title: Control ChIP-seq from SK-N-SH (ENCLB565HMH)

description:
https://www.encodeproject.org/experiments/ENCSR566WAB/
***************
biological replicate number: 1
technical replicate number: 1
description: 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.
experiment encode accession: ENCSR566WAB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB565HMH
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting ARNTL treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: cell line

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ARNTL.

value: child

value: 4 year

value: Michael Snyder, Stanford

value: ENCBS873CMF at ENCODE; https://www.encodeproject.org/ENCBS873CMF/


title: Control ChIP-seq from left ventricle myocardium inferior (ENCLB535MIV)

status: Public on May 23 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR608IVH/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR608IVH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB535MIV
size range: 200-600

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male adult (60 years) left ventricle myocardium inferior tissue

value: left ventricle myocardium inferior

value: tissue

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 60 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Shin Lin

tag: health state

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

tag: link

value: ENCBS267RXN at ENCODE; https://www.encodeproject.org/ENCBS267RXN/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: Control ChIP-seq from left ventricle myocardium inferior (ENCLB708NCT)

description:
https://www.encodeproject.org/experiments/ENCSR608IVH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR608IVH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB708NCT
size range: 200-600

value: ENCBS672IKS at ENCODE; https://www.encodeproject.org/ENCBS672IKS/


title: Control ChIP-seq from left ventricle myocardium inferior (ENCLB312FJK)

description:
https://www.encodeproject.org/experiments/ENCSR608IVH/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR608IVH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB312FJK
size range: 200-600


title: Control ChIP-seq from left ventricle myocardium inferior (ENCLB693UBC)

description:
https://www.encodeproject.org/experiments/ENCSR608IVH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR608IVH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB693UBC
size range: 200-600


title: Histone ChIP-seq from middle frontal area 46 (ENCLB242QMB)

description:
https://www.encodeproject.org/experiments/ENCSR039TGB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR039TGB
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR086BNR
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB242QMB
size range: 200-600

source_name: Homo sapiens male adult (78 years) middle frontal area 46 tissue

tag: antibody

value: middle frontal area 46

value: 78 year

value: Rush University

value: ENCBS375CUK at ENCODE; https://www.encodeproject.org/ENCBS375CUK/

value: Derived from ENCODE donor ENCDO623FPG; https://www.encodeproject.org/ENCDO623FPG/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB450TFB)

description:
https://www.encodeproject.org/experiments/ENCSR039TGB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR039TGB
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR086BNR
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB450TFB
size range: 200-600


title: Control ChIP-seq from SK-N-SH (ENCLB419OJF)

description:
https://www.encodeproject.org/experiments/ENCSR540RTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR540RTZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB419OJF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting BNC2 treated with 6uM all-trans-retinoic acid for 48 hours

tag: line

value: SK-N-SH

value: cell line

value: female

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS028RXB at ENCODE; https://www.encodeproject.org/ENCBS028RXB/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: Histone ChIP-seq from adrenal gland (ENCLB829TUD)

description:
https://www.encodeproject.org/experiments/ENCSR038KST/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR038KST
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB829TUD
size range: 200-600

source_name: Homo sapiens female adult (41 years) adrenal gland tissue

value: adrenal gland

value: tissue

value: adult

value: 41 year

value: Bradley Bernstein, Broad

value: Shin Lin

value: DM:no; HTN:no; CAD:no

value: ENCBS648AMG at ENCODE; https://www.encodeproject.org/ENCBS648AMG/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: Histone ChIP-seq from adrenal gland (ENCLB696TTZ)

description:
https://www.encodeproject.org/experiments/ENCSR038KST/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR038KST
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB696TTZ
size range: 200-600

value: female


title: Histone ChIP-seq from adrenal gland (ENCLB884QTJ)

description:
https://www.encodeproject.org/experiments/ENCSR038KST/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR038KST
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB884QTJ
size range: 200-600

source_name: Homo sapiens female adult (41 years) adrenal gland tissue, preserved by flash-freezing

value: Yiing Lin, MD, PhD

value: ENCBS491ORA at ENCODE; https://www.encodeproject.org/ENCBS491ORA/


title: Control ChIP-seq from foreskin keratinocyte (ENCLB032WTC)

description:
https://www.encodeproject.org/experiments/ENCSR528SMB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq control (input DNA) on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR528SMB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB032WTC

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 5.5 days

value: foreskin keratinocyte

value: primary cell

tag: description

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: Healthy

tag: passage number

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: Histone ChIP-seq from adrenal gland (ENCLB536GQC)

description:
https://www.encodeproject.org/experiments/ENCSR038KST/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR038KST
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB536GQC
size range: 200-600

value: adrenal gland

value: tissue

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: DM:no; HTN:no; CAD:no


title: Histone ChIP-seq from middle frontal area 46 (ENCLB980JSH)

description:
https://www.encodeproject.org/experiments/ENCSR055JGU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR055JGU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR617ONQ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB980JSH
size range: 200-600

source_name: Homo sapiens female adult (81 years) middle frontal area 46 tissue with Alzheimer's disease

value: middle frontal area 46

value: female

value: 81 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS554ZGD at ENCODE; https://www.encodeproject.org/ENCBS554ZGD/

value: Derived from ENCODE donor ENCDO097MEH; https://www.encodeproject.org/ENCDO097MEH/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB387IWV)

description:
https://www.encodeproject.org/experiments/ENCSR589CXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR589CXZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR258GSA
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB387IWV
size range: 200-600

source_name: Homo sapiens female adult (84 years) middle frontal area 46 tissue

value: 84 year

value: ENCBS224FBK at ENCODE; https://www.encodeproject.org/ENCBS224FBK/

value: Derived from ENCODE donor ENCDO461DJY; https://www.encodeproject.org/ENCDO461DJY/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB103KMK)

description:
https://www.encodeproject.org/experiments/ENCSR053KIS/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR053KIS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR153LYY
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB103KMK
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with mild cognitive impairment

value: 90 or above year

value: ENCBS835TES at ENCODE; https://www.encodeproject.org/ENCBS835TES/

value: Derived from ENCODE donor ENCDO672KST; https://www.encodeproject.org/ENCDO672KST/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB690VAE)

description:
https://www.encodeproject.org/experiments/ENCSR055JGU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR055JGU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR617ONQ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB690VAE
size range: 200-600

value: tissue

value: adult


title: TF ChIP-seq from endothelial cell (ENCLB781OKL)

description:
https://www.encodeproject.org/experiments/ENCSR031PXV/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on endothelial cell
experiment encode accession: ENCSR031PXV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR233WMP
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB781OKL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (53 years) endothelial in vitro differentiated cells, preserved by cryopreservation

extract_protocol: not provided

value: CTCF

value: endothelial cell

value: in vitro differentiated cells

value: PGP1 derived endothelial cells

value: male

value: 53 year

value: George Church

value: ENCBS239VAD at ENCODE; https://www.encodeproject.org/ENCBS239VAD/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB305QFP)

description:
https://www.encodeproject.org/experiments/ENCSR589CXZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR589CXZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR258GSA
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305QFP
size range: 200-600

value: middle frontal area 46

value: female

value: 84 year

value: Bradley Bernstein, Broad

value: Rush University


title: TF ChIP-seq from endothelial cell (ENCLB040CQJ)

description:
https://www.encodeproject.org/experiments/ENCSR031PXV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on endothelial cell
experiment encode accession: ENCSR031PXV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR233WMP
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB040CQJ
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from foreskin keratinocyte (ENCLB524RVV)

description:
https://www.encodeproject.org/experiments/ENCSR528SMB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq control (input DNA) on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR528SMB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB524RVV

