01

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: b cells

tag: current stress

tag: beck depression inventory total score

tag: race/ethnicity


title: MINO H3K27ac

status: Public on Aug 04 2015

type: SRA

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
Paired-end sequencing of H3K27ac ChIP and an unenriched chromatin control library was performed on a HiSeq 2500 or NextSeq for all primary lymphoma samples and for 8 cell lines, with read lengths of 36 bp + 25 bp or 42 bp + 42 bp. Single-end sequencing was used for other samples.
Reads were aligned to hg19 using BWA.
The resulting alignment files were then filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq density tracks were generated with ‘igvtools count’ and visualized with IGV.
Genome_build: hg19
Supplementary_files_format_and_content: TDF density files were generated by igvtools

source_name: MINO H3K27ac

growth_protocol: Cell lines were grown in IMDM + 20% FCS (Oci-Ly-7 and Oci-Ly-1) or RPMI + 20% FCS (all others)

extract_protocol:
For histone modification and transcription factor ChIP-Seq in cell lines, 10-20 million cells were crosslinked in growth media + 1% formaldehyde for 10 minutes at 37 C, quenched for 5 minutes with 125 mM glycine, washed twice in cold PBS with protease inhibitors (complete PI, Roche), and stored at -80 C. Pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted  at 3000g , resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes, sonicated to an average fragment size of 200-400 bp on a Branson sonifier, and cleared of debris by centrifugation. Samples were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 0.25% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4 C overnight with 2-5 ug of the appropriate antibody. Antigen-antibody complexes were collected with protein G Dynabeads (Life technologies) for 4 hours at 4 C, and sequentially washed with RIPA buffer (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 140 Mm NaCl), RIPA/High salt (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 360 mM NaCl), LiCl Wash Buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.0), and TE Buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Beads were resuspended in Low SDS ChIP elution buffer (10mM Tris-HCl pH 8.0, 0.5M EDTA, 300mM NaCl, 0.1% SDS, 5mM DTT) and incubated for 6 hours at 65 C to elute DNA and reverse crosslinking. Samples were treated with RNAase for 30 minutes and proteinase K for 2 hours at 37 C. ChIP DNA was then purified from supernatants with AMPure beads (Beckman-Coulter). Input DNA was prepared in parallel by adding unenriched, diluted chromatin directly into the elution / reverse crosslinking step. For primary lymphoma samples, tumor cellularity from the frozen block was confirmed by H&E frozen section by a board-certified hematopathologist (RR), and the block was trimmed as needed to remove low tumor cellularity regions. 25 micron sections were then cut to a total of ~50 mg of tissue for each ChIP-Seq chromatin prep. Frozen sections were resuspended and dissociated in PBS + PI + 10 mM Na butyrate, formaldehyde was added to 1%, and crosslinking and quenching were performed as above. Subsequent steps were identical to those performed in cell lines except that 1) the cytoplasmic lysis step was omitted, and 2) following lysis in SDS lysis buffer, the sample was diluted 1:2 to 1:5 with ChIP dilution buffer prior to sonication, and to a final dilution of 1:10 afterwards. Prior to immunoprecipitation, DNA was quantified from sonicated chromatin, and an equivalent of 2-5 million cells was used per ChIP.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated to barcoded illumina adaptors (Quick T4 DNA ligase, NEB). Each reaction was followed by clean-up with AMPure beads (Beckman-Coulter). Ligation products were amplified by PCR for 14-18 cycles with illumina primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection or gel purification (E-Gel SizeSelect 2%, Life technologies).

treatment_protocol: See individual samples

tag: material type

value: Cell line

tag: transgene

tag: treatment

tag: chip antibody

value: H3K27ac (39133, Active Motif)


title: OCI-LY-7 H3K27ac

source_name: OCI-LY-7 H3K27ac


title: REC-1 H3K27ac

source_name: REC-1 H3K27ac


title: DOHH2 H3K27ac

source_name: DOHH2 H3K27ac


title: KARPAS-422 H3K27ac

source_name: KARPAS-422 H3K27ac


title: JEKO-1 H3K27ac

source_name: JEKO-1 H3K27ac


title: ChIP SPI1/PU.1

status: Public on Jun 23 2015

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description:
chromatin IP (ChIP-seq)
C20F8ACXX_3_3792

