title: ChIA-PET from HCT116 (ENCLB791GOR)

description:
https://www.encodeproject.org/experiments/ENCSR332LKV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, CTCF tag and IAA untreated, control
experiment encode accession: ENCSR332LKV
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB791GOR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

value: not applicable

value: male

value: adult

value: ENCBS166IPG at ENCODE; https://www.encodeproject.org/ENCBS166IPG/


title: ChIA-PET from HCT116 (ENCLB153EWY)

status: Public on Sep 07 2023

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/ENCSR106EOT/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, CTCF tag and IAA untreated, control
experiment encode accession: ENCSR106EOT
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB153EWY
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

tag: antibody

value: CTCF

tag: line

value: cell line

tag: biosample encode accession

tag: collection date

tag: geographic location

tag: encode accession

tag: Sex

tag: health state

value: colorectal carcinoma

tag: dev stage

tag: age

value: 48 year

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Dr. Masato Kanemaki

tag: link

value: ENCBS540XPU at ENCODE; https://www.encodeproject.org/ENCBS540XPU/


title: ChIA-PET from WTC11 (ENCLB777MDG)

description:
https://www.encodeproject.org/experiments/ENCSR779QAB/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in WTC11_clone28
experiment encode accession: ENCSR779QAB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB777MDG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR

value: 30 year

value: Charles Lee

value: Coriell

value: ENCBS628BTJ at ENCODE; https://www.encodeproject.org/ENCBS628BTJ/


title: ChIA-PET from A673 (ENCLB679GLW)

description:
https://www.encodeproject.org/experiments/ENCSR549TMF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in A673
experiment encode accession: ENCSR549TMF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-05-30
lab: Charles Lee
library encode accession: ENCLB679GLW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens A673 cell line

value: female

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS574NPV at ENCODE; https://www.encodeproject.org/ENCBS574NPV/


title: ChIA-PET from WTC11 (ENCLB795MQR)

description:
https://www.encodeproject.org/experiments/ENCSR353ASS/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in WTC11_clone6
experiment encode accession: ENCSR353ASS
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB795MQR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: not applicable

value: male

value: adult

value: ENCBS700IYD at ENCODE; https://www.encodeproject.org/ENCBS700IYD/


title: ChIA-PET from WTC11 (ENCLB331IJG)

description:
https://www.encodeproject.org/experiments/ENCSR543HLV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in WTC11_clone28
experiment encode accession: ENCSR543HLV
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-11-03
lab: Charles Lee
library encode accession: ENCLB331IJG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: cell line

value: ENCBS346YDA at ENCODE; https://www.encodeproject.org/ENCBS346YDA/


title: ChIA-PET from HCT116 (ENCLB217ZKV)

description:
https://www.encodeproject.org/experiments/ENCSR779BUF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, CDK7 tag and IAA untreated, control
experiment encode accession: ENCSR779BUF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB217ZKV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS806XLE at ENCODE; https://www.encodeproject.org/ENCBS806XLE/


title: ChIA-PET from PC-9 (ENCLB224YSX)

description:
https://www.encodeproject.org/experiments/ENCSR274ZVY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in PC-9
experiment encode accession: ENCSR274ZVY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB224YSX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens PC-9 cell line

value: not collected

value: unknown

value: Charles Lee

value: Sigma

value: ENCBS806KKT at ENCODE; https://www.encodeproject.org/ENCBS806KKT/


title: ChIA-PET from HCT116 (ENCLB815OEX)

description:
https://www.encodeproject.org/experiments/ENCSR066MHC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, MED14 tag and IAA untreated, control
experiment encode accession: ENCSR066MHC
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB815OEX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14

value: ENCBS804TFD at ENCODE; https://www.encodeproject.org/ENCBS804TFD/


title: ChIA-PET from HCT116 (ENCLB476MDZ)

description:
https://www.encodeproject.org/experiments/ENCSR779BUF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, CDK7 tag and IAA untreated, control
experiment encode accession: ENCSR779BUF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB476MDZ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: not applicable

value: ENCBS693PBI at ENCODE; https://www.encodeproject.org/ENCBS693PBI/


title: ChIA-PET from HCT116 (ENCLB675VDR)

description:
https://www.encodeproject.org/experiments/ENCSR758BJW/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, CDK7 tag and IAA untreated, control
experiment encode accession: ENCSR758BJW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB675VDR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: male

value: adult

value: ENCBS949SWI at ENCODE; https://www.encodeproject.org/ENCBS949SWI/


title: ChIA-PET from T-cell (ENCLB056DIO)

description:
https://www.encodeproject.org/experiments/ENCSR545NUL/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD3_Resting_donor4
experiment encode accession: ENCSR545NUL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB056DIO
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens female adult (21 years) T-cell primary cell

value: T-cell

value: primary cell

value: female

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS256PFL at ENCODE; https://www.encodeproject.org/ENCBS256PFL/


title: ChIA-PET from HCT116 (ENCLB738MBR)

description:
https://www.encodeproject.org/experiments/ENCSR066MHC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, MED14 tag and IAA untreated, control
experiment encode accession: ENCSR066MHC
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB738MBR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS283IKE at ENCODE; https://www.encodeproject.org/ENCBS283IKE/


title: ChIA-PET from HCT116 (ENCLB959MYL)

description:
https://www.encodeproject.org/experiments/ENCSR281XBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, RAD21 tag and IAA treated
experiment encode accession: ENCSR281XBJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB959MYL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: CTCF

value: not applicable

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS858CFF at ENCODE; https://www.encodeproject.org/ENCBS858CFF/


title: ChIA-PET from AG04450 (ENCLB983YPK)

description:
https://www.encodeproject.org/experiments/ENCSR037FPN/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in AG04450
experiment encode accession: ENCSR037FPN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Yijun Ruan, JAX
library encode accession: ENCLB983YPK
size range: 300-600

source_name: Homo sapiens AG04450 cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/f7779792-9403-4396-9ff6-8e859edd608c/@@download/attachment/In-situ%20chiapet_Ruan%20Lab_final.pdf
extraction method: SDS

value: male

value: apparently healthy

value: embryonic

value: 12 week

value: Yijun Ruan, JAX

value: Coriell

value: ENCBS452VFY at ENCODE; https://www.encodeproject.org/ENCBS452VFY/

value: Derived from ENCODE donor ENCDO001AAA; https://www.encodeproject.org/ENCDO001AAA/


title: ChIA-PET from activated T-cell (ENCLB279XTI)

description:
https://www.encodeproject.org/experiments/ENCSR038GON/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD3_Activated_donor1
experiment encode accession: ENCSR038GON
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB279XTI
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens male adult (43 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: primary cell

value: adult

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS415KTK at ENCODE; https://www.encodeproject.org/ENCBS415KTK/


title: ChIA-PET from HCT116 (ENCLB178UCW)

description:
https://www.encodeproject.org/experiments/ENCSR758BJW/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, CDK7 tag and IAA untreated, control
experiment encode accession: ENCSR758BJW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB178UCW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: cell line

value: not applicable

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS730DRB at ENCODE; https://www.encodeproject.org/ENCBS730DRB/


title: ChIA-PET from WTC11 (ENCLB108GVO)

description:
https://www.encodeproject.org/experiments/ENCSR543HLV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in WTC11_clone28
experiment encode accession: ENCSR543HLV
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-11-03
lab: Charles Lee
library encode accession: ENCLB108GVO
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: male

value: 30 year

value: Charles Lee

value: Coriell

value: ENCBS012LZU at ENCODE; https://www.encodeproject.org/ENCBS012LZU/


title: ChIA-PET from WTC11 (ENCLB682VWG)

description:
https://www.encodeproject.org/experiments/ENCSR016VPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in WTC11
experiment encode accession: ENCSR016VPZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-11-03
lab: Charles Lee
library encode accession: ENCLB682VWG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens WTC11 cell line

value: adult

value: ENCBS433ADF at ENCODE; https://www.encodeproject.org/ENCBS433ADF/


title: ChIA-PET from HCT116 (ENCLB701NBW)

description:
https://www.encodeproject.org/experiments/ENCSR326KGW/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SUPT16H tag and IAA treated
experiment encode accession: ENCSR326KGW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB701NBW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS815ASY at ENCODE; https://www.encodeproject.org/ENCBS815ASY/


title: ChIA-PET from embryonic stem cell (ENCLB300BAQ)

description:
https://www.encodeproject.org/experiments/ENCSR995XUW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in C57BL6J
experiment encode accession: ENCSR995XUW
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB300BAQ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600
instrument models: Illumina MiSeq,Illumina NovaSeq 6000

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J male embryo embryonic stem primary cell

value: embryonic stem cell

value: primary cell

value: embryonic

value: unknown

value: The Jackson Laboratory

value: ENCBS943SIL at ENCODE; https://www.encodeproject.org/ENCBS943SIL/


title: ChIA-PET from WTC11 (ENCLB646DDC)

description:
https://www.encodeproject.org/experiments/ENCSR016VPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in WTC11
experiment encode accession: ENCSR016VPZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-11-03
lab: Charles Lee
library encode accession: ENCLB646DDC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: cell line

value: not applicable

value: ENCBS965HLB at ENCODE; https://www.encodeproject.org/ENCBS965HLB/


title: ChIA-PET from HCT116 (ENCLB804QLF)

description:
https://www.encodeproject.org/experiments/ENCSR010NWN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, SMARCA5 tag and IAA untreated, control
experiment encode accession: ENCSR010NWN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB804QLF
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS928PTW at ENCODE; https://www.encodeproject.org/ENCBS928PTW/


title: ChIA-PET from embryonic stem cell (ENCLB023MOI)

description:
https://www.encodeproject.org/experiments/ENCSR179IQN/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in C57BL6J
experiment encode accession: ENCSR179IQN
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB023MOI
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600
instrument models: Illumina MiSeq,Illumina NovaSeq 6000

value: Charles Lee

value: ENCBS016RGR at ENCODE; https://www.encodeproject.org/ENCBS016RGR/


title: ChIA-PET from Patski (ENCLB575KSG)

description:
https://www.encodeproject.org/experiments/ENCSR564BAB/
***************
biological replicate number: 3
technical replicate number: 1,2
description: RNAPII ChIA-PET in Patski
experiment encode accession: ENCSR564BAB
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB575KSG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600
instrument models: Illumina MiSeq,Illumina NovaSeq 6000

source_name: Mus musculus strain Patski Patski cell line

value: Patski

value: ENCBS511XEM at ENCODE; https://www.encodeproject.org/ENCBS511XEM/


title: ChIA-PET from HCT116 (ENCLB181HWL)

description:
https://www.encodeproject.org/experiments/ENCSR010NWN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, SMARCA5 tag and IAA untreated, control
experiment encode accession: ENCSR010NWN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB181HWL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: adult

value: ENCBS839SOR at ENCODE; https://www.encodeproject.org/ENCBS839SOR/


title: ChIA-PET from Patski (ENCLB631VGJ)

description:
https://www.encodeproject.org/experiments/ENCSR045WUV/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Patski
experiment encode accession: ENCSR045WUV
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB631VGJ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600
instrument models: Illumina MiSeq,Illumina NovaSeq 6000

value: embryonic

value: unknown

value: The Jackson Laboratory

value: ENCBS670EOS at ENCODE; https://www.encodeproject.org/ENCBS670EOS/


title: ChIA-PET from Patski (ENCLB211KLL)