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: Healthy

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: Histone ChIP-seq from pancreas (ENCLB031KCQ)

description:
https://www.encodeproject.org/experiments/ENCSR029SIG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on pancreas female child (16 years)
experiment encode accession: ENCSR029SIG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR067CHO
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB031KCQ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female child (16 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS375CIT at ENCODE; https://www.encodeproject.org/ENCBS375CIT/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: Histone ChIP-seq from pancreas (ENCLB710RHZ)

description:
https://www.encodeproject.org/experiments/ENCSR029SIG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on pancreas female child (16 years)
experiment encode accession: ENCSR029SIG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR067CHO
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB710RHZ
size range: 200-600

source_name: Homo sapiens female child (16 years) pancreas tissue

value: female

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS022HXP at ENCODE; https://www.encodeproject.org/ENCBS022HXP/


title: Histone ChIP-seq from testis (ENCLB020BIT)

description:
https://www.encodeproject.org/experiments/ENCSR503QSX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR503QSX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB020BIT
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) testis tissue

value: testis

value: male

value: adult

value: 37 year

value: Kristin Ardlie

value: ENCBS631HJF at ENCODE; https://www.encodeproject.org/ENCBS631HJF/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Histone ChIP-seq from pancreas (ENCLB731NWT)

description:
https://www.encodeproject.org/experiments/ENCSR029SIG/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac ChIP-seq on pancreas female child (16 years)
experiment encode accession: ENCSR029SIG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR067CHO
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB731NWT
size range: 200-600

value: pancreas

value: tissue

value: child

value: DM:no; HTN:no; CAD:no


title: Histone ChIP-seq from testis (ENCLB515APT)

description:
https://www.encodeproject.org/experiments/ENCSR503QSX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR503QSX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515APT
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from pancreas (ENCLB068AZR)

description:
https://www.encodeproject.org/experiments/ENCSR029SIG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on pancreas female child (16 years)
experiment encode accession: ENCSR029SIG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR067CHO
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB068AZR
fragmentation methods: sonication (generic)
size range: 200-600

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS375CIT at ENCODE; https://www.encodeproject.org/ENCBS375CIT/


title: Control ChIP-seq from middle frontal area 46 (ENCLB796VVF)

description:
https://www.encodeproject.org/experiments/ENCSR557HEX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR557HEX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB796VVF
size range: 200-600

source_name: Homo sapiens male adult (89 years) middle frontal area 46 tissue with mild cognitive impairment

value: middle frontal area 46

value: 89 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS273TDM at ENCODE; https://www.encodeproject.org/ENCBS273TDM/

value: Derived from ENCODE donor ENCDO697SWU; https://www.encodeproject.org/ENCDO697SWU/


title: Control ChIP-seq from middle frontal area 46 (ENCLB066FQA)

description:
https://www.encodeproject.org/experiments/ENCSR557HEX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR557HEX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB066FQA
size range: 200-600

value: male

value: adult


title: Histone ChIP-seq from pancreas (ENCLB303JBP)

description:
https://www.encodeproject.org/experiments/ENCSR571RCH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on pancreas tissue female adult (61 years)
experiment encode accession: ENCSR571RCH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR130HAG
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB303JBP
size range: 200-600

source_name: Homo sapiens female adult (61 years) pancreas tissue, preserved by flash-freezing

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: ENCBS297KRV at ENCODE; https://www.encodeproject.org/ENCBS297KRV/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB369DAC)

description:
https://www.encodeproject.org/experiments/ENCSR025KPY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR025KPY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR086BNR
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB369DAC
size range: 200-600

value: tissue

value: 78 year

value: ENCBS375CUK at ENCODE; https://www.encodeproject.org/ENCBS375CUK/

value: Derived from ENCODE donor ENCDO623FPG; https://www.encodeproject.org/ENCDO623FPG/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB528UHF)

description:
https://www.encodeproject.org/experiments/ENCSR025KPY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR025KPY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR086BNR
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB528UHF
size range: 200-600

value: middle frontal area 46


title: Histone ChIP-seq from middle frontal area 46 (ENCLB321WEM)

description:
https://www.encodeproject.org/experiments/ENCSR555HJT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR555HJT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR739QEI
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB321WEM
size range: 200-600

source_name: Homo sapiens male adult (87 years) middle frontal area 46 tissue

value: 87 year

value: ENCBS552HSQ at ENCODE; https://www.encodeproject.org/ENCBS552HSQ/

value: Derived from ENCODE donor ENCDO203ASI; https://www.encodeproject.org/ENCDO203ASI/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB102YSZ)

description:
https://www.encodeproject.org/experiments/ENCSR555HJT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR555HJT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR739QEI
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB102YSZ
size range: 200-600

value: Bradley Bernstein, Broad

value: Rush University


title: Histone ChIP-seq from middle frontal area 46 (ENCLB819UPY)

description:
https://www.encodeproject.org/experiments/ENCSR549BWF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR549BWF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR917XOL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB819UPY
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with Alzheimer's disease

value: 90 or above year

value: ENCBS837PKE at ENCODE; https://www.encodeproject.org/ENCBS837PKE/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB270XZL)

description:
https://www.encodeproject.org/experiments/ENCSR549BWF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR549BWF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR917XOL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB270XZL
size range: 200-600

value: female

value: adult


title: Histone ChIP-seq from middle frontal area 46 (ENCLB718CNE)

description:
https://www.encodeproject.org/experiments/ENCSR548QRE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR548QRE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR617ONQ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB718CNE
size range: 200-600

value: 81 year

value: ENCBS554ZGD at ENCODE; https://www.encodeproject.org/ENCBS554ZGD/

value: Derived from ENCODE donor ENCDO097MEH; https://www.encodeproject.org/ENCDO097MEH/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB676RBI)

description:
https://www.encodeproject.org/experiments/ENCSR548QRE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR548QRE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR617ONQ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB676RBI
size range: 200-600

value: tissue


title: Histone ChIP-seq from middle frontal area 46 (ENCLB134XLL)

description:
https://www.encodeproject.org/experiments/ENCSR538GXY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR538GXY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB134XLL
size range: 200-600

source_name: Homo sapiens female adult (87 years) middle frontal area 46 tissue with Alzheimer's disease, Cognitive impairment

value: ENCBS592YXK at ENCODE; https://www.encodeproject.org/ENCBS592YXK/

value: Derived from ENCODE donor ENCDO940VNT; https://www.encodeproject.org/ENCDO940VNT/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB092LEF)

description:
https://www.encodeproject.org/experiments/ENCSR022FAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR022FAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR518COE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB092LEF
size range: 200-600

source_name: Homo sapiens female adult (78 years) middle frontal area 46 tissue

value: middle frontal area 46

value: 78 year

value: ENCBS882DOK at ENCODE; https://www.encodeproject.org/ENCBS882DOK/

value: Derived from ENCODE donor ENCDO236YSH; https://www.encodeproject.org/ENCDO236YSH/


title: Histone ChIP-seq from uterus (ENCLB373MPJ)

description:
https://www.encodeproject.org/experiments/ENCSR839SAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR839SAN
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR859LXC
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB373MPJ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) uterus tissue

value: uterus

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS443NGH at ENCODE; https://www.encodeproject.org/ENCBS443NGH/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB691XAR)

description:
https://www.encodeproject.org/experiments/ENCSR022FAQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR022FAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR518COE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB691XAR
size range: 200-600

value: female

value: Rush University


title: Histone ChIP-seq from pancreas (ENCLB550HGZ)

description:
https://www.encodeproject.org/experiments/ENCSR571RCH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on pancreas tissue female adult (61 years)
experiment encode accession: ENCSR571RCH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR130HAG
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB550HGZ
size range: 200-600

value: pancreas

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS297KRV at ENCODE; https://www.encodeproject.org/ENCBS297KRV/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB341VEC)