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the hg18 genome assembly (see characteristics) BWA/ELAND
Peaks were called using MACS2 on settings: p value = 10-6
Genome_build: All ChIP-seq tracks were mapped to genome build HG18
Supplementary_files_format_and_content: wig files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps

growth_protocol: TSU-1621-MT cells were cultured in RPMI 1640 supplemented with 10% FCS, 10 ng/ml of G-CSF and incubated at 37 °C and 5% CO2 (Shikami et al., 1999).

extract_protocol:
Chromatin was sonicated and used for ChIP seq using specific antibodies. RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and  total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.
ChIP seq and RNA-seq libraries were prepared according to  Illumina's standard protocol.

treatment_protocol: ChIP-seq: ChIP seq experiments of ATRA treated cells were performed in TSU-1621-MT cells treated with 1 uM ATRA for 24 hours. For shRNA from RNA-seq experiments: TSU-1621-MT FUS-ERG cells were grown in the absence of tetracycline for induction of shRNA targeting FUS-ERG. shRNA expression was induced in TSU-1621-MT using dox.

tag: cell line

tag: antibody target

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: RNA-seq control shRNA

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the hg18 genome assembly  BWA/ELAND
Peaks were called using MACS2 on settings: p value = 10-6
Genome_build: All ChIP-seq tracks were mapped to genome build HG18
Supplementary_files_format_and_content: wig files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps

molecule: total RNA

source_name: TSU-1621-MT_RNA-seq control shRNA

extract_protocol:
Chromatin was sonicated and used for ChIP seq using specific antibodies.
RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and  total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.
ChIP seq and RNA-seq libraries were prepared according to  Illumina's standard protocol.

treatment_protocol:
ChIP-seq: ChIP seq experiments of ATRA treated cells were performed in TSU-1621-MT cells treated with 1 uM ATRA for 24 hours.
For shRNA from RNA-seq experiments: TSU-1621-MT FUS-ERG cells were grown in the absence of tetracycline for induction of shRNA targeting FUS-ERG. shRNA expression was induced in TSU-1621-MT using dox.

