title: ChIP-seq from A549 (ENCLB697OQG)

description:
https://www.encodeproject.org/experiments/ENCSR102XUM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR102XUM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR491TAD
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB697OQG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS823HFB at ENCODE; https://www.encodeproject.org/ENCBS823HFB/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB941PAJ)

status: Public on Jan 10 2017

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/ENCSR078POK/
***************
biological replicate number: 2
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR078POK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR690JTW
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB941PAJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 4 hours

tag: antibody

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: dev stage

value: adult

tag: age

value: 58 year

tag: Sex

value: male

tag: lab

value: Tim Reddy, Duke

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

tag: link

value: ENCBS427FJS at ENCODE; https://www.encodeproject.org/ENCBS427FJS/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB441GVO)

description:
https://www.encodeproject.org/experiments/ENCSR382EJS/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR382EJS
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB441GVO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 12 hours

value: Control

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS617TCT at ENCODE; https://www.encodeproject.org/ENCBS617TCT/


title: ChIP-seq from A549 (ENCLB864YRR)

description:
https://www.encodeproject.org/experiments/ENCSR366VPA/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR366VPA
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB864YRR
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 6 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS833LTI at ENCODE; https://www.encodeproject.org/ENCBS833LTI/


title: ChIP-seq from A549 (ENCLB548XQG)

description:
https://www.encodeproject.org/experiments/ENCSR366VPA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR366VPA
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB548XQG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS664XGI at ENCODE; https://www.encodeproject.org/ENCBS664XGI/


title: ChIP-seq from A549 (ENCLB596AMB)

description:
https://www.encodeproject.org/experiments/ENCSR336VBV/
***************
biological replicate number: 3
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR336VBV
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB596AMB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 10 hours

value: CTCF

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS424FNE at ENCODE; https://www.encodeproject.org/ENCBS424FNE/


title: DNase-seq from A549 (ENCLB660YJR)

description:
https://www.encodeproject.org/experiments/ENCSR077EYC/
***************
biological replicate number: 5
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR077EYC
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB660YJR

value: immortalized cell line

value: ENCBS675TOV at ENCODE; https://www.encodeproject.org/ENCBS675TOV/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB218EDN)

description:
https://www.encodeproject.org/experiments/ENCSR067XTW/
***************
biological replicate number: 1
technical replicate number: 1
description: FOSL2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR067XTW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR005CRY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB218EDN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: male

value: ENCBS493WOG at ENCODE; https://www.encodeproject.org/ENCBS493WOG/


title: polyA mRNA RNA-seq from A549 (ENCLB730MGF)

description:
https://www.encodeproject.org/experiments/ENCSR070IYV/
***************
biological replicate number: 4
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR070IYV
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB730MGF
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 30 minutes

extract_protocol:
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS561DRV at ENCODE; https://www.encodeproject.org/ENCBS561DRV/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB745SQD)

description:
https://www.encodeproject.org/experiments/ENCSR067XTW/
***************
biological replicate number: 2
technical replicate number: 1
description: FOSL2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR067XTW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR005CRY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB745SQD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS130SLA at ENCODE; https://www.encodeproject.org/ENCBS130SLA/


title: ChIP-seq from A549 (ENCLB674ZAA)

description:
https://www.encodeproject.org/experiments/ENCSR366VPA/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR366VPA
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB674ZAA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS848UWA at ENCODE; https://www.encodeproject.org/ENCBS848UWA/


title: ChIP-seq from A549 (ENCLB734WGN)

description:
https://www.encodeproject.org/experiments/ENCSR109KEL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR109KEL
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR491TAD
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB734WGN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS626ALW at ENCODE; https://www.encodeproject.org/ENCBS626ALW/


title: ChIP-seq from A549 (ENCLB793QJK)

description:
https://www.encodeproject.org/experiments/ENCSR047EVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR047EVQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR711MVL
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB793QJK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 3 hours

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS935QKL at ENCODE; https://www.encodeproject.org/ENCBS935QKL/


title: ChIP-seq from A549 (ENCLB625GUO)

description:
https://www.encodeproject.org/experiments/ENCSR047EVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR047EVQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR711MVL
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB625GUO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS091RAT at ENCODE; https://www.encodeproject.org/ENCBS091RAT/


title: ChIP-seq from A549 (ENCLB630RBO)

description:
https://www.encodeproject.org/experiments/ENCSR336VBV/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR336VBV
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB630RBO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: 58 year

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS974GKC at ENCODE; https://www.encodeproject.org/ENCBS974GKC/


title: ChIP-seq from A549 (ENCLB081UNB)

description:
https://www.encodeproject.org/experiments/ENCSR336VBV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR336VBV
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB081UNB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS922MBD at ENCODE; https://www.encodeproject.org/ENCBS922MBD/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB960UDM)

description:
https://www.encodeproject.org/experiments/ENCSR037DAC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR037DAC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB960UDM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS615RCL at ENCODE; https://www.encodeproject.org/ENCBS615RCL/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB898INY)

description:
https://www.encodeproject.org/experiments/ENCSR328BXP/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR328BXP
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB898INY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: ENCBS013HOT at ENCODE; https://www.encodeproject.org/ENCBS013HOT/


title: ChIP-seq from A549 (ENCLB773WFC)

description:
https://www.encodeproject.org/experiments/ENCSR332WDQ/
***************
biological replicate number: 2
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR332WDQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB773WFC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: JUNB

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS889EQG at ENCODE; https://www.encodeproject.org/ENCBS889EQG/


title: ChIP-seq from A549 (ENCLB575XBT)

description:
https://www.encodeproject.org/experiments/ENCSR332WDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR332WDQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB575XBT
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS362CIG at ENCODE; https://www.encodeproject.org/ENCBS362CIG/


title: ChIP-seq from A549 (ENCLB694EEF)

description:
https://www.encodeproject.org/experiments/ENCSR032SCO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR032SCO
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB694EEF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: 58 year