description:
https://www.encodeproject.org/experiments/ENCSR045WUV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Patski
experiment encode accession: ENCSR045WUV
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB211KLL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600
instrument models: Illumina MiSeq,Illumina NovaSeq 6000

value: CTCF

value: cell line

value: not applicable

value: ENCBS251CCX at ENCODE; https://www.encodeproject.org/ENCBS251CCX/


title: ChIA-PET from embryonic stem cell (ENCLB744JKM)

description:
https://www.encodeproject.org/experiments/ENCSR780SBE/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in 129S1SvImJ
experiment encode accession: ENCSR780SBE
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB744JKM
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600
instrument models: Illumina MiSeq,Illumina NovaSeq 6000

source_name: Mus musculus strain 129S1/SvImJ male embryo embryonic stem primary cell

value: embryonic stem cell

value: primary cell

value: male

value: ENCBS614IRR at ENCODE; https://www.encodeproject.org/ENCBS614IRR/


title: ChIA-PET from H1 (ENCLB489ARY)

description:
https://www.encodeproject.org/experiments/ENCSR095SXC/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in H1
experiment encode accession: ENCSR095SXC
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR095SXC
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB489ARY
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens H1 cell line

value: healthy

value: Charles Lee

value: WiCell

value: ENCBS514AVJ at ENCODE; https://www.encodeproject.org/ENCBS514AVJ/


title: ChIA-PET from HCT116 (ENCLB773BWD)

description:
https://www.encodeproject.org/experiments/ENCSR771PKY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, RAD21 tag and IAA treated
experiment encode accession: ENCSR771PKY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB773BWD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS727VJX at ENCODE; https://www.encodeproject.org/ENCBS727VJX/


title: ChIA-PET from activated T-cell (ENCLB226IEE)

description:
https://www.encodeproject.org/experiments/ENCSR038GON/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIA-PET in CD3_Activated_donor1
experiment encode accession: ENCSR038GON
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB226IEE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: activated T-cell

value: not applicable

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS415KTK at ENCODE; https://www.encodeproject.org/ENCBS415KTK/


title: ChIA-PET from H1 (ENCLB750BBG)

description:
https://www.encodeproject.org/experiments/ENCSR782EKZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in H1
experiment encode accession: ENCSR782EKZ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR782EKZ
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB750BBG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: male

value: healthy

value: embryonic

value: unknown

value: Charles Lee

value: WiCell

value: ENCBS319TTP at ENCODE; https://www.encodeproject.org/ENCBS319TTP/


title: R26-CreERT2 Tp53fl/fl derived cells, Day 21 rep 3

status: Public on Apr 26 2023

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

library_source: transcriptomic

data_processing:
Preprocessing: Sequenced reads (150bp) were trimmed for adaptor sequence and low quality reads using fastp (v 0.19.5, Shifu Chen, fastp: A fast FASTQ preprocessor with full features, (2017), GitHub repository, https://github.com/OpenGene/fastp ). Command line used: fastp  --trim_front1 10 --trim_front2 10
Preprocessing: Reads mapping to rRNA were removed using Bbmap . Command line used: bbsplit.sh minratio=0.56 minhits=1 maxindel=16000
Gene expression: Trimmeds reads were aligned using Salmon (version v1.4.0) against mm10 (Annotation: gencode.mm10.vM22).
Gene expression: Data was normalised in Degust (http://victorian-bioinformatics-consortium.github.io/degust/) using voom with sample weighting. Genes with count >1 and CPM > 1 in at least 2 samples of a given genotype were considered for further analysis.
RNA Editing: Calling of differential editing in known sites (RNA genotype vs RNA genotype) was performed using JACUSA 2.0.0-RC5. Briefly, call-2 was used to determine the difference in editing level for all known sites (all replicates of genotype A vs all replicates of genotype B). Duplicate reads were removed.
Assembly: mm10
Supplementary files format and content: txt: JACUSA call-1 and call-2 RNA editing output files. xlsx: supplementary_gene_expression: Differential expression results. : supplementary_editing: Processed RNA editing results.

molecule: total RNA

source_name: Osteoblasts

growth_protocol: Murine osteoblasts immortalised from primary long bone derived osteoblasts with engineered deletion of p53 (R26-CreERT2 Tp53fl/fl derived cells) were collected at day 7, 14 and 21 post tamoxifen addition. RNA samples were diluted in nuclease-free water to a concentration ranging between 100-270ng/µL. was lysed in Trisure and purified using DirectZol columns.  >2.5 ug of total RNA was used for the construction of sequencing libraries.

extract_protocol:
RNA-Seq
library and sequencing performed by Novogene (Singapore)).

treatment_protocol: The total RNA used for poly(A) enrichment and library preparation following by sequencing on the Illumina platform (150bpPE; library and sequencing performed by Novogene (Singapore)).

tag: genotype

value: R26-Adar1KI/+ x R26-CreERT2 Tp53fl/fl

value: 12 week old

tag: replicate

tag: tissue

value: Osteoblasts

value: female

tag: strain


title: ChIA-PET from H1 (ENCLB550BMH)

description:
https://www.encodeproject.org/experiments/ENCSR095SXC/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in H1
experiment encode accession: ENCSR095SXC
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR095SXC
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB550BMH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

tag: antibody

value: CTCF

tag: line

value: not applicable


title: intact Hi-C from lower lobe of left lung (ENCLB383FPB)

status: Public on Jul 24 2023

description:
https://www.encodeproject.org/experiments/ENCSR446NJD/
***************
biological replicate number: 1
technical replicate number: 1
description: w73 lower lobe of left lung intact dnase hic
experiment encode accession: ENCSR446NJD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB383FPB
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (59 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

value: tissue

tag: biosample encode accession

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

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS614CBB at ENCODE; https://www.encodeproject.org/ENCBS614CBB/

value: derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: R26-CreERT2 Tp53fl/fl derived cells, Day 21 rep 2

value: male


title: R26-CreERT2 Tp53fl/fl derived cells, Day 14 rep 2


title: R26-CreERT2 Tp53fl/fl derived cells, Day 14 rep 3


title: R26-CreERT2 Tp53fl/fl derived cells, Day 21 rep 1


title: intact Hi-C from right lobe of liver (ENCLB214ZIG)

description:
https://www.encodeproject.org/experiments/ENCSR874EIH/
***************
biological replicate number: 1
technical replicate number: 2
description: w61 right lobe of liver
experiment encode accession: ENCSR874EIH
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB214ZIG
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue, preserved by flash-freezing

value: right lobe of liver

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

value: 41 year

value: ENCBS482GVK at ENCODE; https://www.encodeproject.org/ENCBS482GVK/

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


title: R26-CreERT2 Tp53fl/fl derived cells, Day 7 rep 2

value: R26-Adar1KI/+ x R26-CreERT2 Tp53fl/fl

value: 12 week old

value: Osteoblasts


title: R26-CreERT2 Tp53fl/fl derived cells, Day 7 rep 1


title: R26-CreERT2 Tp53fl/fl derived cells, Day 7 rep 3

value: female


title: WT_r3_L3

description:
WT replicate 1 (WT_r1)
WT replicate 2 (WT_r2)

data_processing:
Preprocessing: Sequenced reads (150bp) were trimmed for adaptor sequence and low quality reads using fastp (v 0.19.5, Shifu Chen, fastp: A fast FASTQ preprocessor with full features, (2017), GitHub repository, https://github.com/OpenGene/fastp ). Command line used: fastp  --trim_front1 10 --trim_front2 10
Preprocessing: Reads mapping to rRNA were removed using Bbmap . Command line used: bbsplit.sh minratio=0.56 minhits=1 maxindel=16000
Gene expression: Trimmeds reads were aligned using Salmon (version v1.4.0) against mm10 (Annotation: gencode.mm10.vM22).
Assembly: mm10
Supplementary files format and content: txt: JACUSA call-1 and call-2 RNA editing output files. xlsx: supplementary_gene_expression: Differential expression results. : supplementary_editing: Processed RNA editing results.

source_name: Liver

growth_protocol: Whole liver from tamoxifen treated mice of the indicated genotypes was used to purify RNA for RNA-seq. RNA samples were diluted in nuclease-free water to a concentration ranging between 100-270ng/µL.

extract_protocol:
RNA-Seq
The total RNA used for poly(A) enrichment and library preparation following by sequencing on the Illumina platform (150bpPE; library and sequencing performed by Novogene (Singapore)).

tag: adar1 genotype

value: WT

tag: full genotype

value: UBC-CreERtg/+,WT

value: 10-12 weeks

tag: time post tamixofen

value: 2 weeks

value: Liver


title: WT_r2_L2

tag: Sex


title: ChIA-PET from H1 (ENCLB144DJE)

description:
https://www.encodeproject.org/experiments/ENCSR782EKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in H1
experiment encode accession: ENCSR782EKZ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR782EKZ
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB144DJE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: health state

value: healthy

tag: dev stage

value: embryonic

value: unknown

value: Charles Lee

value: WiCell

value: ENCBS514AVJ at ENCODE; https://www.encodeproject.org/ENCBS514AVJ/


title: R26-CreERT2 Tp53fl/fl derived cells, Day 14 rep 1

value: R26-Adar1KI/+ x R26-CreERT2 Tp53fl/fl

tag: age

value: male


title: E861AKI_r3_L16

description:
ADAR1 E861A overexpression replicate 1 E861AKI_r1)
ADAR1 E861A overexpression replicate 3 E861AKI_r3)


title: WT_r1_L1

description:
WT replicate 1 (WT_r1)
WT replicate 1 (WT_r1)


title: E861AKI_r1_L14

description:
ADAR1 E861A overexpression replicate 1 E861AKI_r1)
ADAR1 E861A overexpression replicate 1 E861AKI_r1)


title: Adar1_p150KI_r2_L9

description:
ADAR1 p150 overexpression replicate 1 (Adar1_p150KI_r1)
ADAR1 p150 overexpression replicate 2 (Adar1_p150KI_r2)

value: UBC-CreERtg/+,R26-Adar1 p150KI/+


title: E861AKI_r2_L15

description:
ADAR1 E861A overexpression replicate 1 E861AKI_r1)
ADAR1 E861A overexpression replicate 2 E861AKI_r2)


title: Adar1_p150KI_r3_L10

description:
ADAR1 p150 overexpression replicate 1 (Adar1_p150KI_r1)
ADAR1 p150 overexpression replicate 3 (Adar1_p150KI_r3)

value: female


title: WT_R26-Adar1p150KI/+_r1_L4

description:
Cre -ve Control replicate 1 (WT_R26-Adar1p150KI/+_r1_L4_r1)
Cre -ve Control replicate 1 (WT_R26-Adar1p150KI/+_r1_L4_r1)

value: WT

value: WT,R26-Adar1 p150KI/+


title: Adar1_p150KI_r1_L8

description:
ADAR1 p150 overexpression replicate 1 (Adar1_p150KI_r1)
ADAR1 p150 overexpression replicate 1 (Adar1_p150KI_r1)

value: 10-12 weeks


title: Adar1_p110KI_r3_L13

description:
ADAR1 p110 overexpression replicate 1 (Adar1_p110KI_r1)
ADAR1 p110 overexpression replicate 3 (Adar1_p110KI_r3)