tag: treated with

value: control shRNA


title: RNA-seq shRNA FUS-ERG

source_name: TSU-1621-MT_RNA-seq shRNA FUS-ERG

value: shRNA FUS-ERG


title: GRANTA-519 H3K27ac

source_name: GRANTA-519 H3K27ac


title: ChIP TAL1/SCL

source_name: TSU-1621-MT_ChIP TAL1/SCL


title: RNA-seq control_B

source_name: TSU-1621-MT_RNA-seq control


title: ChIP LYL1

source_name: TSU-1621-MT_ChIP LYL1


title: ChIP RUNX1

source_name: TSU-1621-MT_ChIP RUNX1

value: Abcam


title: RNA-seq control_A


title: ChIP CTD of RNA polymerase II ATRA

source_name: TSU-1621-MT_ChIP CTD of RNA polymerase II ATRA

value: 1 uM ATRA for 24 hrs

value: RNAPII

value: Diagenode


title: ChIP N-terminal FUS/TLS

source_name: TSU-1621-MT_ChIP N-terminal FUS/TLS

value: FUS

value: Bethyl


title: OCI-LY-1 H3K27ac

source_name: OCI-LY-1 H3K27ac


title: ChIP LMO2

source_name: TSU-1621-MT_ChIP LMO2


title: RNA-seq ATRA

source_name: TSU-1621-MT_RNA-seq ATRA


title: ChIP ERG 1/2/3 ATRA

source_name: TSU-1621-MT_ChIP ERG 1/2/3 ATRA

value: ERG


title: ChIP FLI-1

source_name: TSU-1621-MT_ChIP FLI-1


title: ChIP GATA2

source_name: TSU-1621-MT_ChIP GATA2


title: ChIP RXR

source_name: TSU-1621-MT_ChIP RXR

value: RXR


title: ChIP RAR alpha

source_name: TSU-1621-MT_ChIP RAR alpha

value: RAR


title: ChIP ERG 1/2/3

source_name: TSU-1621-MT_ChIP ERG 1/2/3


title: ChIP N-terminal FUS/TLS ATRA

source_name: TSU-1621-MT_ChIP N-terminal FUS/TLS ATRA


title: 7305

description:
HumanMethylation450 BeadChip - standard protocol
6229068094_R02C01

source_name: Whole Blood

tag: Sex

value: Male

tag: age

tag: childhood sexual/physical abuse moderate to extreme

value: No

tag: treatment for depression

tag: treatment for anxiety disorder

tag: kreek-mchugh-schluger-kellogg scale score for current alcohol use

tag: kreek-mchugh-schluger-kellogg scale score for current tobacco use

tag: kreek-mchugh-schluger-kellogg scale score for current cocaine use

tag: kreek-mchugh-schluger-kellogg scale score for current heroin use

tag: kreek-mchugh-schluger-kellogg scale score for current marijuana use

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: monocytes

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index

value: whole Blood


title: 6706

description:
HumanMethylation450 BeadChip - standard protocol
6229068094_R01C01

tag: Sex

value: Female

tag: age

tag: childhood sexual/physical abuse moderate to extreme

value: Yes

tag: treatment for depression

tag: treatment for bipolar disorder

tag: treatment for posttraumatic stress disorder

tag: treatment for anxiety disorder

tag: b cells

tag: current stress

tag: beck depression inventory total score

tag: tissue

tag: race/ethnicity

value: African American


title: nrde-4 transilencing

status: Public on Apr 01 2015

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using the fastX toolkit fastx_collapser module
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed to give only unique sequence, along with read count for each, the using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: Fasta header: id_number of reads

organism: Caenorhabditis elegans

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions and followed by an overnight precipitation at -20C using isopropanol and glycogen as a carrier.  For RIP, custom Anti HRDE-1 polyclonal antibody was generated by Genomic Antibody Technology(GAT) by SDIX (Newark USA) against amino acids 12-161 of HRDE-1.
Before library preparation, 1-5ug of total RNA was treated with 1ul of RNA polyphosphatase (Epicentre) for 30 minutes at 37C.  RNA was then extracted using Phenol/chloroform and precipitated overnight at -20C using Ethanol and Sodium Acetate.  Following this we followed the Illumina Truseq small RNA protocol according to the manufacturer's instructions

tag: genotype/variation

tag: developmental stage

value: adult

tag: transgenes

value: "operon" +GFP piRNA sensor

value: whole animal


title: nrde-3 trans-silencing

description: 5' polyphosphatase treated


title: drh-3 GFP sensor

description: 5' polyphosphatase treated

value: GFP piRNA sensor


title: nrde-1 trans-silencing

description: 5' polyphosphatase treated


title: trans-silenced operon

description: 5' polyphosphatase treated

value: WT


title: ChIP CTD of RNA polymerase II

source_name: TSU-1621-MT_ChIP CTD of RNA polymerase II

tag: cell line

tag: antibody target

value: RNAPII

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat. #


title: control siRNA 4h sample3

status: Public on Mar 26 2015

type: RNA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: gene expression data from N1E-115 cells

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized by RMA (oligo package from Bioconductor).

organism: Mus musculus

source_name: N1E-115 cells

label_protocol: 270ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Mouse N1E-115 cells (American Tissue Culture Collection) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 2% L-glutamine and 1% penicillin/streptomycin (all reagents from Sigma Aldrich). For differentiation, cells were starved overnight in Neurobasal medium (Invitrogen) with 2% L-glutamine and 1% penicillin/streptomycin. After starvation, cells were replated on 10 μg/ml laminin (Millipore)- coated coverlisps.

extract_protocol: Total RNA from whole cell preparations was isolated with the Nucleospin RNA II kit (Macherey-Nagel).