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS599ALV at ENCODE; https://www.encodeproject.org/ENCBS599ALV/


title: ChIP-seq from A549 (ENCLB939QOL)

description:
https://www.encodeproject.org/experiments/ENCSR013KHB/
***************
biological replicate number: 1
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR013KHB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR467GRT
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB939QOL
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: Tim Reddy, Duke

value: ENCBS340RXI at ENCODE; https://www.encodeproject.org/ENCBS340RXI/


title: ChIP-seq from A549 (ENCLB505LJO)

description:
https://www.encodeproject.org/experiments/ENCSR016PSC/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR016PSC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB505LJO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 7 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS163NSQ at ENCODE; https://www.encodeproject.org/ENCBS163NSQ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB058EMR)

description:
https://www.encodeproject.org/experiments/ENCSR016PSC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR016PSC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB058EMR
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS747KQQ at ENCODE; https://www.encodeproject.org/ENCBS747KQQ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB724BMT)

description:
https://www.encodeproject.org/experiments/ENCSR328BXP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR328BXP
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB724BMT
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS985AGQ at ENCODE; https://www.encodeproject.org/ENCBS985AGQ/


title: ChIP-seq from A549 (ENCLB368KMX)

description:
https://www.encodeproject.org/experiments/ENCSR067XTW/
***************
biological replicate number: 3
technical replicate number: 1
description: FOSL2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR067XTW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR005CRY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB368KMX
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS152DKS at ENCODE; https://www.encodeproject.org/ENCBS152DKS/


title: ChIP-seq from A549 (ENCLB386MTU)

description:
https://www.encodeproject.org/experiments/ENCSR328BXP/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR328BXP
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB386MTU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: 58 year

value: male

value: ENCBS102TQY at ENCODE; https://www.encodeproject.org/ENCBS102TQY/


title: ChIP-seq from A549 (ENCLB166LNY)

description:
https://www.encodeproject.org/experiments/ENCSR013KHB/
***************
biological replicate number: 3
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR013KHB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR467GRT
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB166LNY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS364GKY at ENCODE; https://www.encodeproject.org/ENCBS364GKY/


title: ChIP-seq from A549 (ENCLB136DQQ)

description:
https://www.encodeproject.org/experiments/ENCSR013KHB/
***************
biological replicate number: 2
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR013KHB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR467GRT
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB136DQQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS312TVA at ENCODE; https://www.encodeproject.org/ENCBS312TVA/


title: ChIP-seq from A549 (ENCLB473MNX)

description:
https://www.encodeproject.org/experiments/ENCSR287UXS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR287UXS
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB473MNX
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS613WNR at ENCODE; https://www.encodeproject.org/ENCBS613WNR/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB561HXX)

description:
https://www.encodeproject.org/experiments/ENCSR287UXS/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR287UXS
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB561HXX
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS255WLF at ENCODE; https://www.encodeproject.org/ENCBS255WLF/


title: ChIP-seq from A549 (ENCLB385LFU)

description:
https://www.encodeproject.org/experiments/ENCSR005CRY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR005CRY
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB385LFU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: ENCBS574IVR at ENCODE; https://www.encodeproject.org/ENCBS574IVR/


title: ChIP-seq from A549 (ENCLB077QOO)

description:
https://www.encodeproject.org/experiments/ENCSR145YCX/
***************
biological replicate number: 2
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR145YCX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR690JTW
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB077QOO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS431KOR at ENCODE; https://www.encodeproject.org/ENCBS431KOR/


title: ChIP-seq from A549 (ENCLB756RSJ)

description:
https://www.encodeproject.org/experiments/ENCSR266YIS/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR266YIS
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB756RSJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: 58 year

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS624HVD at ENCODE; https://www.encodeproject.org/ENCBS624HVD/


title: ChIP-seq from A549 (ENCLB002KVA)

description:
https://www.encodeproject.org/experiments/ENCSR249JOH/
***************
biological replicate number: 3
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR249JOH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB002KVA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 1 hour

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS582BMI at ENCODE; https://www.encodeproject.org/ENCBS582BMI/


title: TEM H3K4me1 R2

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the hg19 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
For ChIP-Seq, reads were mapped using BowTie and islands were identified using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: csv file includes RPKM values for each sample

source_name: Blood

growth_protocol: T cells were purified from lymphopaks obtained from NIH Blood Center or blood filters obtained from University of Cincinnati Hoxworth Blood Center. Cells from 2-4 healthy donors were combined for each experiment. Human CD4 T cells were enriched by negative selection using Invitrogen or Miltenyi Untouched CD4 T cell Purification Kit. Cells were further sorted into populations: (1) Naïve T cells (CD4+CD45RO-CD27+); (2) TCM (CD4+CD45RO+CD27+); and (3) TEM (CD4+CD45RO+CD27-).

extract_protocol:
RNA was harvested using BioRad total RNA extraction kit with DNaseI treatment. For ChIP cells were fixed with 0.8-1%% formaldehyde for 8 min at RT and DNA was sonicated using Covaris or probe sonicators.
RNA  libraries for single read sequencing were prepared by using standard Illumina protocols. ChIP libraries were prepared by using ThruPLEX DNA kit (Rubicon).

treatment_protocol: Activation was performed with anti-CD3/28 beads (Invitrogen) for 40 min, 150min or 15hrs.