value: 2 weeks


title: Adar1_p110KI_r1_L11

description:
ADAR1 p110 overexpression replicate 1 (Adar1_p110KI_r1)
ADAR1 p110 overexpression replicate 1 (Adar1_p110KI_r1)

value: Liver


title: Adar1_p110KI_r2_L12

description:
ADAR1 p110 overexpression replicate 1 (Adar1_p110KI_r1)
ADAR1 p110 overexpression replicate 2 (Adar1_p110KI_r2)


title: Adar1KI_r3_L7

description:
ADAR1 overexpression replicate 1 (Adar1KI_r1)
ADAR1 overexpression replicate 3 (Adar1KI_r3)


title: Adar1KI_r2_L6

description:
ADAR1 overexpression replicate 1 (Adar1KI_r1)
ADAR1 overexpression replicate 2 (Adar1KI_r2)


title: Adar1KI_r1_L5

description:
ADAR1 overexpression replicate 1 (Adar1KI_r1)
ADAR1 overexpression replicate 1 (Adar1KI_r1)


title: WT3

status: Public on Apr 24 2023

city: Edinburgh

first: Marcus

last: Keatinge

state: Midlothian

address: Ground Floor, Chancellors building, little france

country: United Kingdom

institute: University of Edinburgh

data_processing:
Per-lane fastq files were merged using the bcbio_prepare_samples.py script from bcbio
Annotation files were download from Ensembl  GRCz11 version) and used for quantification with salmon version 0.9.1 (default parameters)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include TPM values and raw reads for each Sample

organism: Danio rerio

growth_protocol: RNA was prepared from brain tissue of 12-week-old zebrafish

extract_protocol:
TRIzol_x0002_based protocol was used to extract RNA from the tissue. Briefly, individual brains were homogenised in 250 µl TRI Reagent (Sigma-Aldrich) and incubated at room temperature before adding 50 µl chloroform (Thermo Fisher Scientific). The samples were centrifuged at 13,300 g and the top aqueous phase was collected and transferred to a separate tube. RNA was precipitated from the aqueous phase by mixing with an equal volume of isopropanol (Thermo Fisher Scientific) and centrifugation at 13,300 g. The precipitated RNA was resuspended in DEPC-treated water (Thermo Fisher Scientific), and its concentration and quality were quantified using the Nanodrop 1000 Spectrophotomete
Approximately 750 ng of high-quality total RNA, with an RNA integrity number of 9 or above, was used in the preparation of sequencing libraries using the NEB Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760), following the polyA mRNA workflo

value: brain

tag: genotype

tag: batch

value: 12 weeks old


title: WT1

tag: tissue


title: WT2


title: S2


title: S1


title: WT4


title: GS3


title: S4


title: G2


title: GS4


title: G4


title: G1


title: S3


title: G3


title: WTC11 iPSC, differentiated to VICs, rep 1

status: Public on Mar 03 2023

city: New York

first: Clifford

middle: Z.

last: Liu

state: NY

address: 1470 Madison Ave, Hess 8-301

institute: Icahn School of Medicine at Mount Sinai

data_processing:
2-pass mapping with STAR v2.7.10a
Duplicate reads removed with Picard v2.26.10.
Read counts generated with HTSeq v 2.0.2.
Assembly: NCBI build 38/ UCSC hg38
Supplementary files format and content: Gene counts, .txt file

extract_protocol:
Total RNA extracted with the Qiagen RNeasy Kit, following proteinase K incubation.
Poly A selection without strand specificity (performed by Novogene)
RNAseq (performed by Novogene)

tag: cell line

tag: cell type

value: Valvular Interstitial Cells


title: WTC11 iPSC, differentiated to endothelial cells (control), rep 1

value: Endothelial Cell


title: WTC11 iPSC, differentiated to VECs, rep 1

value: Valvular Endothelial Cells


title: Healthy_control_2

status: Public on Apr 03 2023

city: Tainan

first: Yu-Chen

last: Lin

address: 138 Sheng-Li Rd

country: Taiwan

institute: National Cheng Kung University

data_processing:
Quality control and data filtering were done using fastp.
Alignment of the reads to the human genome was done using HISAT2.
The raw reads generated was counted using featureCounts.
Differential analysis of the gene counts was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts for each Sample.

source_name: Skin

extract_protocol:
RNA was extracted by the RNeasy Mini Kit (QIAGEN, Hilden, Germany).
Library was prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

value: Skin

tag: diagnosis

value: Healthy

tag: treatment


title: Healthy_control_1


title: MSN02-4 iPSC, differentiated to VECs, rep1


title: MSN02-4 iPSC, differentiated to VICs, rep 1


title: MSN02-4 iPSC, differentiated to endothelial cells (control), rep 1


title: MSN02-4 iPSC, differentiated to endocardial cells, rep 1

value: Endocardial Cell


title: Whole Brain P195A/- rep 3 (ZL13_310)

status: Public on Feb 13 2023

description: ADAR1 P195A/- rep 3

data_processing:
Preprocessing: Sequenced reads (150bp) were trimmed for adaptor sequence and low quality reads using fastp (v 0.19.5, Shifu Chen, fastp: A fast FASTQ preprocessor with full features, (2017), GitHub repository, https://github.com/OpenGene/fastp ). Command line used: fastp  --trim_front1 10 --trim_front2 10
Preprocessing: Reads mapping to rRNA were removed using Bbmap . Command line used: bbsplit.sh minratio=0.56 minhits=1 maxindel=16000
Gene expression: Trimmeds reads were aligned using Salmon (version v1.6.0) against mm11 (Annotation: gencode.mm11.vM28).
Gene expression: Data was normalised in Degust (http://victorian-bioinformatics-consortium.github.io/degust/) using EdgeR (McCarthy, J. D, Chen, Yunshun, Smyth and K. G (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), pp. -9.). Genes with count >1 and CPM > 1 in at least 3/3 samples of a given genotype were considered for further analysis. Each comparison (P195A/+ vs WT, P195A/P195A vs WT, P195A/- vs WT, P195A/P195A vs  P195A/- ) was performed seperately. Differential expression was performed in Degust using EdgeR.
RNA Editing: Calling of differential editing in known sites (RNA genotype vs RNA genotype) was performed using JACUSA 2.0.0-RC5. Briefly, call-2 was used to determine the difference in editing level for all known sites (all replicates of genotype A vs all replicates of genotype B). Duplicate reads were removed.
Assembly: mm10
Supplementary files format and content: txt: JACUSA call-1 and call-2 RNA editing output files. xlsx: supplementary_gene_expression: Differential expression results. : supplementary_editing: Processed RNA editing results.

source_name: Adult Brain

growth_protocol: Samples used for RNA-seq were from whole brain samples of 42 to 74 days old mice of Adar1+/+ (2F/1M; n=3); Adar1P195A/+ (2F/1M; n=3); Adar1P195A/P195A (3F/1M; n=4); Adar1P195A/-  (2F/1M; n=3). Brain samples were collected, snap-frozen in liquid nitrogen, and stored at -80C. Frozen tissues were homogenized in Trisure reagent (Bioline) using IKA T10 basic S5 Ultra-turrax Disperser.

extract_protocol:
RNA was extracted using Direct-Zol columns (Zymo Research) as per manufacturer’s instruction.
Each sample contained 2500 ng RNA and was sent for sequencing in a dry powder form using Novogne RNA Ambient Tube following the Manufacturer's instruction. cDNA library preparation and sequencing were performed by Novogene LAB (Novogeneait Genomics Singapore PTE LTD).

tag: adar1 genotype

value: Adar (P195A)PM/Adar (P195A)PM,AdarKO/+

tag: adar1 genotype simple

value: M

tag: weaning weight

value: 8.4g at  weaning 20 days old

value: 42 days

tag: replicate

value: Whole Brain

tag: strain


title: Whole Brain P195A/- rep 2 (ZL12_313)

description: ADAR1 P195A/- rep 2

tag: Sex

value: F

value: 8.2g at  weaning 20 days old


title: Whole Brain P195A/- rep 1 (ZL11_317)

description: ADAR1 P195A/- rep 1

value: 7.9g at  weaning 20 days old


title: Whole Brain P195A/P195A rep 4 (ZL10_298)

description: ADAR1 P195A/P195A rep 4

value: Adar (P195A)PM/Adar (P195A)PM,WT

value: 8.0g at weaning 19 days old

value: 48 days


title: GS2

value: brain

value: 12 weeks old


title: GS1


title: Whole Brain P195A/P195A rep 2 (ZL8_309)

description: ADAR1 P195A/P195A rep 2


title: Whole Brain P195A/P195A rep 3 (ZL9_301)

description: ADAR1 P195A/P195A rep 3

value: 7.3g at weaning 19 days old


title: Whole Brain P195A/+ rep 2 (ZL5_306)

description: ADAR1 P195A/+ rep 2

value: Adar (P195A)PM/+,WT

value: 10.3g at  weaning 21 days old

value: 43 days


title: Whole Brain P195A/+ rep 1 (ZL4_307)

description: ADAR1 P195A/+ rep 1

value: 9.0g at  weaning 21 days old


title: Whole Brain wt rep 2 (ZL2_297)

description: wt rep 2

value: WT,WT

value: wt

value: 10.5g at weaning 19 days old


title: OCIAML3_RNA_selinexor_100nM_6h_REP2_220622_TCGAAG_S5

status: Public on Jan 30 2023

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Assembly: GRCh38/hg38
Supplementary files format and content: DESeq2 differential expression summary data (Excel .xlsx format)

source_name: Cell Line OCI-AML3

growth_protocol: Human cell lines were cultured in RPMI with 10% FBS.

extract_protocol:
For RNA isolation, cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) was used to obtain 1-5´107 unique sequencing paired-end tags

treatment_protocol: Treatment regimens indicated for each sample.

tag: timepoint

value: 6 hours

value: 100nM selinexor


title: OCIAML3_RNA_selinexor_100nM_6h_REP1_220622_TCCCGA_S4


title: Whole Brain wt rep 1 (ZL1_300)

description: wt rep 1

value: F

value: 9.0g at weaning 19 days old

value: Whole Brain


title: Whole Brain P195A/+ rep 3 (ZL6_304)

description: ADAR1 P195A/+ rep 3

value: M

value: 10.7g at  weaning 21 days old


title: OCIAML3_RNA_DMSO_6h_REP3_220622_TCATTC_S3

value: DMSO


title: WTC11 iPSC, differentiated to endocardial cells, rep 1

value: Endocardial Cell

value: WT


title: OCIAML3-NPM1c-FKBP_ChIP_RNAPol2_dTAG13_500nM_24h_REP1_220531_GTTTCG_S10

description: ChIPseq_MACS2_peak_bedtools_coverage_diffrpk_OCIAML3-NPM1c-FKBP_Supp_S1.xlsx