treatment_protocol: For KD cells were transfected with 80 nM either control or Hmgn5 siRNA (Dharmacon siRNA smartpool Plus)

tag: sirna

value: control siRNA

tag: differentiation time


title: hmgn5 siRNA 24h sample1

description: gene expression data from N1E-115 cells

value: hmgn5 siRNA


title: control siRNA 24h sample3

description: gene expression data from N1E-115 cells


title: 6590

description:
HumanMethylation450 BeadChip - standard protocol
6164647059_R05C01

tag: Sex

tag: age

tag: childhood sexual/physical abuse moderate to extreme

tag: treatment for depression

tag: treatment for bipolar disorder

tag: dna methylation-predicted age

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: monocytes

tag: granulocytes

tag: cumulative life stress

tag: network life stress

tag: personal life stress

tag: childhood trauma questionnaire total score

tag: posttraumatic stress disorder symptom scale total score

tag: body mass index


title: control siRNA 4h sample2

description: gene expression data from N1E-115 cells

tag: sirna

tag: differentiation time


title: hmgn5 siRNA 24h sample2

description: gene expression data from N1E-115 cells


title: hmgn5 siRNA 24h sample3

description: gene expression data from N1E-115 cells


title: control siRNA 24h sample2

description: gene expression data from N1E-115 cells


title: control siRNA 24h sample1

description: gene expression data from N1E-115 cells


title: control siRNA 4h sample1

description: gene expression data from N1E-115 cells


title: 1045.8wk.CD16

status: Public on Nov 21 2014

scan_protocol: BeadStudio

data_processing: non-normalized, background subtracted

tag: timepoint

value: Week 8

tag: celltype

tag: obesity

value: Obese


title: 1049.8wk.CD16


title: 1050.8wk.CD16


title: 1040.8wk.CD16

value: Normal Weight


title: 1039.8wk.WB

value: Whole Blood


title: 1038.BL.CD16

value: Baseline


title: 1039.BL.WB


title: 1038.8wk.WB


title: 1039.BL.CD16


title: 1047.8wk.CD16


title: 1039.8wk.CD16


title: 1031.BL.WB


title: 1038.BL.WB


title: 1031.BL.CD16


title: 1030.8wk.CD16


title: 1047.BL.CD16


title: 1038.8wk.CD16


title: 1050.BL.CD16


title: 1045.BL.CD16


title: 1031.8wk.WB


title: 1040.8wk.WB


title: 1030.8wk.WB


title: 1030.BL.WB


title: 1040.BL.WB


title: 1049.BL.CD16


title: 1040.BL.CD16


title: 1029.BL.CD16


title: 1029.BL.WB


title: 1029.8wk.WB


title: 1026.BL.WB


title: 1026.BL.CD16


title: 1025.8wk.CD16


title: 1029.8wk.CD16


title: 1018.BL.WB


title: 1008.8wk.WB


title: 1012.8wk.CD16


title: 1008.8wk.CD16


title: 1012.BL.CD16


title: 1008.BL.WB


title: Input_3xF_LIMB

status: Public on Nov 11 2014

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses.
Low-complexity reads were filtered out based on their dinucleotide entropy.
Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using cutom Perl script; Scores represent weighted number of reads in 100bp window

source_name: limb buds

growth_protocol:
Fore- and hindlimb buds, hearts and branchial arches of approximately 150 Hand2-3xFLAG embryos and 150 wild-type control embryos at E10.5 were collected in ice-cold PBS (samples 1 to 4). Fore- and hindlimb buds from 250 Hand2-3xFLAG embryos at E10.5 were similarly collected (samples 5 to 6).
Single nuclei suspensions were cross-linked for 5min with 1% formaldehyde and processed as described (Visel et al., 2009). The ChIP procedure was performed using established protocols with minor modifications (Kim et al. 2007, Lopez-Rios et al. 2012)

extract_protocol:
A modified ChIP protocol was used based on the protocols described in Kim et al. 2007 (PMID: 18265397) and Visel et al. 2009 (PMID: 19212405)
DNA library Prep Kit from New England Biolabs