description:
https://www.encodeproject.org/experiments/ENCSR538GXY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR538GXY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB341VEC
size range: 200-600

value: middle frontal area 46

value: tissue

value: 87 year

value: ENCBS592YXK at ENCODE; https://www.encodeproject.org/ENCBS592YXK/

value: Derived from ENCODE donor ENCDO940VNT; https://www.encodeproject.org/ENCDO940VNT/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB588VWH)

description:
https://www.encodeproject.org/experiments/ENCSR548QRE/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR548QRE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR617ONQ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB588VWH
size range: 200-600

value: 81 year

value: Bradley Bernstein, Broad

value: ENCBS554ZGD at ENCODE; https://www.encodeproject.org/ENCBS554ZGD/

value: Derived from ENCODE donor ENCDO097MEH; https://www.encodeproject.org/ENCDO097MEH/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB237WUT)

description:
https://www.encodeproject.org/experiments/ENCSR011BHU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR011BHU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR258GSA
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB237WUT
size range: 200-600

value: female

value: 84 year

value: Rush University

value: ENCBS224FBK at ENCODE; https://www.encodeproject.org/ENCBS224FBK/

value: Derived from ENCODE donor ENCDO461DJY; https://www.encodeproject.org/ENCDO461DJY/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB252XZO)

description:
https://www.encodeproject.org/experiments/ENCSR532STE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR532STE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR799VTP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB252XZO
size range: 200-600

source_name: Homo sapiens female adult (83 years) middle frontal area 46 tissue with mild cognitive impairment

value: adult

value: 83 year

value: ENCBS104CPK at ENCODE; https://www.encodeproject.org/ENCBS104CPK/

value: Derived from ENCODE donor ENCDO832DBZ; https://www.encodeproject.org/ENCDO832DBZ/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB432PCP)

description:
https://www.encodeproject.org/experiments/ENCSR011BHU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR011BHU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR258GSA
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB432PCP
size range: 200-600

value: middle frontal area 46

value: tissue


title: Histone ChIP-seq from middle frontal area 46 (ENCLB564VEV)

description:
https://www.encodeproject.org/experiments/ENCSR532STE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR532STE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR799VTP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB564VEV
size range: 200-600


title: Histone ChIP-seq from middle frontal area 46 (ENCLB790HXC)

description:
https://www.encodeproject.org/experiments/ENCSR524MPL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR524MPL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR613JAK
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790HXC
size range: 200-600

value: 90 or above year

value: ENCBS345MLG at ENCODE; https://www.encodeproject.org/ENCBS345MLG/

value: Derived from ENCODE donor ENCDO660TGP; https://www.encodeproject.org/ENCDO660TGP/


title: Control ChIP-seq from left lung (ENCLB791YXU)

description:
https://www.encodeproject.org/experiments/ENCSR519WCC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on left lung tissue female child (16 years)
experiment encode accession: ENCSR519WCC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB791YXU
size range: 200-600

source_name: Homo sapiens female child (16 years) left lung tissue

value: left lung

value: child

value: 16 year

value: Bradley Bernstein, Broad

value: Shin Lin

value: DM:no; HTN:no; CAD:no

value: ENCBS892NYC at ENCODE; https://www.encodeproject.org/ENCBS892NYC/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: TF ChIP-seq from adrenal gland (ENCLB035IAJ)

description:
https://www.encodeproject.org/experiments/ENCSR408ZEE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR408ZEE
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB035IAJ
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) adrenal gland tissue

value: CTCF

value: adrenal gland

value: EnTEX:Adrenal Gland

value: female

value: adult

value: 51 year

value: Kristin Ardlie

value: ENCBS458UEH at ENCODE; https://www.encodeproject.org/ENCBS458UEH/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: TF ChIP-seq from adrenal gland (ENCLB039DUD)

description:
https://www.encodeproject.org/experiments/ENCSR408ZEE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR408ZEE
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039DUD
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Histone ChIP-seq from uterus (ENCLB241BMA)

description:
https://www.encodeproject.org/experiments/ENCSR839SAN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR839SAN
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR859LXC
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB241BMA
fragmentation methods: sonication (generic)
size range: 200-600

value: uterus

value: ENCBS443NGH at ENCODE; https://www.encodeproject.org/ENCBS443NGH/


title: RS411 nascent RNA-seq MLL-AF4 siRNA rep3

city: Oxford

first: Thomas

last: Milne

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
Nascent RNA-seq in RS4;11 cells treated with non-targeting siRNA
RS411_MLL-AF4_siRNA_feature_counts.txt

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using Picard MarkDuplicates
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: Leukemia cell line (RS4;11)

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7765).

treatment_protocol: Cells were electroporated with non-targeting or MLL-AF4 targeting siRNA

tag: sirna

value: siMARS (Thomas et al 2005)

tag: cell type

value: B-cell line derived from adult ALL with t(4;11)(q21;q23) translocation


title: Histone ChIP-seq from stomach (ENCLB929FZJ)

description:
https://www.encodeproject.org/experiments/ENCSR819DOR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR819DOR
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB929FZJ
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) stomach tissue

value: stomach

value: Bradley Bernstein, Broad

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/


title: RS411 nascent RNA-seq MLL-AF4 siRNA rep2


title: RS411 nascent RNA-seq control rep1

value: siMM (Thomas et al 2005)


title: RS411 nascent RNA-seq control rep3


title: RS411 nascent RNA-seq MLL-AF4 siRNA rep1


title: Control ChIP-seq from middle frontal area 46 (ENCLB321GGH)

description:
https://www.encodeproject.org/experiments/ENCSR518COE/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR518COE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB321GGH
size range: 200-600

value: middle frontal area 46

value: 78 year

value: Rush University

value: ENCBS882DOK at ENCODE; https://www.encodeproject.org/ENCBS882DOK/

value: Derived from ENCODE donor ENCDO236YSH; https://www.encodeproject.org/ENCDO236YSH/


title: RS411 nascent RNA-seq control rep2


title: Histone ChIP-seq from middle frontal area 46 (ENCLB248MBX)

description:
https://www.encodeproject.org/experiments/ENCSR524MPL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR524MPL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR613JAK
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB248MBX
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with mild cognitive impairment

value: female

value: adult

value: 90 or above year

value: ENCBS345MLG at ENCODE; https://www.encodeproject.org/ENCBS345MLG/

value: Derived from ENCODE donor ENCDO660TGP; https://www.encodeproject.org/ENCDO660TGP/


title: HELA_EGF_PPP2R1A_rep3

city: Philadelphia

first: Sarah

middle: A

last: Welsh

state: PA

address: 3601 Spruce St

institute: Wistar Institute

description: PPP2R1A ChIP-seq was performed in HeLa cells treated with EGF

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment (ChIPseq): BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

growth_protocol: HeLa cells were maintained in DMEM high glucose media, supplemented with 10%(v/v) super calf serum (GEMcell) and 2 mM of L-glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei (Covaris S220), and protein-DNA complexes were isolated with antibody-conjugated Dynabeads
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Inc.)

treatment_protocol: HeLa cells were grown in 0.3% serum for 72hrs, then treated with 0.1ug/mL recombinant Epidermal Growth Factor (EGF) for 15min.