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human(Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM  atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and ngs.plot (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
Peak-associated signals were assessed using the bedtools coverage function. Single peaks were chosen as representative of change in gene signal, using the peak overlapping the gene body which showed the greatest differential signal between treated and control ChIP samples. Signal values were normalized based on the ratio of hg38-aligning reads in treated and control samples, after deduplication.
Assembly: GRCh38/hg38
Supplementary files format and content: MACS2 peak interval signal summary (from bedtools coverage; Excel .xlsx format); Broad IGV (.tdf) files for visualization

source_name: Derivative of cell line OCI-AML3

extract_protocol:
Cells were crosslinked with 1% methanol-free formaldehyde (ThermoFisher) for 7-10 min at room temperature, followed by quenching with 100 mM Tris pH8.0 and 25 mM Glycine, and the cells were lysed in SDS buffer. Cytoplasm was lysed using 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1% SDS for 10 min and nuclei were precipitated by centrifugation at 10,000´g. Nuclei were resuspended in 66 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1.7% Triton X-100, 0.5% SDS and sheared using E100S (Covaris) to chromatin fragments of 200-400 base-pair DNA size.
1-10 ng of DNA was used in preparation of Illumina-compatible libraries using ThruPlex DNA kit (Rubicon Genomics)
Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) was used to obtain 1-5´107 unique sequencing paired-end tags

tag: antibody

tag: antibody manufacturer

value: Cell Signaling

tag: antibody catalog number

tag: agent

value: 500nM dTAG13

value: 24 hours


title: OCIAML3_RNA_selinexor_100nM_6h_REP3_220622_TCGGCA_S6


title: OCIAML3-NPM1c-FKBP_ChIP_NPM1c_dTAG13_500nM_24h_REP1_220623_CGATGT_S2

value: ThermoFisher


title: OCIAML3-NPM1c-FKBP_ChIP_input_DMSO_24h_REP1_220907_ATTCCT_S5


title: OCIAML3-NPM1c-FKBP_ChIP_input_DMSO_24h_REP1_220623_GGCTAC_S11


title: OCIAML3-NPM1c-FKBP_ChIP_NPM1_dTAG_500nM_24h_REP1_220907_ACTGAT_S4


title: OCIAML3-NPM1c-FKBP_ChIP_H3K27ac_dTAG13_500nM_24h_REP1_220623_ACTTGA_S8

value: Abcam


title: Whole Brain P195A/P195A rep 1 (ZL7_314)

description: ADAR1 P195A/P195A rep 1

value: Adar (P195A)PM/Adar (P195A)PM,WT

value: 6.4g at  weaning 20 days old

tag: age

value: 42 days


title: OCIAML3-NPM1c-FKBP_ChIP_RNAPol2_DMSO_24h_REP1_220531_GTGGCC_S9


title: OCIAML3-NPM1c-FKBP_ChIP_DOT1L_dTAG13_500nM_24h_REP1_220623_GCCAAT_S6


title: OCIAML3-NPM1c-FKBP_ChIP_H3K27ac_DMSO_24h_REP1_220623_CAGATC_S7


title: Whole Brain wt rep 3 (ZL3_290)

description: wt rep 3

value: WT,WT

value: wt

value: 10.3g at  weaning 24 days old

value: 74 days

tag: tissue


title: OCIAML3-NPM1c-FKBP_ChIP_DOT1L_DMSO_24h_REP1_220623_ACAGTG_S5

tag: cell line


title: OCIAML3-NPM1c-FKBP_ChIP_CDK9_dTAG13_500nM_24h_REP1_220623_TAGCTT_S10

value: Santa Cruz


title: OCIAML3_ChIP_NPM1wt_VTP_330nM_4d_REP1_220623_ATGTCA_S15

description: ChIPseq_MACS2_peak_bedtools_coverage_diffrpk_OCIAML3_selinexor_VTP_Supp_S11.xlsx

value: 4 days


title: OCIAML3-NPM1c-FKBP_ChIP_CDK9_DMSO_24h_REP1_220623_GATCAG_S9

value: DMSO


title: OCIAML3_ChIP_NPM1c_VTP_330nM_4d_REP1_220623_AGTCAA_S13


title: OCIAML3_ChIP_NPM1c_DMSO_4d_REP1_220623_CTTGTA_S12


title: OCIAML3_RNA_DMSO_6h_REP2_220622_TATAAT_S2

value: 6 hours


title: OCIAML3_ChIP_MLL1_VTP_330nM_4d_REP1_220301_CGATGT_S2

value: Bethyl


title: OCIAML3_ChIP_MLL1_DMSO_4d_REP1_220301_ATCACG_S1


title: OCIAML3_ChIP_NPM1wt_DMSO_4d_REP1_220623_AGTTCC_S14


title: OCIAML3-NPM1c-FKBP_ChIP_NPM1_DMSO_24h_REP1_220907_GAGTGG_S3


title: OCIAML3_ChIP_MEN1_VTP_330nM_4d_REP1_220301_TGACCA_S4


title: OCIAML3_ChIP_MEN1_DMSO_4d_REP1_220301_TTAGGC_S3


title: OCIAML3_RNA_DMSO_6h_REP1_220622_TACAGC_S1


title: OCIAML3_ChIP_input_DMSO_4d_REP1_220623_GTGAAA_S16


title: OCIAML3_ChIP_input_VTP_330nM_4d_REP1_220301_GCCAAT_S5


title: OCIAML3-NPM1c-FKBP_ChIP_input_DMSO_24h_REP1_220531_CGTACG_S11


title: OCIAML3_ChIP_input_DF_VTP_330nM_96h_REP1_210322_CCGTCC_S6


title: OCIAML3_ChIP_input_DF_DMSO_96h_REP1_210322_ATGTCA_S5


title: OCIAML3_ChIP_CRM1_DF_DMSO_96h_REP1_210322_GTCCGC_S7

value: Cell Signaling


title: 293T-MIG-NPM1c_ChIP_HA_steadystate_REP1_210903_ACTTGA_S8

description: ChIPseq_MACS2_peak_bedtools_coverage_diffrpk_293T_CRM1_HA_Supp_S9.xlsx

source_name: Cell line 293T

value: HA

value: untreated

value: steadystate


title: 293T-MIG-NPM1c-HA_ChIP_HA_steadystate_REP1_210903_GATCAG_S9


title: OCIAML3-NPM1c-FKBP_ChIP_NPM1c_DMSO_24h_REP1_220623_ATCACG_S1

value: ThermoFisher

value: 24 hours


title: OCIAML3_ChIP_CRM1_DF_VTP_330nM_96h_REP1_210322_GTGAAA_S8


title: 293T-MIG-AS1-HA_ChIP_HA_steadystate_REP1_210903_CTTGTA_S11


title: 293T-MIG_ChIP_input_steadystate_REP1_210903_ATCACG_S1


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_3h_REP1_210819_TACCTT_S16

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
SLAMseq FASTQ files were analyzed using the Slamdunk pipeline, described elsewhere.
Differential SLAMseq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using Slamdunk converted counts.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: DESeq2 differential gene expression summary using Slamdunk pipeline output (Excel .xlsx format)

molecule: polyA RNA

extract_protocol:
Cells were harvested at 300 g for 5 min at 4°C, washed with PBS and the RNA was extracted from the cell pellet using QIAshredders (Qiagen) and RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. 5ug of the extracted RNA was Iodoacetamide treated according to the SLAM-Seq Metabolic Labeling kit (Lexogen) manual instructions
Libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Preparation kit (Lexogen)
SLAMseq, Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 75bp, single-end reads.

value: 500nM dTAG13


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_3h_REP2_210819_TCTTAA_S17


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_3h_REP3_210819_GTCAGG_S18


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_30m_REP3_210819_TCAGGA_S9


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_30m_REP2_210819_TGTGCA_S8


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_2h_REP3_210819_GGCTGC_S15


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_2h_REP1_210819_CCTAAG_S13


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_1h_REP3_210819_ATGAAC_S12


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_1h_REP2_210819_TTAACT_S11


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_1h_REP1_210819_CGGTTA_S10


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_15m_REP3_210819_GTGTAG_S6


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_15m_REP2_210819_ACATTA_S5


title: OCIAML3-NPM1c-FKBP_SLAM_DMSO_0m_REP3_210819_ACCAGT_S3


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_15m_REP1_210819_TGCACG_S4


title: OCIAML3-NPM1c-FKBP_SLAM_DMSO_0m_REP2_210819_GATCAC_S2


title: OCIAML3-NPM1c-FKBP_SLAM_DMSO_0m_REP1_210819_CAGCGT_S1


title: OCIAML3_PRO_DMSO_0m_REP2_211124_GTAGAG_S8

data_processing:
Library strategy: PRO-seq
FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the hg38 reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl).
For promoter reads, annotated transcription start sites were obtained from human (GRCh38.99) GTFs from Ensembl. After removing transcripts with {immunoglobulin, Mt, Mt_tRNA, rRNA} biotypes, PRO-seq signal in each sample was calculated in the window from the annotated TSS to +150 nt downstream, using a custom script, make_heatmap.pl.
For differential expression analysis, reads were summed within the TSS to TES window for each active gene.  DEseq2, using the Wald test, was used to determine statistically significant differentially expressed genes. Unless otherwise noted, the default size factors determined by DEseq2 were used.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Differential expression (Excel .xlsx format)

source_name: Cell line OCI-AML3

extract_protocol:
10 million cells were harvested and washed once with ice cold PBS, cell pellets were resuspended in 250uL wash buffer to get single-cell suspensions. 10mL permealization buffer was added and samples were incubated on ice for 5 min. Cells were spun down and pellets were washed in 10mL wash buffer. Cells were spun again and resuspended in freezing buffer. Cells were counted and permealization was visualized using tryphan blue. 5 million permealized cells were snap-frozen in 500ul freezing buffer in liquid nitrogen and stored at -80°C. All subsequent steps were performed by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA. In brief, run-on reactions were performed at 37°C.  Adenylated 3' adapter was prepared using the 5' DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturers instructions with 15% PEG-8000 final) and incubated at 16°C overnight.  180uL of betaine blocking buffer with 0.6 uM blocking oligo was mixed with ligations and incubated for 5 min at 65°C and 2 min on ice prior to addition of streptavidin beads.  After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and blocking oligo wash solutions and resuspended in 5' adapter mix.
Eluted cDNA was amplified 5-cycles (NEBNext Ultra II Q5 master mix (NEB)) with Illumina TruSeq PCR primers RP-1 and RPI-X following the manufacturer's suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries.
Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) was used.


title: OCIAML3_PRO_VTP_48h_REP1_211124_GTCCGC_S9


title: 293T-MIG-NPM1wt-HA_ChIP_HA_steadystate_REP1_210903_GGCTAC_S10


title: OCIAML3_NPM1c-FKBP_PRO_dTAG13_30m_REP1_211124_CTTGTA_S3


title: OCIAML3_NPM1c-FKBP_PRO_dTAG13_60m_REP2_211124_ATGTCA_S6


title: OCIAML3_NPM1c-FKBP_PRO_dTAG13_60m_REP1_211124_AGTTCC_S5


title: OCIAML3_NPM1c-FKBP_PRO_DMSO_0m_REP2_211124_GGCTAC_S2


title: OCIAML3_NPM1c-FKBP_PRO_DMSO_0m_REP1_211124_TAGCTT_S1


title: OCIAML3_NPM1c-FKBP_PRO_dTAG13_30m_REP2_211124_AGTCAA_S4


title: OCIAML3_NPM1c-FKBP_RNA_dTAG13_24h_REP3_200122_GATCAG_S9

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: DESeq2 differential expression summary data (Excel .xlsx format)