tag: developmental stage

tag: antibody

value: mouse monoclonal anti-FLAG , M2 (Sigma, Cat.-No.:F1804)

tag: strain

value: NMRI

tag: genotype


title: 3xF_LIMB


title: 1017.BL.WB


title: 1017.BL.CD16


title: 1025.BL.CD16


title: 1004.BL.WB


title: Input_WT

source_name: limb bud, hearts, branchial arches

extract_protocol:
Fore- and hindlimb buds, hearts and branchial arches of approximately 150 Hand2-3xFLAG embryos and 150 wild-type control embryos at E10.5 were collected in ice-cold PBS. Single nuclei suspensions were cross-linked for 5min with 1% formaldehyde and processed as described (Visel et al., 2009). The ChIP procedure was performed using established protocols with minor modifications (Kim et al. 2007, Lopez-Rios et al. 2012)
Library was constructed using the DNA library Prep Kit (New England Biolabs). Following end repair and adaptor ligation, DNA fragments were size selected (200-250bp) by agarose gel electrophoresis and PCR amplified (18 cycles) using Illumina primers. After purification, samples were loaded on an Illumina flow cell for solid-phase amplification. SR50 sequencing of libraries was carried out on a HiSeq 2000 system (Illumina)

tag: genotype/variation

value: wild type


title: 1004.BL.CD16


title: 1017.8wk.WB


title: 1026.8wk.CD16


title: 1004.8wk.CD16


title: 1008.BL.CD16


title: 1012.BL.WB


title: posterior_limb

status: Public on Jun 19 2014

description: 4C PCR product

data_processing:
Only first 50bp from each 4C-seq read were analyzed using “4Cseqpipe” (Landan et al., 2012).
Briefly, sequenced reads were mapped to a pre-built database of restriction fragment locations and fragment end sequences, representing a reduced genome defined by the primary and secondary restriction enzymes.
Mapping takes into account fragment end uniqueness and mappability, and utilizes base-calling qualities to partially apportion reads according to mismatch probabilities.
Dense genomic profiles were created for four distinct classes of fragment ends by linear interpolation of mapped reads.
One interpolated profile was selected and the three other profiles were quantile-normalized to match its distribution. Resulting profiles were combined by direct summation, resulting in a coverage profile.
Finally, medians of normalized coverage, as well as 20th and 80th percentiles, were calculated for sliding windows ranging from 2kb to 50kb in size.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: ID.nearcis.norm.median.scales – Median of normalized contact intensity in 1kb genomic bins.  Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns:
Supplementary_files_format_and_content: column 1 – the starting coordinate of the 1kb bin
Supplementary_files_format_and_content: column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin
Supplementary_files_format_and_content: column 3 – the 80th percentile of values in the window
Supplementary_files_format_and_content: column 4 – the 20th percentile of values in the window
Supplementary_files_format_and_content: Column 5-145 – as columns 2-4, but with linearly increasing window size, going up to 50kb

source_name: Posterior Limb

growth_protocol: E11.5 mouse embryos were collected in ice cold 10% FCS in PBS.

extract_protocol:
A single cell suspension was achieved by digestion of the dissected tissues with 1mg/ml Collagenase D in HBSS at 37°C and gentle pippeting.
The procedure was performed as previously described (Simonis et al., Nature Methods, 2006; van de Werken et al., Methods in Enzymology, 2012). Briefly, dissociated cells were cross-linked with 2% formaldehyde for 10 min at room temperature in PBS containing 10%FC. After nuclei isolation, chromatin was digested with NlaIII as primary restriction enzyme and subsequently ligated under dilute conditions. After crosslink reversal,  DNA was purified and digested with the second restriction enzyme (DpnII). After a second re-ligation step the sample was purified and a 4C inverse PCR was performed using primers annealing to the viewpoint fragment-end of interest. Primers contained non-annealing dangles with Illumina adapter sequences, allowing immediate sequencing of purified PCR products.