tag: cell line

value: HeLa

tag: treatment

value: EGF

tag: chip target

tag: antibody catalog #

value: Bethyl A300-962A


title: HELA_EGF_PP2CA

description: PP2CA ChIP-seq was performed in HeLa cells treated with EGF

value: Millipore Sigma Cat#05-421


title: Control ChIP-seq from left lung (ENCLB157RNR)

description:
https://www.encodeproject.org/experiments/ENCSR519WCC/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on left lung tissue female child (16 years)
experiment encode accession: ENCSR519WCC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB157RNR
size range: 200-600

value: left lung

value: tissue

tag: biosample encode accession

tag: Sex

tag: dev stage

value: child

value: 16 year

value: Bradley Bernstein, Broad

value: Shin Lin

value: DM:no; HTN:no; CAD:no

value: ENCBS892NYC at ENCODE; https://www.encodeproject.org/ENCBS892NYC/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: HELA_EGF_PPP2R1A_rep2


title: HELA_CTRL_PP2CA

description: PP2CA ChIP-seq was performed in untreated HeLa cells

value: untreated


title: HELA_CTRL_PPP2R1A_rep3

description: PPP2R1A ChIP-seq was performed in untreated HeLa cells


title: Control ChIP-seq from middle frontal area 46 (ENCLB571XMK)

description:
https://www.encodeproject.org/experiments/ENCSR518COE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR518COE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB571XMK
size range: 200-600

value: middle frontal area 46

value: female

value: adult

tag: age

value: 78 year

tag: lab

tag: source

value: Rush University

value: ENCBS882DOK at ENCODE; https://www.encodeproject.org/ENCBS882DOK/

value: Derived from ENCODE donor ENCDO236YSH; https://www.encodeproject.org/ENCDO236YSH/


title: HELA_EGF_POL2_rep2

description: RNAPII ChIP-seq was performed in HeLa cells treated with EGF

value: HeLa

value: EGF

value: RNAPII


title: TF ChIP-seq from stomach (ENCLB555OYJ)

description:
https://www.encodeproject.org/experiments/ENCSR361KVZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR361KVZ
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB555OYJ
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

value: CTCF

value: stomach

value: tissue

value: 51 year

value: Kristin Ardlie

tag: link

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from stomach (ENCLB324SYI)

description:
https://www.encodeproject.org/experiments/ENCSR819DOR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR819DOR
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB324SYI
fragmentation methods: sonication (generic)
size range: 200-600

value: Bradley Bernstein, Broad


title: HELA_CTRL_PPP2R1A_rep2

value: untreated

value: Bethyl A300-962A


title: Histone ChIP-seq from vagina (ENCLB286GKL)

description:
https://www.encodeproject.org/experiments/ENCSR346FVK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR346FVK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB286GKL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) vagina tissue

value: vagina

value: female

value: adult

value: ENCBS468YOF at ENCODE; https://www.encodeproject.org/ENCBS468YOF/


title: HELA_EGF_POL2

value: HeLa


title: HELA_CTRL_POL2_rep2

description: RNAPII ChIP-seq was performed in untreated HeLa cells


title: HELA_CTRL_PPP2R1A


title: HELA_EGF_INPUT

description: chromatin from HeLa cells treated with EGF

value: EGF

value: Input


title: Histone ChIP-seq from vagina (ENCLB358LCR)

description:
https://www.encodeproject.org/experiments/ENCSR346FVK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR346FVK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB358LCR
fragmentation methods: sonication (generic)
size range: 200-600


title: HELA_CTRL_POL2


title: THP1 Acute INTS6 Knockout

city: Melbourne

first: Stephin

middle: J

last: Vervoort

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Fastq files were aligned to a Hg19 or dm3 reference genome performed with Bowtie2 (v2.3.4.1) to generate SAM files
SAM files converted to BAM files using Samtools (v1.9) using view command. BAM files were sorted, indexed and potential PCR duplicates removed using rmdup function
bigWig files were generated from sorted, indexd BAM files using the Deeptools (v3.0.0) BamCoverage function (--normalize using CPM, --smoothLength 150 --binSize 50 -e 200 scaleFactor 1)
Average read density across defined genomic regions were defined using the Deeptools computeMatrix function and plotHeatmap function was used to generate chromatin occupancy heatmaps
Subread (v2.0.0) featureCounts function (-O -M -T 16 -F SAF) was used to count reads within TSS and gene body regions using bedtools (v2.27.1) slop function using UCSC Hg19 or dm3 chromosome sizes
Read density was calculated as RPKM in Rstudio (v3.6.1) using limma (v3.40.6) and edgeR (v.3.26.8) and visualized using ggplot2 (v3.3.1)
Genome_build: Hg19 or dm3
Supplementary_files_format_and_content: bigWig files of RNAPII, CDK9, INTS11, INTS6, BRD4 and RNAPII phospho-ser 2 occupancy across the genome in CPM

source_name: Acute myeloid leukemia cell line

growth_protocol: THP-1 cells were cultured in RPMI-1640 supplemented with 10-20 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at 37 degrees celciuus and 5 percent carbon dioxide. S2 cells were cultured in Schneider's Drosophila medium supplemented with 10 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at room temperature and atmospheric carbon dioxide

extract_protocol:
Cells were cross-linked with formaldehyde solution, nuclei were extracted and sonicated using a Covaris. Protein-bound chromatin was isolated using indicated antibody and decrosslinked DNA was isolated using the Zymogen ChIP DNA Clean and Concentrator Kit
ChIP-seq librarys were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) and 200 - 500 base pair fragments were selected using a Pippin Prep (1.5% agarose, Sage Science)

treatment_protocol: Cells were treated with DMSO (untreated control), CDK9i (AZ5576, 100nM or 170nM 2 hours) or DBK-1154 (10µM 2 hours 15 minutes)

value: THP-1 cell line

tag: chip antibody

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)

value: 60 hours post-electroporation with Cas9 and INTS6 targeting sgRNA


title: HELA_EGF_PPP2R1A


title: Histone ChIP-seq from thyroid gland (ENCLB276DDW)

description:
https://www.encodeproject.org/experiments/ENCSR309UVT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR309UVT
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR347VUG
encode release date: 2018-12-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB276DDW
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) thyroid gland tissue

value: thyroid gland

value: tissue

tag: description

value: 51 year

value: ENCBS541DMP at ENCODE; https://www.encodeproject.org/ENCBS541DMP/


title: Histone ChIP-seq from thyroid gland (ENCLB679OHI)

description:
https://www.encodeproject.org/experiments/ENCSR309UVT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR309UVT
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR347VUG
encode release date: 2018-12-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB679OHI
fragmentation methods: none
size range: 200-600

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: THP1 Acute Control

value: 60 hours post-electroporation with Cas9 and non-targeting sgRNA


title: THP1 Input Pooled

value: Pool for 60 hours post-electroporation with Cas9 and non-targeting or INTS6 targeting sgRNA


title: THP-1 DBK-1154 RNAPII CTD4H8

value: DBK-1154 10uM 2 hours 15 minutes


title: THP-1 CDK9i + DBK-1154 RNAPII CTD4H8

value: CDK9i (AZ5576) 170nM 2 hours + DBK-1154 10uM 2 hours 15 minutes


title: THP-1 DMSO RNAPII CTD4H8

value: DMSO (untreated control) 2 hours


title: TF ChIP-seq from stomach (ENCLB405UOM)

description:
https://www.encodeproject.org/experiments/ENCSR361KVZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR361KVZ
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB405UOM
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: stomach

value: female

value: adult

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/


title: THP-1 sgINTS6A DMSO RNAPII phospho-CTD Ser2

source_name: Acute myeloid leukemia cell line expressing Cas9 and INTS6 targeting sgRNA

value: THP-1 cell line

tag: genotype

value: RNA polymerase II subunit B1, phospho-CTD Ser-2, clone 3E10 (Millipore 04-1571-I)


title: THP-1 sgINTS6A CDK9i RNAPII phospho-CTD Ser2

value: expressing Cas9 and INTS6 targeting sgRNA

value: CDK9i (AZ5576) 170nM 2 hours


title: THP-1 sgSCR DMSO RNAPII phospho-CTD Ser2

source_name: Acute myeloid leukemia cell line expressing Cas9 and non-targeting (Scramble) sgRNA