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_30m_REP1_210819_CTAGTC_S7


title: OCIAML3_NPM1c-FKBP_RNA_dTAG13_24h_REP2_200122_ACTTGA_S8


title: OCIAML3_NPM1c-FKBP_RNA_dTAG13_24h_REP1_200122_CAGATC_S7


title: OCIAML3_NPM1c-FKBP_RNA_DMSO_3h_REP3_200122_TTAGGC_S3

value: 3 hours


title: OCIAML3_NPM1c-FKBP_RNA_DMSO_3h_REP2_200122_CGATGT_S2


title: OCIAML3_NPM1c-FKBP_RNA_DMSO_3h_REP1_200122_ATCACG_S1


title: OCIAML3-NPM1c-FKBP_SLAM_dTAG13_500nM_2h_REP2_210819_AATCCG_S14


title: 293T-trns-NPM1wt-HA_RNA_steadystate_REP3_211122_TCGAAG_S11


title: 293T-trns-NPM1wt-HA_RNA_steadystate_REP1_211122_CCAACA_S3


title: 293T-trns-NPM1c-HA_RNA_steadystate_REP3_211122_TATAAT_S10


title: 293T-trns-NPM1c-HA_RNA_steadystate_REP1_211122_CATTTT_S2


title: OCIAML3_PRO_DMSO_0m_REP1_211124_CCGTCC_S7


title: 293T-trns-MSCV-Puro-HA_RNA_steadystate_REP1_211122_CATGGC_S1


title: 293T-trns-AS1-HA_RNA_steadystate_REP3_211122_TCGGCA_S12


title: 293T-trns-AS1-HA_RNA_steadystate_REP1_211122_CGGAAT_S4


title: 293T-trns-MSCV-Puro-HA_RNA_steadystate_REP2_211122_CTAGCT_S5


title: OCIAML3-NPM1-FKBP_ChIP_MLL1_dTAG_500nM_48h_REP1_201208_GAGTGG_S20

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human(Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM  atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and ngs.plot (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
Peak-associated signals were assessed using the bedtools coverage function. Single peaks were chosen as representative of change in gene signal, using the peak overlapping the gene body which showed the greatest differential signal between treated and control ChIP samples. Signal values were normalized based on the ratio of hg38-aligning reads in treated and control samples, after deduplication.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: MACS2 peak interval signal summary (from bedtools coverage; Excel .xlsx format); Broad IGV (.tdf) files for visualization