tag: cell type

value: Resting TEM CD4 purified cells

tag: chip antibodies

value: H3K4me1 (Abcam ab8895)

tag: biowardrobe ids


title: ChIP-seq from A549 (ENCLB392KHA)

description:
https://www.encodeproject.org/experiments/ENCSR266YIS/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR266YIS
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB392KHA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS366BMB at ENCODE; https://www.encodeproject.org/ENCBS366BMB/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: TEM H2A.z R2

value: H2A.z (Abcam ab4174)


title: TEM RNA Polymerase II

value: RNA Polymerase II (Active Motif, 4H8)


title: ChIP-seq from A549 (ENCLB414LJG)

description:
https://www.encodeproject.org/experiments/ENCSR005CRY/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR005CRY
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB414LJG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS579YWF at ENCODE; https://www.encodeproject.org/ENCBS579YWF/


title: ChIP-seq from A549 (ENCLB533LKN)

description:
https://www.encodeproject.org/experiments/ENCSR266YIS/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR266YIS
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB533LKN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS972YKN at ENCODE; https://www.encodeproject.org/ENCBS972YKN/


title: TEM H3K27ac

value: H3K27Ac  (Diagenode, pAb-196-060)


title: TEM H3K4me3 R2

value: H3K4Me3 (Millipore,17-614)


title: TCM RNA Polymerase II

value: Resting TCM CD4 purified cells


title: TCM H2A.z R2


title: ChIP-seq from A549 (ENCLB062KAV)

description:
https://www.encodeproject.org/experiments/ENCSR249JOH/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR249JOH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB062KAV
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: male

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS924DBS at ENCODE; https://www.encodeproject.org/ENCBS924DBS/


title: TCM H3K4me1 R2

value: H3K4me1 (Abcam ab8895)


title: ChIP-seq from A549 (ENCLB579MEV)

description:
https://www.encodeproject.org/experiments/ENCSR384KPP/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR384KPP
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB579MEV
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 2 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS291IYO at ENCODE; https://www.encodeproject.org/ENCBS291IYO/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB939QPW)

description:
https://www.encodeproject.org/experiments/ENCSR233BJW/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR233BJW
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB939QPW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 8 hours

value: Control

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

value: ENCBS506NAT at ENCODE; https://www.encodeproject.org/ENCBS506NAT/


title: TCM H3K27ac


title: 4OHT_BMAL1_ChIP_rep2

city: Taichung

first: Yi-Ying

last: Chiou

address: No.145, Xingda Rd., South Dist.

department: Graduate Institute of Biochemistry

country: Taiwan

institute: National Chung Hsing University

description:
processed data file:
BMAL1_ChIPseq_Peak_RPKM.txt

data_processing:
Sequence reads were trimmed to remove adaptor sequences using BBDuk tool (bbmap/35.82) using parameters “ktrim = r k = 23 hdist = 1 minlen = 50".
For RNA-seq, sequence reads were mapped to mouse genome (mm10) by bbmap/35.82 with the option “maxindel = 100000 intronlen = 10 ambig = random qin = 33”. For ChIP-Seq, sequence reads were mapped to mouse genome (mm10) byBowtie2/2.2.8 (37) using default parameters.
For ChIP-seq, peaks were called by MACS/2015–04-20 with options “-f BAM -g mm -B -q 0.01". Common peaks were determine using intersect function in Bedtools/2.25.0.
For RNA-seq, mapped reads were quantified by featureCounts with option “-T 4 -t exon” and then were analyzed by Deseq2. For ChIP-Seq, binding strength of peaks were quantified by intersect function in in Bedtools/2.25.0 with option "-c" and then normalized to RPKM
Genes contolled by BMAL1 were defined by the distance bwtween peak center and gene less than 5 kb
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw counts of RNA-Seq, bed files of common BMAL1 binding sites with raw counts at the last column, tab-delimited text file include RPKM values of each peak for each ChIP-seq sample and tab-delimited text file include Deseq2 analysis of BMAL1 controled genes

organism: Mus musculus

growth_protocol: Cells were routinely generated by replating to new plates when cells were 80% confluent in DMEM (Gibco) with 10% FBS (Sigma)

extract_protocol:
For RNA-seq, cells were lysed with Trizol (Thermo Fisher Scientiic). After phase separation, RNA was purified by  PureLink RNA Mini Kit (Thermo Fisher Scientific). For ChIP-Seq, protein-DNA complex  were crosslinked by formaldehyde, sonicated, immunoprecipitated and extracted after reverse-crosslinking (see details in 2016 PNAS 113, E6072)  Fisher Scientific)
For RNA-seq, use TruSeq stranded mRNA preparation kit (Illumina). For ChIP-seq, use ThruPLEX DNA-seq Kit (RUBICON GENOMICS).

treatment_protocol: Cells were treated with 1 micro M 4-hydroxy-tamoxifen (4-OHT) or 0.1% EtOH (solvent of 4-OHT) for 4 hours before collection

tag: strain background

value: embryonic fibroblast

tag: genotype/variation

tag: transgene

tag: treated with

tag: chip antibody

value: BMAL1 (Bethyl, A302-616A)

tag: molecule subtype

value: BMAL1 ChIPed DNA


title: 4OHT_BMAL1_ChIP_rep1


title: ChIP-seq from A549 (ENCLB899CGR)

description:
https://www.encodeproject.org/experiments/ENCSR005CRY/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR005CRY
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB899CGR
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: antibody

tag: line

value: adult

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS794TLJ at ENCODE; https://www.encodeproject.org/ENCBS794TLJ/


title: ChIP-seq from A549 (ENCLB926ORZ)

description:
https://www.encodeproject.org/experiments/ENCSR269RPR/
***************
biological replicate number: 3
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR269RPR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB926ORZ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: JUNB

tag: biosample encode accession

tag: dev stage

value: male

value: Tim Reddy, Duke

value: ENCBS977SDW at ENCODE; https://www.encodeproject.org/ENCBS977SDW/


title: ChIP-seq from A549 (ENCLB529TNY)

description:
https://www.encodeproject.org/experiments/ENCSR233BJW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR233BJW
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB529TNY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: age

tag: Sex

value: ENCBS515ZMK at ENCODE; https://www.encodeproject.org/ENCBS515ZMK/


title: ChIP-seq from A549 (ENCLB545IUE)

description:
https://www.encodeproject.org/experiments/ENCSR216DMN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR216DMN
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB545IUE
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: lab