title: Histone ChIP-seq from Peyer's patch (ENCLB553ANR)

description:
https://www.encodeproject.org/experiments/ENCSR249IKQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR249IKQ
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR773UBR
encode release date: 2019-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB553ANR
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 years) Peyer's patch tissue

value: Peyer's patch

value: tissue

value: EnTEX:Small Intestine - Terminal Ileum

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS654VYQ at ENCODE; https://www.encodeproject.org/ENCBS654VYQ/


title: THP-1 sgSCR CDK9i BRD4

value: expressing Cas9 and non-targeting (Scramble) sgRNA

value: BRD4 (Bethyl Laboratories, A301-985A)


title: Histone ChIP-seq from Peyer's patch (ENCLB734XIO)

description:
https://www.encodeproject.org/experiments/ENCSR249IKQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR249IKQ
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR773UBR
encode release date: 2019-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB734XIO
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: THP-1 sgSCR DMSO BRD4

value: DMSO (untreated control) 2 hours


title: THP-1 sgSCR CDK9i INTS6

value: DICE1 (INTS6) clone H-6 (Santa Cruz, sc-376524)


title: THP-1 sgSCR DMSO INTS6


title: THP-1 sgINTS6A DMSO CDK9

value: CDK9 (Cell Signaling Technologies, 2316)


title: THP-1 sgSCR DMSO INTS11

value: THP-1 cell line

value: INTS11 (Bethyl Laboratories, A301-274A)


title: THP-1 sgSCR DMSO CDK9


title: THP-1 sgINTS6A CDK9i CDK9

value: expressing Cas9 and INTS6 targeting sgRNA


title: THP-1 sgSCR CDK9i CDK9

value: CDK9i (AZ5576) 170nM 2 hours


title: THP-1 sgSCR CDK9i INTS11


title: THP-1 sgINTS6A CDK9i RNAPII CTD4H8

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)


title: THP-1 sgSCR CDK9i RNAPII CTD4H8


title: THP-1 sgINTS6 CDK9i 6 hours replicate 2

description:
5-T6-2
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv

data_processing:
library strategy: 4sU-seq
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Fastq files were aligned to a combined Hg19/dm3 genome performed with Bowtie2 (v2.3.4.1) to generate SAM filles
SAM files converted to BAM files using Samtools (v1.9) using view command. BAM files were sorted and indexed
For normalization of hg19 reads to Drosophila spike-in, reads mapping to Hg19 and dm3 genomes were calculated using Subread (v2.0.0) featureCounts function. A scale factor was determined by calculating the proportion of reads mapping to the dm3 genome relative to the combined Hg19/dm3 genome
bigWig files were generated from sorted, indexd BAM files using the Deeptools (v3.0.0) BamCoverage function (--normalize using CPM, --smoothLength 150 --binSize 50 -e 200) using the appropriate scaleFactor
Scaled bigWig files were visualized in IGV and analyzed using the Deeptools (v3.0.0) bigwigCompare function
Data was visualized in Rstudio using ggplot2 (v3.3.1), ggrepel (v3.3.1) and ggfortify (v0.4.10)
Genome_build: Hg19 / dm3
Supplementary_files_format_and_content: bigWig files of nascent RNA coverage in cpm across the genome; text files of featureCounts counts; text file of S2 normalized counts

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction and isopropanol precipitation. 4-thiouridine labelled RNA was isolated from total RNA of THP-1 (human) and S2 (Drosophila; 5 percent) cells following biotinylation with EZ-Link HPDP Biotin (ThermoFisher Scientific) and strepavidin µMACs enrichment (Miltenyi). Biotin-enriched 4-thiouridine labelled nascent RNA was isolated using the Qiagen RNAeasy MinElute kit.
RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB E7760S)

treatment_protocol: THP-1 cells were treated with DMSO for 6 hours (untreated control; CDK9i 0 hours) or CDK9i (AZ5576) 170nM for 2 hours and 6 hours; cells were labelled with 4-thiouridine during the final 30 minutes of CDK9i treatment. S2 cells were labelled with 4-thiouridine for 30 minutes.

value: CDK9i (AZ5576) 170nM for 6 hours, 500µM 4-thiouridine for final 30 minutes

tag: spike-in

value: Drosophila melanogaster spike-in


title: THP-1 CDK9i RNAPII CTD4H8


title: THP-1 sgINTS6 CDK9i 2 hours replicate 2

description:
5-T2-2
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv

value: CDK9i (AZ5576) 170nM for 2 hours, 500µM 4-thiouridine for final 30 minutes


title: THP-1 sgSCR DMSO RNAPII CTD4H8


title: TF ChIP-seq from heart left ventricle (ENCLB460ABR)

description:
https://www.encodeproject.org/experiments/ENCSR718SDR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR718SDR
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR178FVP
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460ABR
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) heart left ventricle tissue

value: CTCF

value: heart left ventricle

value: tissue

value: EnTEX:Heart - Left Ventricle

value: female

value: adult

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS684IAD at ENCODE; https://www.encodeproject.org/ENCBS684IAD/


title: THP-1 sgINTS6 CDK9i 6 hours replicate 1

description:
5-T6-1
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv

value: THP-1 cell line


title: TF ChIP-seq from heart left ventricle (ENCLB148OBL)

description:
https://www.encodeproject.org/experiments/ENCSR718SDR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR718SDR
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR178FVP
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB148OBL
fragmentation methods: none
size range: 200-600

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from upper lobe of left lung (ENCLB406UMM)

description:
https://www.encodeproject.org/experiments/ENCSR229GEL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR229GEL
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR774MLK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406UMM
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: male

value: 54 year

value: Kristin Ardlie

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: THP-1 sgINTS6 CDK9i 0 hours replicate 1

description:
5-T0-1
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv

value: expressing Cas9 and INTS6 targeting sgRNA

value: DMSO (untreated) for 6 hours, 500µM 4-thiouridine for final 30 minutes

value: Drosophila melanogaster spike-in


title: THP-1 sgINTS6 CDK9i 2 hours replicate 1

description:
5-T2-1
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv

value: CDK9i (AZ5576) 170nM for 2 hours, 500µM 4-thiouridine for final 30 minutes


title: THP-1 sgSCR CDK9i 6 hours replicate 2

description:
scr-T6-2
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv

value: expressing Cas9 and non-targeting (Scramble) sgRNA

value: CDK9i (AZ5576) 170nM for 6 hours, 500µM 4-thiouridine for final 30 minutes


title: THP-1 sgINTS6 CDK9i 0 hours replicate 2

description:
5-T0-2
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv


title: THP-1 sgSCR CDK9i RNAPII phospho-CTD Ser2

value: RNA polymerase II subunit B1, phospho-CTD Ser-2, clone 3E10 (Millipore 04-1571-I)

value: CDK9i (AZ5576) 170nM 2 hours


title: THP-1 sgSCR CDK9i 6 hours replicate 1

description:
scr-T6-1
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv


title: THP-1 sgSCR CDK9i 0 hours replicate 2

description:
scr-T0-2
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv


title: THP-1 sgSCR CDK9i 2 hours replicate 2

description:
scr-T2-1
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv


title: THP-1 sgSCR CDK9i 0 hours replicate 1

description:
scr-T0-1
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv


title: THP-1 sgSCR CDK9i 2 hours replicate 1

description:
scr-T2-2
featureCounts_output_hg19-dm3.txt
201202_4sUseq_SpikeIn_normalisedCounts.csv


title: THP-1 sgINTS6A DMSO RNAPII CTD4H8

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)

value: DMSO (untreated control) 2 hours


title: Histone ChIP-seq from upper lobe of left lung (ENCLB342XOO)