treatment_protocol: Forelimbs from 20 embryos were split into posterior and anterior parts. Telencephalic vesicles were processed in parallel as a control tissue

tag: tissue

value: Posterior Limb

tag: 1st restriction enzyme

value: NlaIII

tag: 2nd restriction enzyme

value: DpnII

tag: viewpoint

value: Ptch1 promoter – chr13:63669139


title: anterior_limb

description: 4C PCR product

source_name: Anterior Limb

value: Anterior Limb


title: telencephalon

description: 4C PCR product

source_name: Telencephalon

value: Telencephalon


title: 1017.8wk.CD16


title: 1018.8wk.CD16


title: ChIP_Tead2_biological rep2

status: Public on Mar 12 2014

source_name: Py2T breast cancer cells

growth_protocol: Py2T cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with glutamine, penicillin, streptomycin and 10% FCS (Sigma-Aldrich)

extract_protocol:
Cross-linked chromatin was sonicated to achieve an average fragment size of 500 bp. 150 ug of Chromatin and 5 ug of anti-Tead2 antibody were used for ChIP.
The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina’s instructions and sequenced on the Genome Analyzer 2 following the manufacturer’s protocols.

treatment_protocol: Py2T cells were treated with TGFβ for 5 days (2ng/ml)

tag: cell line

value: Py2T, breast cancer cells

tag: chip antibody

value: Tead2 (affinity purified, polyclonal rabbit anti-Tead2 antibody (amino acids 16-32)


title: ChIP_Tead2_biological rep1


title: 3xF

value: mouse monoclonal anti-FLAG (M2) (Sigma,F1804)


title: 1003.BL.CD16


title: Py2T 5 days TGFβ, biological rep.1

description: Gene expression data from Py2T cells treated with TGFβ for 5 days(2ng/ml)

source_name: Py2T breast cancer cells treated with TGFβ for 5 days(2ng/ml)

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

extract_protocol: RNA was extracted using Rneasy kit (Qiagen)

treatment_protocol: Py2T cells were either kept untreated or treated with TGFβ for 5 days (2ng/ml)

tag: treatment

value: 5 days TGFβ (2ng/ml)


title: Patient_CBFb ChIP-Seq

status: Public on Sep 09 2013

description: chromatin IP (ChIP-seq)

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the hg18 or hg19 genome assembly (see characteristics) using ELAND/BWA
Peaks were called using MACS 1.3.3 on settings:mfold =8, tsize=32, p value = e-6
Genome_build: hg18
Supplementary_files_format_and_content: wig or bedgraph files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps

source_name: Patient AML cells

growth_protocol: ME-1 cells were cultured in normal cell culture containing 10% serum. U937 cells were cultured in tet free culture media for maintenance.

extract_protocol:
Chromatin was sonicated and used for ChIP seq using specific antibodies (avialable on suplementry table).
Libraries were prepared according to Illumina's standard protocol.

treatment_protocol: U937 CBFβ-MYH11 cells were maintained in the presence of tetracyclin and grown in the absence of tetracycline for induction of CBFβ-MYH11. shRNA expression was induced in  ME-1 using dox.

tag: cell type

value: Patient AML cells

tag: antibody target

value: CBFB

tag: antibody company

value: Diagenode

tag: antibody catalogue number


title: U937CM, CBFb_uninduced ChIP-Seq

description: chromatin IP (ChIP-seq)

source_name: U937CM cell line (leukemic)

value: leukemic cell line

value: Tet (1 mM) containing medium


title: Py2T untreated, biological rep.2

description: Gene expression data from Py2T cells


title: 1018.8wk.WB

tag: timepoint

value: Week 8

tag: celltype

value: Whole Blood

tag: obesity

value: Normal Weight


title: ME-1, H3K9K14ac ChIP-Seq

description: chromatin IP (ChIP-seq)

source_name: ME-1 cell line (leukemic)


title: 1003.8wk.CD16

value: Obese


title: ME-1, PU.1 ChIP-Seq

description: chromatin IP (ChIP-seq)

value: Santa Cruz


title: ME-1 RNA-Seq

description: RNA-seq

source_name: ME-1 (leukemic)

extract_protocol:
RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and  total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.
Libraries were prepared according to Illumina's standard protocol.