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS302TDW at ENCODE; https://www.encodeproject.org/ENCBS302TDW/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: EtOH_BMAL1_ChIP_rep2

tag: cell type

value: EtOH


title: TCM H3K4me3 R2

value: Resting TCM CD4 purified cells

tag: chip antibodies

value: H3K4Me3 (Millipore,17-614)


title: Naïve RNA Polymerase II

value: Resting naive CD4 purified cells

value: RNA Polymerase II (Active Motif, 4H8)

tag: biowardrobe ids


title: ChIP-seq from A549 (ENCLB904DHG)

description:
https://www.encodeproject.org/experiments/ENCSR226UQG/
***************
biological replicate number: 2
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR226UQG
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB904DHG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

tag: link

value: ENCBS710NDE at ENCODE; https://www.encodeproject.org/ENCBS710NDE/


title: Naïve H2A.z R2

value: H2A.z (Abcam ab4174)


title: Naïve H3K27ac

value: H3K27Ac  (Diagenode, pAb-196-060)


title: ChIP-seq from A549 (ENCLB073MNR)

description:
https://www.encodeproject.org/experiments/ENCSR226UQG/
***************
biological replicate number: 3
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR226UQG
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB073MNR
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: JUNB

value: 58 year

value: male

value: Tim Reddy, Duke

value: ENCBS637RXS at ENCODE; https://www.encodeproject.org/ENCBS637RXS/


title: ChIP-seq from A549 (ENCLB372HCM)

description:
https://www.encodeproject.org/experiments/ENCSR249JOH/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR249JOH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB372HCM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS009OYK at ENCODE; https://www.encodeproject.org/ENCBS009OYK/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB055UEL)

description:
https://www.encodeproject.org/experiments/ENCSR269RPR/
***************
biological replicate number: 2
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR269RPR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB055UEL
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS016CUF at ENCODE; https://www.encodeproject.org/ENCBS016CUF/


title: ChIP-seq from A549 (ENCLB033WCD)

description:
https://www.encodeproject.org/experiments/ENCSR226UQG/
***************
biological replicate number: 1
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR226UQG
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB033WCD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS746SZI at ENCODE; https://www.encodeproject.org/ENCBS746SZI/


title: EtOH_BMAL1_ChIP_rep1

tag: strain background

value: embryonic fibroblast

tag: genotype/variation

value: EtOH

value: BMAL1 (Bethyl, A302-616A)

value: BMAL1 ChIPed DNA


title: 4OHT_Input_rep2

tag: transgene

tag: treated with


title: EtOH_Input_rep1

tag: chip antibody

tag: molecule subtype


title: ChIP-seq from A549 (ENCLB038JIJ)

description:
https://www.encodeproject.org/experiments/ENCSR233BJW/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR233BJW
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB038JIJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: antibody

value: Control

tag: line

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

value: ENCBS751ANS at ENCODE; https://www.encodeproject.org/ENCBS751ANS/


title: EtOH_Input_rep2


title: 4OHT_Input_rep1


title: ChIP-seq from A549 (ENCLB542AGR)

description:
https://www.encodeproject.org/experiments/ENCSR216DMN/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR216DMN
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB542AGR
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: biosample encode accession

tag: dev stage

value: 58 year

value: male

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS652AAX at ENCODE; https://www.encodeproject.org/ENCBS652AAX/


title: ChIP-seq from A549 (ENCLB681PPK)

description:
https://www.encodeproject.org/experiments/ENCSR216DMN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR216DMN
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB681PPK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: age

tag: Sex

value: ENCBS422ZAB at ENCODE; https://www.encodeproject.org/ENCBS422ZAB/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: 4OHT_mRNA_rep2

description:
processed data file:
counts_PN_annot.txt
Deseq2_OHTvsCtl.txt

value: mRNA


title: ChIP-seq from A549 (ENCLB683MOK)

description:
https://www.encodeproject.org/experiments/ENCSR173IEA/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR173IEA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB683MOK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: immortalized cell line

tag: lab

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS582VVW at ENCODE; https://www.encodeproject.org/ENCBS582VVW/


title: Naïve H3K4me1 R2

tag: cell type

value: Resting naive CD4 purified cells

tag: chip antibodies

value: H3K4me1 (Abcam ab8895)


title: AGO2 PARCLIP L7

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: after UV-crosslinking of A673 cells protein G Dynabeads (Invitrogen) were coupled to Ago2 antibody,while cells were lysed and RNA partially digested Then AGO2 IP took place followed by RNA 3´ends dephosphorylation, linker preparation (32P-γ-ATP) and RNA 5´ends labelling, SDS-PAGE in a4-12% NuPAGE Bis-Tris gel (Invitrogen). Protein-RNA complexes were transferred from the gel to a nitrocellulose membrane that was exposed till obtaining a clear image of the band corresponding to Ago2 molecular weight (97kDa). Band was excised and purified and RNA precipitated and resuspended in RNase-free H2O to proceed with 5´RNA linker ligation. Finally RT was done, afterwards took place PCR with Solexa flow-cell adaptors (2` 95°C, 28 cycles of 20´´ 95°C, 30´´ 58°C, 20´´ 68°C, 5´ 68°C, ∞ 4C) and its product was loaded in a 4% low-melt agarose gel and extracted from the gel and eluted using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany. DNA quantity and quality were measured using the Picogreen Assay (Invitrogen) for Nanodrop. cDNAs were then ready for sequencing