description:
https://www.encodeproject.org/experiments/ENCSR229GEL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR229GEL
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR774MLK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB342XOO
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: adult

value: Bradley Bernstein, Broad


title: HT-29 CDK9i + DBK-1154 replicate 2

description:
3RNA-HT-29-AZ-DBK-2_S35
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Sequencing reads were trimmed using cutadapt (v2.1) and aligned to the Hg19 or a combined Hg19/dm3 reference genome using HISAT 2 (v2.1.0)
Read counting across genomic regions was performed using the Subread (v2.0.0) featureCounts function and differential gene expression analysis was performed in Rstudio (v3.6.1) using Voom-Limma (v3.42.2)
Genome_build: Hg19 and dm3
Supplementary_files_format_and_content: Tag density files (TDF) of 3'UTR RNA coverage across the Hg19 genome;  text files of featureCounts counts; text file of normalized (voom) and normalized (voom and S2 spike-in) counts

source_name: Colorectal cancer cell line

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10-20 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at 37 degrees celciuus and 5 percent carbon dioxide

extract_protocol:
Cells were lysed in TriZol reagent and total DNAse-treated RNA isolated using the Zymogen RNA mini-prep kit. For HT-29 cells, total RNA (5 percent) from Drosophila S2 cells was spiked into each human RNA sample.
RNA libraries were prepared using the Lexogen QuantSeq 3'-mRNA Seq Library Prep kit (015)

treatment_protocol: THP-1 cells were treated with LPS (1µg/mL) over a time-course and HT-29 cells were treated with CDK9i (AZ5576, 170nM, 2 hours), DBK-1154 (10µM, 2 hours 15 minutes) or a combination of both

value: HT-29 cell line

value: CDK9i (AZ5576) 170nM 2 hours + DBK-1154 10µM 2 hours 15 minutes


title: HT-29 CDK9i replicate 2

description:
3RNA-HT-29-AZ5576-2_S32
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts


title: HT-29 DBK-1154 replicate 2

description:
3RNA-HT-29-DBK-1154-2_S29
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

value: DBK-1154 10µM 2 hours 15 minutes


title: HT-29 DBK-1154 replicate 1

description:
3RNA-HT-29-DBK-1154-1_S28
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts


title: HT-29 CDK9i + DBK-1154 replicate 1

description:
3RNA-HT-29-AZ-DBK-1_S34
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts


title: HT-29 CDK9i replicate 3

description:
3RNA-HT-29-AZ5576-3_S33
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts


title: TF ChIP-seq from thyroid gland (ENCLB538KNQ)

description:
https://www.encodeproject.org/experiments/ENCSR145HBC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR145HBC
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR347VUG
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB538KNQ
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: thyroid gland

value: female

value: 51 year

value: Kristin Ardlie

value: ENCBS541DMP at ENCODE; https://www.encodeproject.org/ENCBS541DMP/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: HT-29 DBK-1154 replicate 3

description:
3RNA-HT-29-DBK-1154-3_S30
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

value: Drosophila melanogaster spike-in


title: TF ChIP-seq from thyroid gland (ENCLB581FHR)

description:
https://www.encodeproject.org/experiments/ENCSR145HBC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR145HBC
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR347VUG
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB581FHR
fragmentation methods: none
size range: 200-600


title: HT-29 CDK9i replicate 1

description:
3RNA-HT-29-AZ5576-1_S31
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

value: CDK9i (AZ5576) 170nM 2 hours


title: THP-1 sgINTS6 LPS 8 hour replicate 1

description:
KO-LPS8h-1_S46
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: THP-1 cell line

value: expressing Cas9 and INTS6 targeting sgRNA

value: LPS 1µg/mL 8 hour


title: HT-29 DMSO replicate 2

description:
3RNA-HT-29-DMSO-2_S26
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

value: Untreated control


title: THP-1 sgINTS6 LPS 4 hour replicate 2

description:
KO-LPS4h-2_S50
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: LPS 1µg/mL 4 hour


title: HT-29 DMSO replicate 1

description:
3RNA-HT-29-DMSO-1_S25
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

value: HT-29 cell line


title: THP-1 sgINTS6 LPS 4 hour replicate 1

description:
KO-LPS4h-1_S45
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: THP-1 sgINTS6 LPS 8 hour replicate 2

description:
KO-LPS8h-2_S51
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: HT-29 CDK9i + DBK-1154 replicate 3

description:
3RNA-HT-29-AZ-DBK-3_S36
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

value: CDK9i (AZ5576) 170nM 2 hours + DBK-1154 10µM 2 hours 15 minutes


title: THP-1 sgINTS6 LPS 1 hour replicate 1

description:
KO-LPS1h-1_S43
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: LPS 1µg/mL 1 hour


title: THP-1 sgINTS6 LPS 2 hour replicate 2

description:
KO-LPS2h-2_S49
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: LPS 1µg/mL 2 hour


title: THP-1 sgINTS6 LPS 2 hour replicate 1

description:
KO-LPS2h-1_S44
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: THP-1 sgINTS6 untreated replicate 1

description:
KO-UT-1_S42
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: THP-1 sgINTS6 LPS 1 hour replicate 2

description:
KO-LPS1h-2_S48
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: THP-1 sgSCR LPS 8 hour replicate 2

description:
SCR-LPS8h-2_S41
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: expressing Cas9 and non-targeting (Scramble) sgRNA


title: THP-1 sgSCR LPS 8 hour replicate 1

description:
SCR-LPS8h-1_S36
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: THP-1 sgINTS6 untreated replicate 2

description:
KO-UT-2_S47
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: THP-1 sgSCR LPS 2 hour replicate 2

description:
SCR-LPS2h-2_S39
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: THP-1 sgSCR LPS 1 hour replicate 2

description:
SCR-LPS1h-2_S38
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt


title: Histone ChIP-seq from MCF-7 (ENCLB970FUJ)

description:
https://www.encodeproject.org/experiments/ENCSR610IYQ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR610IYQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB970FUJ
fragmentation methods: shearing (Covaris generic)
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

tag: line

value: cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: adult

value: female

tag: health state

value: breast cancer (adenocarcinoma)

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: TF ChIP-seq from vagina (ENCLB524RUQ)

description:
https://www.encodeproject.org/experiments/ENCSR614HHL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR614HHL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB524RUQ
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: vagina

value: tissue

value: 51 year

value: Kristin Ardlie

value: ENCBS468YOF at ENCODE; https://www.encodeproject.org/ENCBS468YOF/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: THP-1 sgSCR LPS 2 hour replicate 1

description:
SCR-LPS2h-1_S34
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

tag: cell line

value: THP-1 cell line

value: expressing Cas9 and non-targeting (Scramble) sgRNA

tag: treatment

value: LPS 1µg/mL 2 hour


title: THP-1 sgSCR LPS 1 hour replicate 1

description:
SCR-LPS1h-1_S33
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: LPS 1µg/mL 1 hour


title: THP-1 sgSCR untreated replicate 2

description:
SCR-UT-2_S37
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt

value: Untreated control


title: TF ChIP-seq from vagina (ENCLB101ECY)

description:
https://www.encodeproject.org/experiments/ENCSR614HHL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR614HHL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB101ECY
fragmentation methods: sonication (generic)
size range: 200-600

tag: biosample encode accession

value: female

value: adult

value: Bradley Bernstein, Broad


title: HT-29 DMSO replicate 3

description:
3RNA-HT-29-DMSO-3_S27
3UTRseq_featureCounts_Exons_HT29
201202_HT29_NormalisedCounts
201202_HT29_SpikeIn_NormalisedCounts

value: HT-29 cell line

value: Drosophila melanogaster spike-in


title: Histone ChIP-seq from upper lobe of left lung (ENCLB318MVO)

description:
https://www.encodeproject.org/experiments/ENCSR038ODI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR038ODI
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR774MLK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB318MVO
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

tag: Sex

value: male

value: 54 year

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from upper lobe of left lung (ENCLB641JOW)

description:
https://www.encodeproject.org/experiments/ENCSR038ODI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR038ODI
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR774MLK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB641JOW
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

tag: dev stage

value: Kristin Ardlie


title: SEM nascent RNA-seq RUNX1 siRNA rep3

description:
Nascent RNA-seq in SEM cells treated with RUNX1 siRNA
SEM_RUNX1_KD3

source_name: Leukemia cell line (SEM)

extract_protocol:
10e8 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7765).