value: 48 hours


title: 293T-trns-NPM1c-HA_RNA_steadystate_REP2_211122_CTATAC_S6


title: 293T-trns-AS1-HA_RNA_steadystate_REP2_211122_TAATCG_S8


title: 293T-trns-MSCV-Puro-HA_RNA_steadystate_REP3_211122_TACAGC_S9


title: OCIAML3_PRO_VTP_48h_REP2_211124_GTGAAA_S10


title: OCIAML3-NPM1-FKBP_ChIP_NPM1c_VTP_330nM_96h_REP1_201208_TGACCA_S3

value: 96 hours


title: OCIAML3-NPM1-FKBP_ChIP_MLL1_DMSO_24h_REP1_200921_AGTCAA_S3


title: OCIAML3-NPM1-FKBP_ChIP_MLL1_dTAG_500nM_24h_REP1_200921_CCGTCC_S6


title: OCIAML3-NPM1-FKBP_ChIP_MLL1_DMSO_48h_REP1_201208_CGTACG_S19


title: OCIAML3-NPM1-FKBP_ChIP_MEN1_dTAG_500nM_24h_REP1_201208_CTTGTA_S10


title: OCIAML3-NPM1-FKBP_ChIP_input_dTAG_500nM_24h_REP1_201208_TAGCTT_S8


title: OCIAML3-NPM1-FKBP_ChIP_input_DMSO_96h_REP2_201208_ACAGTG_S4


title: 293T-trns-NPM1wt-HA_RNA_steadystate_REP2_211122_GACGAC_S7


title: OCIAML3-NPM1-FKBP_ChIP_input_DMSO_48h_REP1_201208_GTGGCC_S17


title: OCIAML3-NPM1-FKBP_ChIP_NPM1c_DMSO_96h_REP1_201208_TTAGGC_S2


title: OCIAML3-NPM1-FKBP_ChIP_NPM1c_dTAG_500nM_24h_REP1_200921_AGTTCC_S4


title: OCIAML3-NPM1-FKBP_ChIP_input_DMSO_24h_REP1_200921_GTCCGC_S7


title: OCIAML3-NPM1-FKBP_ChIP_NPM1c_DMSO_24h_REP1_200921_GGCTAC_S1


title: OCIAML3-NPM1-FKBP_ChIP_input_dTAG_500nM_48h_REP1_201208_GTTTCG_S18


title: OCIAML3-NPM1-FKBP_ChIP_DOT1L_DMSO_24h_REP1_201208_AGTCAA_S11


title: OCIAML3-NPM1-FKBP_ChIP_input_DMSO_96h_REP1_201208_ATCACG_S1


title: OCIAML3-NPM1-FKBP_ChIP_input_DMSO_24h_REP1_201208_GATCAG_S7


title: OCIAML3-NPM1-FKBP_ChIP_H3K27ac_dTAG_500nM_24h_REP1_201208_GTGAAA_S16

value: Abcam


title: OCIAML3-NPM1-FKBP_ChIP_CRM1_VTP_330nM_96h_REP1_201208_ACTTGA_S6


title: OCIAML3-NPM1-FKBP_ChIP_CRM1_DMSO_96h_REP1_201208_CAGATC_S5


title: OCIAML3-NPM1-FKBP_ChIP_MEN1_DMSO_24h_REP1_201208_GGCTAC_S9


title: OCIAML3-NPM1c-FKBP_ChIP_RNAPol2_dfix_dTAG_500nM_24h_REP1_210609_ACTTGA_S8


title: OCIAML3-NPM1c-FKBP_ChIP_RNAPol2_dfix_DMSO_24h_REP1_210609_CAGATC_S7


title: OCIAML3-NPM1c-FKBP_ChIP_LEDGF_dTAG_500nM_24h_REP1_210115_TAGCTT_S6

value: LEDGF


title: OCIAML3-NPM1c-FKBP_ChIP_NPM1_dfix_DMSO_24h_REP1_210420_TTAGGC_S3


title: OCIAML3-NPM1c-FKBP_ChIP_NPM1_dfix_dTAG_500nM_24h_REP1_210420_TGACCA_S4


title: OCIAML3-NPM1c-FKBP_ChIP_input_dTAG_500nM_24h_REP1_210115_GCCAAT_S2


title: OCIAML3-NPM1c-FKBP_ChIP_LEDGF_DMSO_24h_REP1_210115_GATCAG_S5


title: OCIAML3-NPM1c-FKBP_ChIP_input_DMSO_24h_REP1_210115_CGATGT_S1


title: OCIAML3-NPM1c-FKBP_ChIP_input_dfix_DMSO_24h_REP1_210420_ATCACG_S1


title: OCIAML3-NPM1c-FKBP_ChIP_input_dfix_dTAG_500nM_24h_REP1_210609_GCCAAT_S6


title: OCIAML3-NPM1c-FKBP_ChIP_input_dfix_dTAG_500nM_24h_REP1_210420_CGATGT_S2


title: OCIAML3-NPM1c-FKBP_ChIP_CRM1_DMSO_24h_REP1_210115_CAGATC_S3


title: OCIAML3-NPM1c-FKBP_ChIP_CDK9_dfix_dTAG_500nM_24h_REP1_210609_TAGCTT_S10

value: Santa Cruz


title: OCIAML3-NPM1c-FKBP_ChIP_CDK9_dfix_DMSO_24h_REP1_210609_GATCAG_S9


title: OCIAML3-NPM1c-FKBP_ChIP_CRM1_dTAG_500nM_24h_REP1_210115_ACTTGA_S4


title: OCIAML3-FKBP-NPM1c_ChIP_RNAPol2_dTAG13_500nM_60m_REP_211007_TGACCA_S8

value: 60 minutes


title: OCIAML3-FKBP-NPM1c_ChIP_RNAPol2_DMSO_REP_211007_TTAGGC_S7

value: DMSO


title: OCIAML3-FKBP-NPM1c_ChIP_NPM1_dTAG13_500nM_60m_REP_211007_CGATGT_S6


title: OCIAML3-NPM1-FKBP_ChIP_H3K27ac_DMSO_24h_REP1_201208_GTCCGC_S15


title: OCIAML3-FKBP-NPM1c_ChIP_NPM1_DMSO_REP_211007_ATCACG_S5


title: OCIAML3-FKBP-NPM1c_ChIP_input_dTAG13_500nM_60m_REP_211007_TAGCTT_S2


title: OCIAML3-FKBP-NPM1c_ChIP_input_dTAG13_500nM_60m_REP_211007_AGTTCC_S4


title: OCIAML3-FKBP-NPM1c_ChIP_input_DMSO_REP_211007_GATCAG_S1


title: OCIAML3-FKBP-NPM1c_ChIP_CDK9_DMSO_1h_REP1_211213_CTTGTA_S1

value: 1 hour


title: OCIAML3-NPM1c-FKBP_ChIP_input_dfix_DMSO_24h_REP1_210609_ACAGTG_S5


title: OCIAML3-FKBP-NPM1c_ChIP_H3K27ac_DMSO_1h_REP1_211213_GTGAAA_S6


title: OCIAML3-NPM1-FKBP_ChIP_DOT1L_dTAG_500nM_24h_REP1_201208_AGTTCC_S12


title: OCIAML3_ChIP_NPM1_VTP_4d_REP1_220114_ACTGAT_S4

value: 4 days


title: OCIAML3_ChIP_NPM1_DMSO_4d_REP1_220114_GAGTGG_S3


title: OCIAML3_ChIP_NPM1c_DMSO_6h_REP1_220114_CTTGTA_S15

value: 6 hours


title: OCIAML3_ChIP_NPM1c_selinexor_6h_REP1_220114_AGTCAA_S16

value: 100nM Selinexor


title: OCIAML3_ChIP_NPM1c_dfix_VTP_330nM_96h_REP1_210115_CCGTCC_S12


title: OCIAML3_ChIP_input_VTP_330nM_96h_REP1_210115_CTTGTA_S8


title: OCIAML3_ChIP_input_VTP_4d_REP1_220114_GATCAG_S12


title: OCIAML3_ChIP_input_DMSO_96h_REP1_210115_GGCTAC_S7


title: OCIAML3_ChIP_NPM1c_dfix_DMSO_96h_REP1_210115_ATGTCA_S11


title: OCIAML3_ChIP_input_DMSO_4d_REP1_220114_ACTTGA_S11


title: OCIAML3_ChIP_DOT1L_VTP_330nM_4d_REP1_181004_TACAGGAT_S4

value: Cell Signaling


title: OCIAML3_ChIP_CRM1_DMSO_6h_REP1_220114_TAGCTT_S13


title: OCIAML3_ChIP_DOT1L_DMSO_4d_REP1_181004_TAGTGACT_S3


title: OCIAML3_ChIP_CRM1_selinexor_6h_REP1_220114_GGCTAC_S14


title: OCIAML3_ChIP_input_DMSO_4d_REP1_181004_TAGTCTTG_S7


title: DFAM68555_ChIP_NPM1c_untreated_REP1_220114_AGTTCC_S1

source_name: PDX model DFAM68555

value: untreated

value: steadystate


title: OCIAML3_ChIP_RNAPol2_DMSO_4d_REP1_220114_GCCAAT_S9


title: OCIAML3_ChIP_RNAPol2_VTP_4d_REP1_220114_CAGATC_S10


title: DFAM61345_ChIP_NPM1c_untreated_REP1_211213_ACAGTG_S5

source_name: PDX model DFAM61345

value: ThermoFisher


title: DFAM68555_ChIP_input_untreated_REP1_220114_GTGAAA_S5


title: DFAM61345_ChIP_NPM1_untreated_REP1_211213_GCCAAT_S6


title: DFAM22359_ChIP_NPM1_untreated_REP1_211213_TGACCA_S4

source_name: PDX model DFAM22359


title: MSK010R_ChIP_NPM1c_untreated_REP1_211213_ATCACG_S1

source_name: PDX model MSK010R


title: DFAM645419_ChIP_NPM1c_untreated_REP1_211213_CAGATC_S7

source_name: PDX model DFAM645419


title: DFAM22359_ChIP_NPM1c_untreated_REP1_211213_TTAGGC_S3


title: DFAM19969-V1_ChIP_NPM1c_VTP_chow_3d_REP1_211007_GTTTCG_S2

source_name: PDX model DFAM19969

value: 0.1% VTP50469 in chow

value: 3 days


title: DFAM19969_ChIP_NPM1_VTP_chow_6d_REP1_211213_GATCAG_S9

value: 6 days


title: OCIAML3_ChIP_input_VTP_330nM_4d_REP1_181004_TTCCATTG_S8


title: DFAM19969_ChIP_NPM1_untreated_REP1_211213_ACTTGA_S8


title: DFAM19969-V1_ChIP_NPM1c_untreated_REP1_211007_GTGGCC_S1


title: DFAM19969-V1_ChIP_input_untreated_REP1_211007_ATTCCT_S4


title: 293T-trns-NPM1wt-HA_ChIP_HA_steadystate_REP1_210830_GTCCGC_S7

value: HA


title: DFAM68555_ChIP_NPM1_untreated_REP1_220114_CCGTCC_S3


title: DFAM16835_ChIP_input_untreated_REP1_211213_GGCTAC_S11

source_name: PDX model DFAM16835


title: 293T-trns-NPM1c-HA_ChIP_HA_steadystate_REP1_210830_ATGTCA_S5


title: DFAM16835_ChIP_NPM1c_untreated_REP1_211213_CGATGT_S2


title: 293T-trns-NPM1c_ChIP_HA_steadystate_REP1_210830_AGTTCC_S4


title: 293T-trns-AS1-HA_ChIP_HA_steadystate_REP1_210830_GTGAAA_S8


title: 293T-trns-MIG_ChIP_input_steadystate_REP1_210830_CGATGT_S2


title: hs_SkinRaft_Targretin_02uM_Rep2

status: Public on Jan 11 2023

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description: Human skin raft (keratinocytes), treated, Targretin 02uM, RNA-seq replicate 2

data_processing:
Sequencing quality of the single-ended mRNA reads was evaluated by FastQC software and were aligned to the human reference genome (hg19) using HISAT2 with default parameters. Genes were quantified using featureCounts.
Genes with at least 5 Counts Per Million mapped read (CPM) were considered expressed. Statistically significant difference was considered with FDR < 0.05 and fold change > 1.5 using edgeR package in R.
Assembly: hg19
Supplementary files format and content: Counts per million (CPM) normalized gene matrix.

source_name: Keratinocyte

growth_protocol: Stratified cultures of human epidermis were differentiated from primary human keratinocytes and cultured at the air-liquid interface for 9 days.

extract_protocol:
RNA was purified using the Direct-Zol RNA Miniprep Plus from Zymo Research, according to the manufacterurer's protocol
Libraries were prepared using 200ng input total RNA using the NEBNext Ultra II RNA Library Kit

treatment_protocol: Rexinoids were added to the growth medium from 1000x stocks in DMSO (vehicle) on the day following the transfer of the epidermal cultures to the air-liquid interface. Medium was changed every other day, and fresh rexinoids were added to the medium every time.

tag: cell type

value: Keratinocyte

value: Skin raft


title: hs_SkinRaft_Targretin_02uM_Rep1

description: Human skin raft (keratinocytes), treated, Targretin 02uM, RNA-seq replicate 1


title: 293T_DF_ChIP_CRM1_steadystate_REP1_210830_CAGATC_S1


title: hs_SkinRaft_Targretin_02uM_Rep3

description: Human skin raft (keratinocytes), treated, Targretin 02uM, RNA-seq replicate 3


title: hs_SkinRaft_UAB110_02uM_Rep2

description: Human skin raft (keratinocytes), treated, UAB110 02uM, RNA-seq replicate 2


title: hs_SkinRaft_UAB30_1uM_Rep3

description: Human skin raft (keratinocytes), treated, UAB30 1uM, RNA-seq replicate 3


title: hs_SkinRaft_UAB30_1uM_Rep2

description: Human skin raft (keratinocytes), treated, UAB30 1uM, RNA-seq replicate 2


title: hs_SkinRaft_UAB110_02uM_Rep3

description: Human skin raft (keratinocytes), treated, UAB110 02uM, RNA-seq replicate 3


title: hs_SkinRaft_UAB110_02uM_Rep1

description: Human skin raft (keratinocytes), treated, UAB110 02uM, RNA-seq replicate 1


title: hs_SkinRaft_UAB30_1uM_Rep1

description: Human skin raft (keratinocytes), treated, UAB30 1uM, RNA-seq replicate 1


title: hs_SkinRaft_UAB30_02uM_Rep3

description: Human skin raft (keratinocytes), treated, UAB30 0.2uM, RNA-seq replicate 3


title: hs_SkinRaft_UAB30_02uM_Rep2

description: Human skin raft (keratinocytes), treated, UAB30 0.2uM, RNA-seq replicate 2


title: hs_SkinRaft_UAB30_02uM_Rep1

description: Human skin raft (keratinocytes), treated, UAB30 0.2uM, RNA-seq replicate 1


title: hs_SkinRaft_Veh_Rep2

description: Human skin raft (keratinocytes), unstimulated, Vehicle, RNA-seq replicate 2

value: Veh


title: hs_SkinRaft_Veh_Rep1

description: Human skin raft (keratinocytes), unstimulated, Vehicle, RNA-seq replicate 1


title: 17656X12

status: Public on Nov 25 2022

city: Salt Lake City

first: Rodney

last: Stewart

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

institute: University of Utah

data_processing:
The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c.
Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text file containing gene id, log2FC, padj, and raw counts

source_name: tail/posterior to yolk sac

growth_protocol: Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.

extract_protocol:
Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit (Invitrogen 12183016). Homogenization was performed with a 18.5-gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated.
Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold (Illumina 20020598)

treatment_protocol: Tails frozen at -80C in RNA stabilization solution (QIAGEN). Tails rinsed in 1X PBS prior to homogenization and lysis.

value: 24 hpf

tag: genotype

value: 36433 wildtype

value: tail/posterior to yolk sac


title: 17656X10


title: 17656X11

value: 36433 mutant


title: 17656X7


title: 17656X9


title: 293T-trns-MIG_ChIP_HA_steadystate_REP1_210830_AGTCAA_S3


title: 17656X5

value: 23095 mutant


title: 17656X8


title: 17656X3


title: 17656X2

value: 23095 wildtype


title: 17656X4


title: Kasumi-1, CBFB, Ctrl, 17152

status: Public on Nov 09 2022

city: UTRECHT

first: Olaf

last: Heidenreich

state: UTRECHT

address: Prinses Máxima Centrum voor kinderoncologie | Postbus 113| 3720 AC BILTHOVEN | Heidelberglaan 25 |  3584CS UTRECHT | Nederland

country: Netherlands

data_processing:
For CUT&RUN data, the fastq files were trimmed using trim_galore 0.6.5
followed by aligning to the Homo_sapiens GRCh38 reference sequence using bowtie2 version 2.4.5.
Then, we identified duplicate reads and sort the output files with the picard 2.27.4 tool
instrument model: Illumina NextSeq 500/550
Assembly: GRCh38
Supplementary files format and content: bigWigs
Library strategy: CUT&RUN

growth_protocol: Kasumi-1 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), and SKNO-1 were maintaned im RPMI supplemented with 15% fbs and 7 ng/ul GM-CSF in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
cells were bound to magnatic beads and incubated with overnight with the corresponding antibodies, then treatedwith  pAG/MNase for 1 hour at 4 C. DNA fragments were releasted at 37 C and extracted with Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v).
CUT&RUN libraries were prepared using starting from 10-30 ng input and constructed with the KAPA HF polymerase and barcoded with Illumina TruSeq Barcodes.  10-30 ng of DNA was used as starting material  Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were purfied with  Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Cells were treated with 2 µg/ml lipid nanoparticles for 24 hrs then wached with BPS and mainiatened at 0.5 million cells/ml till day 3.

value: acute myeloid leukemia

tag: chip antibody

value: CBFB (Diagenode, #C15310002)

value: Ctrl


title: Kasumi-1, RUNX1, KD, 17149

institute: Prinses Máxima Centrum voor kinderoncologie

value: RUNX1 (abcam, #ab35962)

value: KD


title: 17656X1


title: Kasumi-1, RUNX1/ETO, Ctrl , 17147

value: RUNX1/ETO (Diagenode, #C15310197)


title: Kasumi-1, CBFB, Ctrl, 17144


title: hs_SkinRaft_Veh_Rep3

description: Human skin raft (keratinocytes), unstimulated, Vehicle, RNA-seq replicate 3

tag: treatment


title: Kasumi-1, RUNX1, Ctrl, 17142


title: Kasumi-1, CBFB, KD, 17143


title: Kasumi-1, CBFB, KD, 17151


title: NT G1/S1

status: Public on Dec 31 2022

city: Paris

first: Chunlong

last: Chen

address: 26 rue d’Ulm

country: France

institute: Institut Curie

description: Enrichment of BrdU labelled DNA

data_processing:
Library strategy: Repli-seq
Demultiplexing: bcl2fastq2
Adapter trimming: Cutadapt
Mapping: bwa
PCR duplicates were removed by Picard tools (http://broadinstitute.github.io/picard)
The sequence reads located within the regions likely resulted from the sequencing hotspots (defined as the 0,5% windows with the highest amount of reads within 200bp windows) were also removed.
The read density was them computed for each 50 kb nonoverlapping windows (w) for each sample Si corresponding to different S phase fractions (i = 1–6).
The background levels were them estimated and the density profiles were normalized as described in previous studies (Chen Genome Res 2010, Brison Nat Commun 2019).
The six S-Phase fractions were resized based on a symulation of the number of active forks in each fraction.
A Under-Replication Index (URI) for the average profile of each treated sample was calculated as in Brison Nat Commun 2019
Genome_build: hg19
Supplementary_files_format_and_content: All processed provided data are bigwig: files marked with the prefix URI_ contain the average URI for each condition; files marked as S50_ contain the average replication timing for each condition; files marked as Average_profile_ are the average profiles for each S-phase fraction in each condition.

source_name: human lymphoblastoid cells

growth_protocol: Epstein–Barr-virus-immortalized human B lymphocytes (JEFF cells) were grown in RPMI-1640 plus GlutaMAX-I medium (GIBCO) with 10% fetal calf serum (PAN-Biotech GmbH), 100 µg/ml of penicillin and streptomycin (GIBCO).