data_processing:
Basecalls performed using CASAVA version 1.8
raw reads were quality filtered, trimmed using the fastx toolkit: fastx_clipper -Q33 -a adaptersequence, fastq_quality_filter -Q33  -p 80  -q 25 -v
quality filtered reads were aligned to the hg19 genome assembly using bowtie version  with the following configurations: bowtie -t -v 2  -m 1 --best  --strata --seed 1234  hg19
clusters of AGO2 interaction sites on mRNA were identified using PARalyzer (D. Corcoran,  et al., Genome Biol. 2011 12 8 R79) with the following settings: BANDWIDTH=3, CONVERSION=T>C, MINIMUM_READ_COUNT_PER_GROUP=5, MINIMUM_READ_COUNT_PER_CLUSTER=5, MINIMUM_READ_COUNT_FOR_KDE=5, MINIMUM_CLUSTER_SIZE=10, MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=1, MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=1, MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=5, MINIMUM_READ_LENGTH=13, #MINIMUM_READ_LENGTH=1, MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=0, EXTEND_BY_READ, MAXIMUM_SEED_MATCH_LENGTH=8
Genome_build: hg19
Supplementary_files_format_and_content: output from PARalyzer. https://ohlerlab.mdc-berlin.de/files/duke/PARalyzer/README.txt

source_name: Ewing Sarcoma cellinie

growth_protocol:
A clone of the ES cell line A673 with a stably transfected construct harbouring a doxycyclin inducible shRNA against the EWS-FLI1 fusion protein as previously described (Carrillo, J., Garcia-Aragoncillo, E., Azorin, D., Agra, N., Sastre, A., Gonzalez-Mediero, I., Garcia-Miguel, P., Pestana, A., Gallego, S., Segura, D. et al. (2007). Clinical cancer research, 13, 2429-2440). Cells were transfected using the Lipofectamine Plus reagent (Invitrogen, Groningen, the Netherlands) according to manufacter´s instructions
ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
After UV -crosslinking of A673 cells protein G Dynabeads (Invitrogen) were coupled to Ago2 antibody,while cells were lysed and RNA partially digested Then AGO2 IP took place followed by RNA 3´ends dephosphorylation, linker preparation (32P-γ-ATP) and RNA 5´ends labelling, SDS-PAGE in a4-12% NuPAGE Bis-Tris gel (Invitrogen).
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Protein-RNA complexes were transferred from the gel to a nitrocellulose membrane that was exposed till obtaining a clear image of the band corresponding to Ago2 molecular weight (97kDa). Band was excised and purified and RNA precipitated and resuspended in RNase-free H2O to proceed with 5´RNA linker ligation. Finally RT was done, followed by PCR with Solexa flow-cell adaptors (2` 95°C, 28 cycles of 20´´ 95°C, 30´´ 58°C, 20´´ 68°C, 5´ 68°C, ∞ 4C) and its product was loaded in a 4% low-melt agarose gel then extracted from the gel and eluted using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany. DNA quantity and quality were measured using the Picogreen Assay (Invitrogen) for Nanodrop. cDNAs were then ready for sequencing
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
PARCLIP-Seq

treatment_protocol: In one of these experiments EWS-FLI1 depletion was effectively achieved after 53h doxycycline induction

value: clone the Ewing Sarcoma celline A673 harboring a doxycyclin inducible sh mediated knockdown of EWS-FLI1

tag: treatment

value: doxycycline induction:53h

tag: par-clip antibody

value: anti-AGO2 antibody kindly provided by Gunter Meister (University of Regensburg)


title: ChIP-seq from A549 (ENCLB456PBY)

description:
https://www.encodeproject.org/experiments/ENCSR163EXK/
***************
biological replicate number: 3
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR163EXK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB456PBY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: JUNB

value: adult

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

tag: link

value: ENCBS058HUF at ENCODE; https://www.encodeproject.org/ENCBS058HUF/


title: AGO2 PARCLIP L3

value: no doxycyclin


title: TEM H3K4me1 R1

value: Resting TEM CD4 purified cells

tag: biowardrobe ids


title: AGO2 PARCLIP L1


title: TEM H2A.z R1

value: H2A.z (Abcam ab4174)


title: ChIP-seq from A549 (ENCLB382HBB)

description:
https://www.encodeproject.org/experiments/ENCSR163EXK/
***************
biological replicate number: 2
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR163EXK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB382HBB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: Tim Reddy, Duke

value: ENCBS276FMI at ENCODE; https://www.encodeproject.org/ENCBS276FMI/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB973KEN)

description:
https://www.encodeproject.org/experiments/ENCSR173IEA/
***************
biological replicate number: 3
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR173IEA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB973KEN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS522XYT at ENCODE; https://www.encodeproject.org/ENCBS522XYT/


title: 4OHT_mRNA_rep1

tag: strain background

value: embryonic fibroblast

tag: genotype/variation

tag: transgene

tag: treated with

value: mRNA


title: clone of Ewing Sarcoma cellinie A673 transfected with sponge against miR9, replicate2 of batch2

description: mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with microRNA sponge

data_processing:
Illumina Casava1.8 software used for basecalling.
The STAR aligner was used for alignment of reads to human genome build hg19 (1000 genomes version hs37d5) with settings: --outFilterMultimapNmax 2 --outFilterMismatchNoverLmax 0.05
read counting in genes was performed with "featureCount" function of the Rsubread R-package
batch 1 and 2 were analyzed separately for differential expression
Genome_build: hg19
Supplementary_files_format_and_content: read counts in Entrez Gene Genes

growth_protocol: A clone of the ES cell line A673 with a stably transfected construct harbouring a doxycyclin inducible shRNA against the EWS-FLI1 fusion protein as previously described (Carrillo, J., Garcia-Aragoncillo, E., Azorin, D., Agra, N., Sastre, A., Gonzalez-Mediero, I., Garcia-Miguel, P., Pestana, A., Gallego, S., Segura, D. et al. (2007). Clinical cancer research, 13, 2429-2440). Cells were transfected using the Lipofectamine Plus reagent (Invitrogen, Groningen, the Netherlands) according to manufacter´s instructions

extract_protocol:
Trizol total RNA
RNA-Seq, New England Biolab kit with polyA enrichment

treatment_protocol: CMV-d2eGFP sponge plasmids for CXCR4 and sponge against miR-17-92 (s-α- miR-17-92) were obtained from the Jedlicka Lab (Dylla, L. and Jedlicka, P. (2013), PloS one, 8, e63032.). pBp-Control Sponge (CXCR4 sponge), (Addgene plasmid # 22744), pBabe-puro-miR-10b sponge (Addgene plasmid # 25043) and pBabe-puro-miR-9 sponge were gifts from Bob Weinberg (Addgene plasmid # 25040) (Cell, 137, 1032-1046, Nature biotechnology, 28, 341-347).