title: ME-1, ERG ChIP-Seq

description: chromatin IP (ChIP-seq)

value: ERG


title: 1026.8wk.WB


title: 1031.8wk.CD16


title: 1004.8wk.WB


title: Patient_MYH11 ChIP-Seq

description: chromatin IP (ChIP-seq)

value: Novus


title: 1030.BL.CD16

value: Baseline


title: Input_3xF

tag: developmental stage

tag: strain

value: NMRI

tag: antibody


title: Input_Tead2_biological rep2

value: Py2T, breast cancer cells


title: ME-1_scrambled RNA-Seq

description: RNA-seq

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the hg18 or hg19 genome assembly (see characteristics) using ELAND/BWA
Peaks were called using MACS 1.3.3 on settings:mfold =8, tsize=32, p value = e-6
Genome_build: hg19
Supplementary_files_format_and_content: wig or bedgraph files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps

value: 3 days Dox (1 mM)


title: ME-1, ELF1 ChIP-Seq

description: chromatin IP (ChIP-seq)


title: ME-1_Knockdown RNA-Seq

description: RNA-seq


title: U937CM, MYH11_induced ChIP-Seq

description: chromatin IP (ChIP-seq)

value: 3 days Tet free medium


title: U937CM, CBFb_induced ChIP-Seq

description: chromatin IP (ChIP-seq)


title: ME-1, TAL1 ChIP-Seq

description: chromatin IP (ChIP-seq)


title: ME-1, FLI1 ChIP-Seq

description: chromatin IP (ChIP-seq)


title: ME-1, HDAC1 ChIP-Seq

description: chromatin IP (ChIP-seq)

value: Abcam


title: ME-1, p300 ChIP-Seq

description: chromatin IP (ChIP-seq)


title: 1018.BL.CD16


title: ME-1, GATA2 ChIP-Seq

description: chromatin IP (ChIP-seq)


title: ME-1, HEB ChIP-Seq

description: chromatin IP (ChIP-seq)

value: HEB


title: 1012.8wk.WB


title: ME-1, CBFb_SC ChIP-Seq

description: chromatin IP (ChIP-seq)

value: CBFB

value: Diagenode


title: ME-1, MYH11_A1379 ChIP-Seq

description: chromatin IP (ChIP-seq)

value: leukemic cell line


title: ME-1, CBFb_A1329 ChIP-Seq

description: chromatin IP (ChIP-seq)


title: ME-1, MYH11_Novous ChIP-Seq

description: chromatin IP (ChIP-seq)


title: U937CM_induced RNA-Seq

description: RNA-seq


title: U937CM_control RNA-Seq

description: RNA-seq

value: Tet (1 mM) containing medium


title: WT

tag: genotype/variation

value: wild type

value: mouse monoclonal anti-FLAG (M2) (Sigma,F1804)


title: ME-1, RNAPII ChIP-Seq

description: chromatin IP (ChIP-seq)

value: RNAPII


title: ME-1, TBP ChIP-Seq

description: chromatin IP (ChIP-seq)

value: TBP


title: ME-1, RUNX1 ChIP-Seq

description: chromatin IP (ChIP-seq)


title: USC_ChipSeq_HepG2_TCF7L2_UCDavis

status: Public on Aug 30 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: liver carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment description

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit monoclonal

tag: antibody targetdescription

value: TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following:Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4

tag: antibody vendorname

value: Cell Signaling Technology

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate

tag: replicate description

value: tier 1


title: Py2T 5 days TGFβ, biological rep.2

tag: cell line

value: Py2T, breast cancer cells

tag: treatment

value: 5 days TGFβ (2ng/ml)


title: Py2T untreated, biological rep.1

description: Gene expression data from Py2T cells


title: Input_Tead2_biological rep1

tag: chip antibody