treatment_protocol: Cells were electroporated with non-targeting or RUNX1 targeting siRNA

tag: sirna

value: RUNX1 siRNA (Dharmacon J-003926-05)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: SEM nascent RNA-seq RUNX1 siRNA rep1

description:
Nascent RNA-seq in SEM cells treated with RUNX1 siRNA
SEM_RUNX1_KD1


title: SEM nascent RNA-seq RUNX1 siRNA rep2

description:
Nascent RNA-seq in SEM cells treated with RUNX1 siRNA
SEM_RUNX1_KD2


title: THP-1 sgSCR - Input DNA

value: THP-1 cell line

value: expressing Cas9 and non-targeting (Scramble) sgRNA

value: DMSO (untreated control) 2 hours


title: Histone ChIP-seq from body of pancreas (ENCLB704KGS)

description:
https://www.encodeproject.org/experiments/ENCSR588PZN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR588PZN
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR700CAX
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB704KGS
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) body of pancreas tissue

value: body of pancreas

value: female

tag: age

value: 51 year

tag: lab

value: ENCBS535XPM at ENCODE; https://www.encodeproject.org/ENCBS535XPM/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: TF ChIP-seq from GM23338 (ENCLB767AIO)

description:
https://www.encodeproject.org/experiments/ENCSR591DTH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR591DTH
assay title: TF ChIP-seq
possible controls: ENCSR773IYZ
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB767AIO
fragmentation methods: sonication (generic)
size range: 200-600
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

tag: antibody

value: cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: Histone ChIP-seq from body of pancreas (ENCLB380GIW)

description:
https://www.encodeproject.org/experiments/ENCSR588PZN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR588PZN
assay title: Histone ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR700CAX
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB380GIW
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link


title: SEM nascent RNA-seq control rep2

description:
Nascent RNA-seq in SEM cells treated with non-targeting siRNA
SEM_RUNX1_NT2

value: non-targeting siRNA (Dharmacon D-001810-10-20)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: SEM nascent RNA-seq control rep1

description:
Nascent RNA-seq in SEM cells treated with non-targeting siRNA
SEM_RUNX1_NT1


title: SP3

city: Minato

first: Yosuke

last: Tanaka

state: Tokyo

address: Shirokanedai

country: Japan

institute: IMS, The University of Tokyo

data_processing:
Each obtained read was mapped to the reference sequence “GRCm38/mm10” using CLC genomic workbench v11.0.0 (Qiagen), and expression levels were normalized and subjected to the statistical analyses based on EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: CML progenitors_vehicle

growth_protocol: We developed CML-like mice by tranafer of retorvillaly trasceduced BCR-ABL1 expressinng bone marrow cells into lethally irradiated recipient mice

extract_protocol:
100 sorted cells from bone marrow and spleen were extracted in lysis buffer with NP40 and Rnase inhibitor.
The first strand of cDNA was synthesized using a PrimeScript RT reagent kit (TaKaRa Bio Inc.) and not-so random primers. Following the synthesis of the first strand, the second strand was synthesized by Klenow Fragment (3’, -5’, exo-; New England Biolabs Inc.) and complement chains of the not-so random primers. Using purified double-strand cDNA, the library for RNA-Seq was prepared and amplified using a Nextera XT DNA sample Prep Kit (Illumina Inc.).

treatment_protocol: imatinib treatment by oral gavage once a day

tag: strain

tag: tissue

value: Bone marrow ans spleen

tag: cell type

value: BCR-ABL1+CD27+G0M-KSL cells

value: Vehicle


title: SP2


title: IMSP2

source_name: CML progenitors_Imatinib

value: Imatinib


title: SP1


title: Histone ChIP-seq from testis (ENCLB283NIX)

description:
https://www.encodeproject.org/experiments/ENCSR561MYM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR561MYM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB283NIX
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) testis tissue

value: testis

tag: description

value: male

value: 37 year

value: ENCBS631HJF at ENCODE; https://www.encodeproject.org/ENCBS631HJF/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: IMSP3


title: IMSP1


title: TF ChIP-seq from uterus (ENCLB014GFW)

description:
https://www.encodeproject.org/experiments/ENCSR527TPP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR527TPP
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR859LXC
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB014GFW
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) uterus tissue

value: CTCF

value: uterus

value: female

value: adult

value: 51 year

value: ENCBS443NGH at ENCODE; https://www.encodeproject.org/ENCBS443NGH/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: DP3

source_name: CML stem cells_vehicle

value: BCR-ABL1+CD27+G0M+KSL cells


title: TF ChIP-seq from uterus (ENCLB777BOQ)

description:
https://www.encodeproject.org/experiments/ENCSR527TPP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR527TPP
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR859LXC
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB777BOQ
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad


title: IMDP1

source_name: CML stem cells_Imatinib

value: Bone marrow ans spleen


title: IMDP3

value: Imatinib


title: TAZ-CAMTA1iECs

city: Dallas

first: Jordan

last: Driskill

state: TX

address: 5323 Harry Hines Blvd

department: Physiology

institute: UT Southwestern

description: Treated with Dox until P0

data_processing:
The Cell Ranger Pipeline was utilized to generate the BAM files and the digital expression matrices
Genome_build: mm10
Supplementary_files_format_and_content: GZ file containing filtered feature barcodes, features, and matrix

source_name: Pulmonary endothelial cells

extract_protocol:
Pooled lungs were isolated from three five week-old TRE-H2B;TRE-TAZ-CAMTA1;Cdh5-tTA that had been induced (switched to normal water from 1.5mg/mL doxycycline water) at birth. Lungs were digested in .2% collagenase 1 (Thermo Fisher) and treated with ACK Lysis Buffer before being mixed with the viability stain 7-AAD (BioLegend) and subjected to flow-activated cell sorting (FACS) at the Moody Foundation Flow Cytometry Core on a FACS ARIA II SORP using FACSDiva Software. Approximately 400,000 cells were obtained, and a viability of 80% was estimated with a Countess Automated Cell Counter (Thermo Scientific).
Samples were processed using the 10X genomics platform by the UTSW Next Generation Sequencing Core. The appropriate volume of cells was loaded with Single Cell 3’ Gel Beads into a Next GEM Chip G and run on the Chromium Controller. GEM emulsions were incubated and then broken. Silane magnetic beads were used to clean up the GEM reaction mixture. Read one primer sequence was added during incubation and full-length, barcoded cDNA was then amplified by PCR after cleanup. Sample size is checked on the Agilent Tapestation 4200 using the DNAHS 5000 tape. Concentration was determined by the Qubit 4.0 Fluorimeter (Thermo Scientific) using the DNA HS assay. Samples were enzymatically fragmented and underwent size selection before library construction.  During library preparation, Read 2 primer sequence, sample index and both Illumina adapter sequences were added.  Subsequently, samples were cleaned up using Ampure XP beads and post library preparation quality control was performed using the DNA 1000 tape on the Agilent Tapestation 4200. Final concentration is ascertained using the Qubit DNA HS assay. Samples were loaded at 1.6 pM and run on the Illumina NextSeq500 High Output Flowcell using V2.5 chemistry.  Run configuration is 28x98x8.