tag: batch

tag: strain

value: clone of A673

value: transfected with sponge against miR-9, replicate2


title: EtOH_mRNA_rep2

value: EtOH

tag: chip antibody

tag: molecule subtype


title: clone of Ewing Sarcoma cellinie A673 transfected with sponge against miR10b, replicate1 of batch2

value: transfected with sponge against miR-10b, replicate1


title: ChIP-seq from A549 (ENCLB917NNS)

description:
https://www.encodeproject.org/experiments/ENCSR173IEA/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR173IEA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB917NNS
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: antibody

tag: line

tag: biosample encode accession

tag: dev stage

value: adult

tag: age

value: 58 year

tag: Sex

value: ENCBS802OFY at ENCODE; https://www.encodeproject.org/ENCBS802OFY/


title: Naïve H3K4me3 R2

tag: cell type

value: Resting naive CD4 purified cells

tag: chip antibodies

value: H3K4Me3 (Millipore,17-614)


title: clone of Ewing Sarcoma cellinie A673 transfected with sponge against miR9, replicate1 of batch2

tag: treatment

value: transfected with sponge against miR-9, replicate1


title: TCM H3K4me1 R1

value: Resting TCM CD4 purified cells

value: H3K4me1 (Abcam ab8895)

tag: biowardrobe ids


title: EtOH_mRNA_rep1

tag: strain background

tag: genotype/variation


title: ChIP-seq from A549 (ENCLB269XDK)

description:
https://www.encodeproject.org/experiments/ENCSR130TQM/
***************
biological replicate number: 3
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR130TQM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB269XDK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: immortalized cell line

value: male

tag: lab

value: Tim Reddy, Duke

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

tag: link

value: ENCBS820ONJ at ENCODE; https://www.encodeproject.org/ENCBS820ONJ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB040EKF)

description:
https://www.encodeproject.org/experiments/ENCSR163EXK/
***************
biological replicate number: 1
technical replicate number: 1
description: JunB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR163EXK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB040EKF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: JUNB

value: ENCBS002UWD at ENCODE; https://www.encodeproject.org/ENCBS002UWD/


title: clone of Ewing Sarcoma cellinie A673 transfected with sponge against miR10b, replicate2 of batch2

tag: batch

tag: strain

value: clone of A673

value: transfected with sponge against miR-10b, replicate2


title: clone of Ewing Sarcoma cellinie A673 transfected with CXCR4 control, replicate1 of batch2

description: mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with microRNA control sponge

value: transfected with CXCR4 control sponge


title: TCM H3K4me3 R1

value: H3K4me3 (Abcam ab8580)


title: clone of Ewing Sarcoma cellinie A673 transfected with a sponge against miR 17-92 cluster members, replicateA

value: transfected with sponge against microRNA 17-92 cluster members, replicateA


title: ChIP-seq from A549 (ENCLB900PAQ)

description:
https://www.encodeproject.org/experiments/ENCSR139PCE/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR139PCE
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB900PAQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

tag: antibody

value: Control

value: adult

value: 58 year

value: ENCBS506AEB at ENCODE; https://www.encodeproject.org/ENCBS506AEB/


title: ChIP-seq from A549 (ENCLB997GTW)

description:
https://www.encodeproject.org/experiments/ENCSR139PCE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR139PCE
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB997GTW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: line

value: immortalized cell line

value: ENCBS949VOR at ENCODE; https://www.encodeproject.org/ENCBS949VOR/


title: Naïve H2A.z R1

value: Resting naive CD4 purified cells

value: H2A.z (Abcam ab4174)


title: ChIP-seq from A549 (ENCLB347HHP)

description:
https://www.encodeproject.org/experiments/ENCSR139PCE/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR139PCE
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB347HHP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: biosample encode accession

value: male

value: Tim Reddy, Duke

value: ENCBS419LEN at ENCODE; https://www.encodeproject.org/ENCBS419LEN/


title: TEM CD4  150 min activated

molecule: polyA RNA

value: TEM CD4 purified cells

tag: state

value: 150 min activated with anti-CD3/28 beads


title: TEM H3K4me3 R1

value: Resting TEM CD4 purified cells


title: TCM H2A.z R1

value: Resting TCM CD4 purified cells


title: ChIP-seq from A549 (ENCLB343TOC)

description:
https://www.encodeproject.org/experiments/ENCSR088SOR/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR088SOR
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB343TOC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: dev stage

tag: age

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS535ZFG at ENCODE; https://www.encodeproject.org/ENCBS535ZFG/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: clone of Ewing Sarcoma cellinie A673 transfected with a sponge against miR 17-92 cluster members, replicateB

value: clone of A673

value: transfected with sponge against microRNA 17-92 cluster members, replicateB


title: clone of Ewing Sarcoma cellinie A673 transfected with CXCR4 control, replicateA

description: mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge

value: transfected with CXCR4 control sponge


title: Naïve H3K4me3 R1

tag: cell type

value: H3K4me3 (Abcam ab8580)


title: ChIP-seq from A549 (ENCLB108YQS)

description:
https://www.encodeproject.org/experiments/ENCSR130TQM/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR130TQM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB108YQS
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: immortalized cell line

value: adult

value: 58 year

tag: Sex

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS537WCE at ENCODE; https://www.encodeproject.org/ENCBS537WCE/


title: clone of Ewing Sarcoma cellinie A673 transfected with CXCR4 control, replicate2 of batch2

tag: treatment


title: Naïve H3K4me1 R1

value: Resting naive CD4 purified cells

tag: chip antibodies

value: H3K4me1 (Abcam ab8895)