extract_protocol:
Cells were incubated overnight in lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA, 0.1% SDS, 50 ug/mL RNAse A, 100 ug/mL Proteinase K). DNA was purified from the lysates by phenol extraction.
Four µg of genomic DNA was fragmented to a mean size of 500 bp on a Covaris S220 intrument (peak power: 140, duty factor: 10%, cycle/burst: 200, time: 80 seconds). Fragmented DNA was treated with the End-Repair module (New England BioLabs, E6050) and the A-Tailing module (New England BioLabs, E6053), according to the manufacturer recommendations. Illumina Truseq indexed adapters were ligated on the resulting fragments, using the Quick Ligation module (New England BioLabs, E6056), according to the manufacturer recommendations. Following heat denaturation, BrdU-DNA was isolated by immunoprecipitation using an anti-BrdU monoclonal antibody (BD Biosciences, 347580). Immunoprecipitated fragments were amplified for 10 cycles using the KAPA Hifi DNA polymerase (KAPABiosystems, KK2502) and the resulting libraries were purified with AMPure XP beads (Beckman Coulter, A63881). Illumina libraries were pooled and sequenced on a NextSeq500 instrument on Paired-end 2x43 bp runs, using a NextSeq 500/550 High Output Kit v2 (75 cycles) kit.

treatment_protocol: Exponentially growing lymphoblastoid cells (~200x106), were pulse-labelled with 50 µM BrdU (Merck, B-5002) prior to recovery. Untreated cells were pulse labeled for 1 h, while all the other conditions were labeled for the last 3 h. Cells were then fixed in 70% ethanol and incubated overnight at 4°C in the presence of 15 µg/ml Hoescht 33342 (ThermoFisher Scientific, H3570). Cells were re-suspended in 1X PBS and sorted in six fractions at a time by flow cytometry based on their DNA content using a BD Biosciences INFLUX cell sorter. The first fraction contains cells in the second half of the G1 phase plus very early S (called G1/S1); the rest of the S phase was divided into four fractions (S2 to S5); and the last fraction contains cells in very late S, G2 and M phases (S6/G2/M).Aphidicolin (A0781), RO (CDK1 Inhibitor IV - Calbiochem; 217699), VE-821 (Sigma-Aldrich SML1415) and hydroxyurea (Sigma-Aldrich H8627) were obtained from Merck.

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes

value: Untreated

tag: s phase


title: Kasumi-1, RUNX1/ETO, Ctrl , 17139


title: SKNO-1, KD

data_processing:
The ATAC-seq paired-end raw reads were demultiplexed and trimmed by BBduk (Bushnell) then
aligned to the human reference genome (GRCh38/hg38) by BWA (V: 0.7.17-r1188)
and the mapped reads normalized to the input cell number.
Assembly: GRCh38
Supplementary files format and content: bigWigs

extract_protocol:
Nuclei were extracted from 50000 cells and tagmanted with 2.5 µl of TDE1 Enzyme (Illumina) for 30 minutes at 37C. Tagmented DNA was purfied with MinElute PCR Purification kit  (Qiagen).
ATAC-seq libraries were amplified using 10-14 cycles on the thermocycler. Post amplification libraries were purfied with  Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.


title: Kasumi-1, RUNX1/ETO, KD , 17140


title: Kasumi-1, KD


title: Kasumi-1 cells, LNP/siRE-mod,  in vivo survival, rep1

data_processing:
For RNAseq data, the fastq files were trimmed using trim_galore 0.6.5.
The in vivo data were mapped to Homo_sapiens GRCh37 using using bowtie2 version 2.4.5.
The in vitro data were mapped to the Homo_sapiens GRCh38 reference sequence using STAR 2.7.10a.
RNA-seq in vitro read counts were retrieved with subread/1.6.5.
RNA-seq in vivo read counts were retrieved with htseq.
Assembly: GRCh37, GRCh38
Supplementary files format and content: Matrix table, raw counts, FPKM value for in vivo data

extract_protocol: RNA was harvested using AllPrep DNA/RNA/Protein Mini Kit (Qiagen). 1  µg  of total RNA was used for the construction of sequencing libraries.

treatment_protocol:
Cells were treated with 2 µg/ml lipid nanoparticles for 24 hrs then wached with BPS and mainiatened at 0.5 million cells/ml till day 3.
RG mice were treated with 1 µg/kg lipid nanoparticles on day 1, then 2 µg/kg  on days 3, 5, 7, 9, 12, 15 and 19.

value: RUNX1/ETO knockdown

value: Lipid nanoparticles

tag: time

value: in vivo survival


title: Kasumi-1 cells, LNP/siMM-mod,  in vivo survival, rep2

value: WT


title: SKNO-1, Ctrl


title: Kasumi-1 cells, LNP/siMM-mod,  in vivo survival, rep1


title: Kasumi-1, RUNX1, Ctrl, 17150


title: SKNO-1 cells, LNP/siRE-mod, Day3, rep3

value: Day 3


title: Kasumi-1, RUNX1/ETO, KD , 17148


title: SKNO-1 cells, LNP/siMM-mod, Day3, rep3


title: SKNO-1 cells, LNP/siMM-mod, Day3, rep2


title: Kasumi-1 cells, LNP/siRE-mod, Day3, rep3


title: SKNO-1 cells, LNP/siMM-mod, Day3, rep1


title: Kasumi-1 cells, LNP/siRE-mod, Day3, rep2


title: Kasumi-1 cells, LNP/siRE-mod, Day3, rep1


title: Kasumi-1, RUNX1, KD, 17141


title: Kasumi-1 cells, LNP/siMM-mod, Day3, rep3


title: Kasumi-1 cells, LNP/siMM-mod, Day3, rep2


title: Kasumi-1, Ctrl


title: Kasumi-1 cells, LNP/siRE-mod,  in vivo survival, rep2


title: SKNO-1 cells, LNP/siRE-mod, Day3, rep1


title: Kasumi-1 cells, LNP/siMM-mod, Day3, rep1


title: SKNO-1 cells, LNP/siRE-mod, Day3, rep2


title: OCIAML3-FKBP-NPM1c_ChIP_input_DMSO_REP_211007_AGTCAA_S3

value: DMSO

value: steadystate


title: RNAPII (WT) unstimulated BMDM ChIP-seq rep 1

status: Public on Oct 20 2022

data_processing:
RNA-seq: Raw reads were aligned to the mm10 (GRCm38) genome with STAR using nf-core/rnaseq pipeline version 3.2. Genes counts were quantified with Salmon using default parameters.
ATAC-seq: Raw reads were aligned to the mm10 (GRCm38) genome with BWA using nf-core/atacseq pipeline version 1.2.1. ChIP-seq read alignments were carried out using ChIP-seq command line pipeline [Barta, 2011]. Briefly, reads were mapped to the mouse reference genome (mm10) using the default parameters of BWA MEM aligner. Low mapping quality reads (MAPQ<10), reads mapping to ENCODE mouse blacklisted [ref] regions and duplicated reads are discarded from downstream analysis, using samtools rmdup and bedtools intersectBed. Coverage profiles were calculated using deeptools2 bamCoverage (--binSize 50 --normalizeUsing RPGC –effectiveGenomeSize 2652783500).
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Raw and normalized (TPM) count matrices. ChIP-seq, ATAC-seq: RPGC normalized coverage files (deeptools2, bigwigs).

source_name: Bone marrow derived macrophages

growth_protocol: Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant. Cells were polarized on the 6th day of the differentiation with IL-4 (20ng/ml) for 24 hours. Then, the IL-4-primed and non-polarized macrophages were activated by 1-3 hours lenght LPS stimulation (100ng/ml).

extract_protocol:
For RNA-seq, wild type (C57/B6 or Egr2 +/+), Stat6 -/- and Egr2fl/fl macrophages were differentiated in the presence of M-CSF using L929 cell supernatants for 6 days. On the 6th day, cells were re-plated and treated with IL-4 (20ng/ml) for 24 hours or left untreated. Then, the IL-4-primed and non-polarized macrophages were activated by 3 hours LPS stimulation. Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single ‘A’ base addition and ligation of barcode-indexed adaptors to the DNA fragments. ChIP was performed essentially as previously described (Daniel et al., 2014b), (Daniel et al., 2014a). ATAC-seq was carried out as described earlier with minor modification (Buenrostro et al., 2013).
For RNA-seq adapter-specific PCRs were performed to generate sequencing libraries. Approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

treatment_protocol: ATAC-seq, ChIP-seq and gene expression measurements were performed in macrophages differentiated with M-CSF. On the 6th day, cells were  primed with IL-4 (20ng/ul) for 24 hours and then activated by 1-3 hours lenght LPS stimulation.

value: Bone marrow

value: RNAPII (WT)

value: unstimulated BMDM


title: RNAPII (WT) 1-h LPS treated BMDM ChIP-seq rep 1

value: 1-h LPS treated BMDM


title: BRD4 (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 2

value: BRD4 (WT)