tag: sample type

value: FACS-sorted GFP+ cells from TRE-GFP;Cdh5-tTA;TRE-TAZ-CAMTA1 mouse lungs

value: Endothelial cells

value: 5 week old mice


title: DP1

value: Vehicle


title: SEM nascent RNA-seq control rep3

description:
Nascent RNA-seq in SEM cells treated with non-targeting siRNA
SEM_RUNX1_NT3

value: non-targeting siRNA (Dharmacon D-001810-10-20)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: TF ChIP-seq from OCI-LY1 (ENCLB945GTF)

description:
https://www.encodeproject.org/experiments/ENCSR520VTO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR520VTO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2017-11-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB945GTF
fragmentation methods: shearing (Covaris generic)
size range: 200-600
nucleic acid starting quantity: 32
nucleic acid starting quantity units: ng

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: line

value: cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: male

tag: health state

value: B cell lymphoma

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: TF ChIP-seq from OCI-LY1 (ENCLB089VNB)

description:
https://www.encodeproject.org/experiments/ENCSR520VTO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR520VTO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2017-11-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB089VNB
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: Cop1_sgRNA#2_Cebpd_ChIP_seq_R2_treat_pileup.bw

city: Boston

first: Xiaoqing

last: Wang

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
The Sentieon Bwa-mem aligner was used to map reads to the mm10 reference genome (https://support.sentieon.com/manual/)
ChIP-seq peak calling was then performed using MACS2 v2.1.4 (Zhang et al., 2008), with the following parameters: “-SPMR -B -q 0.01 –keep-dup 1”
Mapped reads were then down sampled to 4 million for subsequent quality control analysis using the ChiLin pipeline (Qin et al., 2016). Quality control consisted of five metrics: 1) the average read quality according to FastQC (Andrews, 2010); 2) the fraction of uniquely mapped reads; 3) a PCR bottleneck coefficient, which is the fraction of locations with one uniquely mapped read; 4) fraction of reads in peaks according to MACS2 (Zhang et al., 2008) (more, the better); 5) overlap of peaks with DNA hypersensitivity sites. All samples were of adequate quality.
Only peaks with at least 5fold enrichment by MACS2 (v2.1.4)  were utilized for downstream analysis
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig scores represent signal per million reads from MACS2

source_name: 4T1 mouse breast cancer cells

growth_protocol: Mouse 4T1 breast cancer cells were seeded (typically 4-5 × 106 cells)  into a 150 mm petri dish with DMEM Complete Medium. Cells will be harvested on day 3.

extract_protocol:
Lysates were clarified from sonicated nuclei and Cebpd-DNA complexes were pulled down with antibody.
Libraries were prepared according toTAKARA's instructions accompanying Smarter Thruplex DNAseq Kit. Briefly, in the first step, Template Preparation, the DNA is repaired and yields molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5' ends are ligated with high efficiency to the 5' end of the genomic DNA, leaving a nick at the 3' end. The adaptors can not ligate to each other and do not have single-strand tails, both of which contribute to non-specific background found with many other NGS preparations. In the final step, the 3' ends of the genomic DNA are extended to complete library synthesis, and Illumina-compatible indexes are added through a high-fidelity amplification. Any remaining free adaptors are destroyed. Hands-on time and the risk of contamination are minimized by using a single tube and eliminating intermediate purifications.

treatment_protocol: No treatment

tag: cell line

value: triple-negative breast cancer cells

tag: genotype/variation

tag: chip antibody

value: Cebpd (Abcam, #ab245214)

tag: treatment

value: untreated


title: ChIP-seq input for MLL-N and AF4-C in RS4;11 cells

description:
ChIP-seq performed using MLL-N and AF4-C antibodies in RS4;11
RS411_MLL-N_peaks.txt

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Supplementary_files_format_and_content: Peak calling using Homer v4.7

source_name: Leukemia cell line (RS4;11)

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (EZH2). For reference normalisation 10% S2 cells were spiked in prior to sonication. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

treatment_protocol: Cells were either untreated, or electroporated with non-targeting or RUNX1 targeting siRNA

value: B-cell line derived from adult ALL with t(4;11)(q21;q23) translocation


title: Cop1_sgRNA#1_Cebpd_ChIP_seq_R1_treat_pileup.bw


title: DP2

value: Bone marrow ans spleen

value: BCR-ABL1+CD27+G0M+KSL cells

value: Vehicle


title: Cop1_sgRNA#2_Cebpd_ChIP_seq_R1_treat_pileup.bw


title: Cop1_sgRNA#1_Cebpd_ChIP_seq_R2_treat_pileup.bw


title: AF4-C ChIP-seq in RS4;11 cells

description:
ChIP-seq performed using AF4-C antibody in RS4;11
RS411_AF4-C_peaks.txt

value: Abcam ab31812


title: Rosa26_sgRNA_Cebpd_ChIP_seq_R2_treat_pileup.bw


title: Reference normalised ChIP-seq input for RUNX1 and MLL-N in SEM cells following KD siRNA treatment

description:
ChIP-seq performed using RUNX1 and MLL-N antibody in SEM cells following KD siRNA treatment
SEM_RUNX1-KD_RUNX1_peaks.txt

value: Bone marrow aspirate from a 15-year old MLL-AF4 ALL patient

tag: sirna

value: RUNX1 siRNA (Dharmacon J-003926-05)


title: Rosa26_sgRNA_Cebpd_ChIP_seq_R1_treat_pileup.bw


title: MS1 cells expressing TAZ-CAMTA1 Rep 3

data_processing:
Demultiplexing performed with bcl2fastq
Quality control assessed by FastQC
Sequencing reads mapped using STAR
Count data generated using featureCounts
EdgeR used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with raw counts
Supplementary_files_format_and_content: tab-delimited text files with normalized transcripts per million

source_name: Ms1 cell line (ATCC)

extract_protocol:
RNA extracted with RNAeasy plus mini kit. RNA was DNAse treated with the Invitrogen Turbo DNA-Free Kit
Libraries were prepared with the Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. Poly-A RNA was purified and fragmented before cDNA synthesis. Adapters were ligated, and then samples were PCR amplified and purified with Ampure XP beads. Samples were normalized, pooled, and run on an Illumina HiSeq 2500 using SBS v3 reagents

value: Ms1 cells

value: endothelial cells (pancreas)

tag: lentiviral backbone used


title: MS1 cells expressing TAZ-CAMTA1 Rep 1


title: Reference normalised MLL-N ChIP-seq in SEM cells following KD siRNA treatment

description:
ChIP-seq performed using MLL-N antibody in SEM cells following KD siRNA treatment
SEM_RUNX1-KD_MLL-N_peaks.txt

value: Bethyl A300-086A


title: MLL-N ChIP-seq in RS4;11 cells

description:
ChIP-seq performed using MLL-N antibody in RS4;11
RS411_MLL-N_peaks.txt


title: IMDP2

value: Imatinib


title: Reference normalised RUNX1 ChIP-seq in SEM cells following KD siRNA treatment

description:
ChIP-seq performed using RUNX1 antibody in SEM cells following KD siRNA treatment
SEM_RUNX1-KD_RUNX1_peaks.txt

value: Abcam ab23980


title: MS1 cells expressing TAZ 4A Rep 3


title: Reference normalised ChIP-seq input for RUNX1 and MLL-N in SEM cells following NT siRNA treatment

description:
ChIP-seq performed using RUNX1 and MLL-N antibody in SEM cells following NT siRNA treatment
SEM_RUNX1-NT_RUNX1_peaks.txt

value: non-targeting siRNA (Dharmacon D-001810-10-20)