tag: biowardrobe ids


title: TEM CD4  40 min activated

value: TEM CD4 purified cells

value: 40 min activated with anti-CD3/28 beads


title: ChIP-seq from A549 (ENCLB767WAP)

description:
https://www.encodeproject.org/experiments/ENCSR090RGB/
***************
biological replicate number: 2
technical replicate number: 1
description: cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR090RGB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB767WAP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: JUN

value: male

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS202SSL at ENCODE; https://www.encodeproject.org/ENCBS202SSL/


title: TEM CD4  15 hrs activated

value: 15 hrs  activated with anti-CD3/28 beads


title: ChIP-seq from A549 (ENCLB284UFR)

description:
https://www.encodeproject.org/experiments/ENCSR090RGB/
***************
biological replicate number: 3
technical replicate number: 1
description: cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR090RGB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB284UFR
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS133PHP at ENCODE; https://www.encodeproject.org/ENCBS133PHP/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB686AMK)

description:
https://www.encodeproject.org/experiments/ENCSR088SOR/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR088SOR
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB686AMK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS057UPO at ENCODE; https://www.encodeproject.org/ENCBS057UPO/


title: ChIP-seq from A549 (ENCLB915RPD)

description:
https://www.encodeproject.org/experiments/ENCSR088SOR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR088SOR
assay title: ChIP-seq
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB915RPD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS173DBY at ENCODE; https://www.encodeproject.org/ENCBS173DBY/


title: ChIP-seq from A549 (ENCLB403GIO)

description:
https://www.encodeproject.org/experiments/ENCSR048CVK/
***************
biological replicate number: 2
technical replicate number: 1
description: cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR048CVK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB403GIO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS148NZA at ENCODE; https://www.encodeproject.org/ENCBS148NZA/


title: ChIP-seq from A549 (ENCLB894JSW)

description:
https://www.encodeproject.org/experiments/ENCSR048CVK/
***************
biological replicate number: 3
technical replicate number: 1
description: cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR048CVK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB894JSW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS514OCX at ENCODE; https://www.encodeproject.org/ENCBS514OCX/


title: ChIP-seq from A549 (ENCLB080NHN)

description:
https://www.encodeproject.org/experiments/ENCSR035OXA/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR035OXA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB080NHN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CTCF

value: ENCBS714GDR at ENCODE; https://www.encodeproject.org/ENCBS714GDR/


title: ChIP-seq from A549 (ENCLB968UIB)

description:
https://www.encodeproject.org/experiments/ENCSR090RGB/
***************
biological replicate number: 1
technical replicate number: 1
description: cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR090RGB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB968UIB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: JUN

value: male

value: Tim Reddy, Duke

value: ENCBS047ROF at ENCODE; https://www.encodeproject.org/ENCBS047ROF/


title: ChIP-seq from A549 (ENCLB162CXO)

description:
https://www.encodeproject.org/experiments/ENCSR130TQM/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR130TQM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB162CXO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS136ZVQ at ENCODE; https://www.encodeproject.org/ENCBS136ZVQ/


title: ChIP-seq from A549 (ENCLB471GQJ)

description:
https://www.encodeproject.org/experiments/ENCSR035OXA/
***************
biological replicate number: 3
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR035OXA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB471GQJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS633XBY at ENCODE; https://www.encodeproject.org/ENCBS633XBY/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: TCM CD4  150 min activated

value: TCM CD4 purified cells

value: 150 min activated with anti-CD3/28 beads


title: TCM CD4  Resting

value: resting


title: ChIP-seq from A549 (ENCLB141HAE)

description:
https://www.encodeproject.org/experiments/ENCSR035OXA/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR035OXA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2016-12-20
lab: Tim Reddy, Duke
library encode accession: ENCLB141HAE
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: 58 year

value: ENCBS218EVW at ENCODE; https://www.encodeproject.org/ENCBS218EVW/


title: naïve CD4  40 min activated

value: naive CD4 purified cells

value: 40 min activated with anti-CD3/28 beads


title: naïve CD4  150 min activated


title: ChIP-seq from A549 (ENCLB268WAJ)

description:
https://www.encodeproject.org/experiments/ENCSR954SQX/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR954SQX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB268WAJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS953UYS at ENCODE; https://www.encodeproject.org/ENCBS953UYS/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: clone of Ewing Sarcoma cellinie A673 transfected with CXCR4 control, replicateB

description: mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with microRNA control sponge

value: clone of A673

value: transfected with CXCR4 control sponge


title: TEM CD4  Resting

value: TEM CD4 purified cells


title: naïve CD4  Resting


title: ChIP-seq from A549 (ENCLB459WHS)

description:
https://www.encodeproject.org/experiments/ENCSR954HUB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR954HUB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB459WHS
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS798DNC at ENCODE; https://www.encodeproject.org/ENCBS798DNC/


title: ChIP-seq from A549 (ENCLB805CCP)

description:
https://www.encodeproject.org/experiments/ENCSR944WVU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR944WVU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR549SVK
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB805CCP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS779CAS at ENCODE; https://www.encodeproject.org/ENCBS779CAS/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: IgG DNA

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

country: China

institute: Shanghai JiaYin Biological technology co., LTD

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19

source_name: human lung cancer cell

growth_protocol: Primary spinal metastasis lung cancer cells were obtained according to the instruction of Ethics Committee of Chang Zheng Hospital. Briefly, primary tumor cells were dispersed using scissors, and dispersed tissues were trypsinzed at 37°C for 30 min and inactivated by DMEM with 10% FBS. Cells were filtered with 0.75 um micro filter and centrifuged at 1000 rpm for 5 mins at room temperature. Finally, cells were re-suspended in DMEM and plated in 10-cm dishes. All the cell lines were cultured in a 5% (v/v) CO2 humidified incubator at 37 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and FOXD3 binding DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Ki. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: IgG


title: FOXD3 ChIP-seq


title: ChIP-seq from A549 (ENCLB101ZEW)

description:
https://www.encodeproject.org/experiments/ENCSR949IDI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR949IDI
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB101ZEW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: 58 year