value: 24-h IL-4 and 1-h LPS treated BMDM


title: BRD4 (WT) 1-h LPS treated BMDM ChIP-seq rep 1


title: BRD4 (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 1


title: RNAPII (WT) 1-h LPS treated BMDM ChIP-seq rep 2


title: RNAPII (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 1


title: RNAPII (WT) 24-h IL-4 treated BMDM ChIP-seq rep 2

value: 24-h IL-4 treated BMDM


title: BRD4 (WT) 1-h LPS treated BMDM ChIP-seq rep 2


title: OCIAML3-FKBP-NPM1c_ChIP_CDK9_dTAG_500nM_1h_REP1_211213_AGTCAA_S2

value: Santa Cruz

value: 1 hour


title: RNAPII (WT) 24-h IL-4 treated BMDM ChIP-seq rep 1


title: RNAPII (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 2


title: RNAPII (WT) unstimulated BMDM ChIP-seq rep 2


title: BRD4 (WT) 24-h IL-4 treated BMDM ChIP-seq rep 1


title: BRD4 (WT) unstimulated BMDM ChIP-seq rep 2


title: p65 EGR2fl/fl (KO) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 2

value: p65 EGR2fl/fl

value: 24-h IL-4 and 1-h LPS treated


title: BRD4 (WT) unstimulated BMDM ChIP-seq rep 1


title: p65 EGR2fl/fl (KO) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 1


title: p65 EGR2fl/fl (KO) 1-h LPS treated BMDM ChIP-seq rep 2


title: BRD4 (WT) 24-h IL-4 treated BMDM ChIP-seq rep 2


title: p65 EGR2fl/fl (KO) unstimulated BMDM ChIP-seq rep 2


title: p65 EGR2fl/fl (KO) 1-h LPS treated BMDM ChIP-seq rep 1


title: p65 EGR2fl/fl (KO) 24-h IL-4 treated BMDM ChIP-seq rep 1


title: p65 EGR2fl/fl (KO) 24-h IL-4 treated BMDM ChIP-seq rep 2


title: p65 EGR2fl/fl (KO) unstimulated BMDM ChIP-seq rep 1


title: p65 EGR2+/+ (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 2


title: p65 EGR2+/+ (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 1


title: p65 EGR2+/+ (WT) 24-h IL-4 treated BMDM ChIP-seq rep 2


title: p65 EGR2+/+ (WT) 1-h LPS treated BMDM ChIP-seq rep 1


title: p65 EGR2+/+ (WT) 1-h LPS treated BMDM ChIP-seq rep 2


title: p65 EGR2+/+ (WT) unstimulated BMDM ChIP-seq rep 2


title: p65 STAT6-/- (KO) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 2


title: p65 STAT6-/- (KO) unstimulated BMDM ChIP-seq rep 1


title: p65 STAT6-/- (KO) 24-h IL-4 treated BMDM ChIP-seq rep 2


title: p65 STAT6WT (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 2

value: p65 STAT6WT


title: p65 STAT6-/- (KO) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 1


title: p65 STAT6-/- (KO) 1-h LPS treated BMDM ChIP-seq rep 2


title: p65 EGR2+/+ (WT) 24-h IL-4 treated BMDM ChIP-seq rep 1


title: p65 STAT6-/- (KO) 24-h IL-4 treated BMDM ChIP-seq rep 1


title: p65 STAT6-/- (KO) 1-h LPS treated BMDM ChIP-seq rep 1


title: p65 EGR2+/+ (WT) unstimulated BMDM ChIP-seq rep 1


title: p65 STAT6WT (WT) 1-h LPS treated BMDM ChIP-seq rep 2


title: p65 STAT6WT (WT) 1-h LPS treated BMDM ChIP-seq rep 1


title: p65 STAT6-/- (KO) unstimulated BMDM ChIP-seq rep 2


title: p65 STAT6WT (WT) unstimulated BMDM ChIP-seq rep 2


title: p65 STAT6WT (WT) 24-h IL-4 treated BMDM ChIP-seq rep 1


title: p65 STAT6WT (WT) 24-h IL-4 treated BMDM ChIP-seq rep 2


title: p65 STAT6WT (WT) unstimulated BMDM ChIP-seq rep 1


title: WT 24-h IL-4 and 1-h LPS treated BMDM ATAC-seq rep 1


title: WT 24-h IL-4 and 1-h LPS treated BMDM ATAC-seq rep 2


title: WT 24-h IL-4 treated BMDM ATAC-seq rep 2


title: WT 1-h LPS treated BMDM ATAC-seq rep 1


title: WT 24-h IL-4 treated BMDM ATAC-seq rep 1


title: OCIAML3-FKBP-NPM1c_ChIP_H3K27ac_dTAG_500nM_1h_REP1_211213_GTGGCC_S7

value: Abcam

value: 500nM dTAG13


title: WT unstimulated BMDM ATAC-seq rep 2

value: WT


title: EGR2fl/fl 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 2

description:
mm_BMDM_RNAseq_EGR2WT_EGR2KO_IL4LPS_RNAseq_raw_counts.txt
mm_BMDM_RNAseq_EGR2WT_EGR2KO_IL4LPS_RNAseq_TPM_counts.txt

value: 24-h IL-4 and 3-h LPS treated BMDM


title: WT unstimulated BMDM ATAC-seq rep 1


title: EGR2fl/fl 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 3


title: EGR2fl/fl 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 1


title: EGR2fl/fl 3-h LPS treated BMDM RNA-seq rep 3

value: 3-h LPS treated BMDM


title: EGR2fl/fl 24-h IL-4 treated BMDM RNA-seq rep 2

value: Bone marrow


title: EGR2fl/fl unstimulated BMDM RNA-seq rep 2


title: EGR2fl/fl unstimulated BMDM RNA-seq rep 3


title: EGR2fl/fl 3-h LPS treated BMDM RNA-seq rep 1


title: EGR2fl/fl 24-h IL-4 treated BMDM RNA-seq rep 1


title: EGR2+/+ (WT) 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 3


title: EGR2+/+ (WT) 3-h LPS treated BMDM RNA-seq rep 3


title: EGR2+/+ (WT) 24-h IL-4 treated BMDM RNA-seq rep 3


title: EGR2+/+ (WT) 3-h LPS treated BMDM RNA-seq rep 2


title: EGR2+/+ (WT) 3-h LPS treated BMDM RNA-seq rep 1


title: EGR2+/+ (WT) 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 2


title: EGR2+/+ (WT) 24-h IL-4 treated BMDM RNA-seq rep 2


title: EGR2+/+ (WT) 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 1


title: EGR2+/+ (WT) 24-h IL-4 treated BMDM RNA-seq rep 1


title: EGR2+/+ (WT) unstimulated BMDM RNA-seq rep 3


title: EGR2+/+ (WT) unstimulated BMDM RNA-seq rep 1


title: EGR2+/+ (WT) unstimulated BMDM RNA-seq rep 2


title: p65 STAT6WT (WT) 24-h IL-4 and 1-h LPS treated BMDM ChIP-seq rep 1


title: STAT6-/- 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 2

description:
mm_BMDM_RNAseq_STAT6WT_STAT6KO_IL4LPS_RNAseq_raw_counts.txt
mm_BMDM_RNAseq_STAT6WT_STAT6KO_IL4LPS_RNAseq_TPM_counts.txt


title: WT 1-h LPS treated BMDM ATAC-seq rep 2


title: STAT6-/- 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 1


title: EGR2fl/fl unstimulated BMDM RNA-seq rep 1


title: EGR2fl/fl 3-h LPS treated BMDM RNA-seq rep 2


title: STAT6-/- 3-h LPS treated BMDM RNA-seq rep 3


title: STAT6-/- 3-h LPS treated BMDM RNA-seq rep 1


title: STAT6-/- 24-h IL-4 treated BMDM RNA-seq rep 3


title: STAT6-/- 3-h LPS treated BMDM RNA-seq rep 2


title: EGR2fl/fl 24-h IL-4 treated BMDM RNA-seq rep 3


title: STAT6-/- 24-h IL-4 treated BMDM RNA-seq rep 1


title: STAT6-/- 24-h IL-4 treated BMDM RNA-seq rep 2


title: STAT6-/- unstimulated BMDM RNA-seq rep 3


title: STAT6-/- unstimulated BMDM RNA-seq rep 1


title: STAT6 (WT) 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 3

value: STAT6 (WT)


title: STAT6 (WT) 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 1


title: STAT6-/- 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 3


title: STAT6 (WT) 24-h IL-4 treated BMDM RNA-seq rep 3


title: STAT6 (WT) 24-h IL-4 treated BMDM RNA-seq rep 1


title: STAT6 (WT) unstimulated BMDM RNA-seq rep 2

value: unstimulated BMDM


title: STAT6 (WT) unstimulated BMDM RNA-seq rep 3


title: STAT6 (WT) 3-h LPS treated BMDM RNA-seq rep 3


title: STAT6 (WT) 3-h LPS treated BMDM RNA-seq rep 1


title: STAT6 (WT) 24-h IL-4 treated BMDM RNA-seq rep 2


title: G_Jag1

status: Public on Sep 06 2022

city: London

first: Paul

last: Evans

address: Charterhouse square

institute: QMUL

data_processing:
bcbio-nextgen,1.0.9
Reads were aligned to reference geneome build GRCh37/hg19 using STAR aligner.
Transcription quantification was performed using salmon 0.9.1.
Annotation combined counts table was created with featurecounts 1.4.4
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited text files

source_name: Primary Human Coronary Artery Endothelial Cells (HCAEC)

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (74104, Qiagen) and reverse transcribed into cDNA using the iScript cDNA synthesis kit (1708891, Bio-Rad).
The purity and integrity of total RNA samples isolated from HCAEC was assessedusing a Bioanalyser (Agilent) and high-quality samples from HCAEC donors were used to prepare RNA-seq libraries that were sequenced on an Illumina HiSeq platform yielding 20 million reads per sample. Library preparation and cDNA sequencing were performed by Novogene.

tag: donor

value: G


title: STAT6 (WT) 3-h LPS treated BMDM RNA-seq rep 2

tag: strain


title: STAT6 (WT) unstimulated BMDM RNA-seq rep 1


title: E_Jag1

value: Primary Human Coronary Artery Endothelial Cells (HCAEC)

value: E


title: SHE-BT-s004-1

library_source: transcriptomic single cell

data_processing:
Reads from Illumina sequencing were aligned to the GRCm38 mouse genome using STAR.
Single-cell transcriptomes generated using Sort-seq were filtered by requiring the total number of genes detected per cell to be more than 1200.
The percentage of reads mapping to ERCC controls was below 35%. Data were not filtered according to mitochondrial reads which werenegligible (minimum: 0.3%, median 0.9%, maximum: 11.0%). After filtering count data andselecting high quality single cells, the data were normalised and the top 2000 highly variable genes in our dataset were selected and used for principal component analysis. The first 12 principal components were retained based on their contribution to overall variability and used for downstream analysis (dimensional reduction and clustering).
Dimensional reduction and clustering of our scRNA-seq dataset were performed using the R package Seurat (v3.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files

source_name: aorta

extract_protocol:
scRNAseq libraries were generated using the SORT-seq protocol.
Single cells were lysed at 65ºC for 5 min,and second-strand mixers and reverse transcriptase were then added to the wells using the Nanodrop II liquid handling platform (GC Biotech). After reverse-transcribing the mRNA of each cell, double-stranded cDNAs from single cells were pooled and in vitro transcription was performed for linear amplification, which resulted in amplified RNA. TruSeq small RNA primers (Illumina) were used to prepare the Illumina sequencing libraries and these DNA libraries were then sequenced paired-end at 75 bp read length using the Illumina NextSeq

value: aorta

value: Jag1 ECWT


title: G_D114


title: SHE-BT-s002-1

value: Jag1 ECKO


title: E_D114


title: G_CTRL

value: CTRL


title: E_CTRL


title: STAT6-/- unstimulated BMDM RNA-seq rep 2


title: STAT6 (WT) 24-h IL-4 and 3-h LPS treated BMDM RNA-seq rep 2


title: SHE-BT-s001-1


title: C_CTRL

value: C


title: A_CTRL

value: A


title: C_D114


title: A_Jag1


title: SHE-BT-s003-1


title: A_D114


title: C_Jag1


title: mpMG_APOE44_6

status: Public on Jun 23 2022

first: Julia

last: TCW

state: Massachusetts

address: 700 Albany St.

institute: Boston University

data_processing:
Paired end reads were trimmed to 100bp reads for Illumina TruSeq adapters and matching read depth of other datasets
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.3a).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1) and DESeq2 (v.3.14)
Genome_build: hg38
Supplementary_files_format_and_content: mouseApoe_featureCounts.txt (Tab-delimited text file of raw read counts)

source_name: APOE44 mouse primary microglia

growth_protocol: Primary microglia and astrocytes from mouse APOE 33, APOE 44, Apoe WT and Apoe KO cells were purified and cultured in human microglia and astrocyte media.

extract_protocol:
Total RNA was extracted from differentiated CNS cells in a single batch using the Total RNA isolation kit (Rneasy kit from Qiagen).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina, and sequenced as paired-end 150bp reads on the Illumina HiSeq 4000.

treatment_protocol: No treatment

value: Microglia

tag: apoe genotype

tag: batch

tag: Sex

value: F

tag: rin


title: mpMG_APOEKO_1

source_name: APOEKO mouse primary microglia

value: KO


title: mpMG_APOE44_5

value: M


title: mpMG_APOEKO_4