tag: lab

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS381CYW at ENCODE; https://www.encodeproject.org/ENCBS381CYW/


title: ChIP-seq from A549 (ENCLB001SBQ)

description:
https://www.encodeproject.org/experiments/ENCSR936UEX/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR936UEX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR344ERJ
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB001SBQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS293IUY at ENCODE; https://www.encodeproject.org/ENCBS293IUY/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB103SGI)

description:
https://www.encodeproject.org/experiments/ENCSR936UEX/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR936UEX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR344ERJ
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB103SGI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: link

value: ENCBS914AZQ at ENCODE; https://www.encodeproject.org/ENCBS914AZQ/


title: ChIP-seq from A549 (ENCLB275ELP)

description:
https://www.encodeproject.org/experiments/ENCSR928FDN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR928FDN
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB275ELP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS996ZFV at ENCODE; https://www.encodeproject.org/ENCBS996ZFV/


title: polyA mRNA RNA-seq from A549 (ENCLB653XDE)

description:
https://www.encodeproject.org/experiments/ENCSR924BHF/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR924BHF
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB653XDE
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Tim Reddy, Duke

value: ENCBS331QMP at ENCODE; https://www.encodeproject.org/ENCBS331QMP/


title: polyA mRNA RNA-seq from A549 (ENCLB413AHN)

description:
https://www.encodeproject.org/experiments/ENCSR924BHF/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR924BHF
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB413AHN
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS191VYO at ENCODE; https://www.encodeproject.org/ENCBS191VYO/


title: ChIP-seq from A549 (ENCLB875ZJH)

description:
https://www.encodeproject.org/experiments/ENCSR944WVU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR944WVU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR549SVK
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB875ZJH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS795HVL at ENCODE; https://www.encodeproject.org/ENCBS795HVL/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB207TQW)

description:
https://www.encodeproject.org/experiments/ENCSR919OXR/
***************
biological replicate number: 2
technical replicate number: 1
description: NR3C1 (GR) ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR919OXR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB207TQW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: ENCBS343YHO at ENCODE; https://www.encodeproject.org/ENCBS343YHO/


title: ChIP-seq from A549 (ENCLB348YKF)

description:
https://www.encodeproject.org/experiments/ENCSR887SZF/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR887SZF
assay title: ChIP-seq
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB348YKF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS684TZE at ENCODE; https://www.encodeproject.org/ENCBS684TZE/


title: ChIP-seq from A549 (ENCLB100FDZ)

description:
https://www.encodeproject.org/experiments/ENCSR905REY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR905REY
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB100FDZ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS299XUO at ENCODE; https://www.encodeproject.org/ENCBS299XUO/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB870ZRM)

description:
https://www.encodeproject.org/experiments/ENCSR873VJA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR873VJA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB870ZRM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS659JPG at ENCODE; https://www.encodeproject.org/ENCBS659JPG/


title: TCM CD4  40 min activated

value: TCM CD4 purified cells

value: 40 min activated with anti-CD3/28 beads


title: naïve CD4  15 hrs activated

value: naive CD4 purified cells

value: 15 hrs  activated with anti-CD3/28 beads


title: ChIP-seq from A549 (ENCLB535GRQ)

description:
https://www.encodeproject.org/experiments/ENCSR868MLT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR868MLT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB535GRQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS714IGN at ENCODE; https://www.encodeproject.org/ENCBS714IGN/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: DNase-seq from A549 (ENCLB326FVP)

description:
https://www.encodeproject.org/experiments/ENCSR837VHE/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR837VHE
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB326FVP
nucleic acid starting quantity: 220
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS549TVN at ENCODE; https://www.encodeproject.org/ENCBS549TVN/


title: TCM CD4  15 hrs activated


title: ChIP-seq from A549 (ENCLB458OFN)

description:
https://www.encodeproject.org/experiments/ENCSR901AAW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR901AAW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB458OFN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS938EZW at ENCODE; https://www.encodeproject.org/ENCBS938EZW/


title: ChIP-seq from A549 (ENCLB901HAL)

description:
https://www.encodeproject.org/experiments/ENCSR834LCU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR834LCU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB901HAL
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: ENCBS018TOF at ENCODE; https://www.encodeproject.org/ENCBS018TOF/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB987SIR)

description:
https://www.encodeproject.org/experiments/ENCSR954SQX/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR954SQX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB987SIR
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS417IIV at ENCODE; https://www.encodeproject.org/ENCBS417IIV/


title: ChIP-seq from A549 (ENCLB360VON)

description:
https://www.encodeproject.org/experiments/ENCSR872BBM/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR872BBM
assay title: ChIP-seq
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB360VON
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: ENCBS011GKY at ENCODE; https://www.encodeproject.org/ENCBS011GKY/


title: ChIP-seq from A549 (ENCLB630YAC)

description:
https://www.encodeproject.org/experiments/ENCSR952GOL/
***************
biological replicate number: 2
technical replicate number: 1
description: NR3C1 (GR) ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR952GOL
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB630YAC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS419HCP at ENCODE; https://www.encodeproject.org/ENCBS419HCP/


title: ChIP-seq from A549 (ENCLB304TNN)

description:
https://www.encodeproject.org/experiments/ENCSR791BNU/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR791BNU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR274VPI
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB304TNN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

value: ENCBS461GBL at ENCODE; https://www.encodeproject.org/ENCBS461GBL/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB434OVF)

description:
https://www.encodeproject.org/experiments/ENCSR791BNU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR791BNU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR274VPI
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB434OVF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS947WTB at ENCODE; https://www.encodeproject.org/ENCBS947WTB/


title: ChIP-seq from A549 (ENCLB991GZJ)

description:
https://www.encodeproject.org/experiments/ENCSR783SNV/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR783SNV
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR838ZAU
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB991GZJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: ENCBS508IUN at ENCODE; https://www.encodeproject.org/ENCBS508IUN/