title: ChIA-PET from CD4-positive, alpha-beta T cell (ENCLB903TIW)

description:
https://www.encodeproject.org/experiments/ENCSR345UIQ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in CD4_Resting
experiment encode accession: ENCSR345UIQ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB903TIW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell

value: CTCF

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS236MDD at ENCODE; https://www.encodeproject.org/ENCBS236MDD/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: ChIA-PET from BJ (ENCLB277XDU)

status: Public on Nov 04 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR956IXE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in BJ
experiment encode accession: ENCSR956IXE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-09-23
lab: Yijun Ruan, JAX
library encode accession: ENCLB277XDU
size range: 300-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens BJ 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

tag: antibody

tag: line

value: BJ

value: cell line

tag: description

value: skin fibroblast, The line was established from skin taken from normal foreskin. - ATCC.

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: normal

tag: dev stage

value: newborn

tag: age

value: not collected

tag: lab

tag: source

value: ATCC

tag: link

value: ENCBS425ZJX at ENCODE; https://www.encodeproject.org/ENCBS425ZJX/

value: Derived from ENCODE donor ENCDO000AAG; https://www.encodeproject.org/ENCDO000AAG/


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCLB124JPL)

description:
https://www.encodeproject.org/experiments/ENCSR731OFF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Naive_CD4_Activated_Day2
experiment encode accession: ENCSR731OFF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB124JPL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (43 years) activated CD4 positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: CTCF

value: primary cell

value: 43 year

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS224WCU at ENCODE; https://www.encodeproject.org/ENCBS224WCU/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from CD4-positive naive resting alpha-beta T cell (ENCLB012TNX)

description:
https://www.encodeproject.org/experiments/ENCSR763OCG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Naive_CD4_Resting
experiment encode accession: ENCSR763OCG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB012TNX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (43 years) CD4-positive naive resting alpha-beta T primary cell

value: adult

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS056PBO at ENCODE; https://www.encodeproject.org/ENCBS056PBO/


title: ChIA-PET from BJ (ENCLB987CLU)

description:
https://www.encodeproject.org/experiments/ENCSR956IXE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in BJ
experiment encode accession: ENCSR956IXE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-09-23
lab: Yijun Ruan, JAX
library encode accession: ENCLB987CLU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: BJ

value: cell line

value: skin fibroblast, The line was established from skin taken from normal foreskin. - ATCC.

value: male

value: ENCBS116BPR at ENCODE; https://www.encodeproject.org/ENCBS116BPR/


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCLB855RNX)

description:
https://www.encodeproject.org/experiments/ENCSR982KEM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD8_Activated_Day2
experiment encode accession: ENCSR982KEM
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB855RNX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: 21 year

value: ENCBS051LKA at ENCODE; https://www.encodeproject.org/ENCBS051LKA/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCLB257TNZ)

description:
https://www.encodeproject.org/experiments/ENCSR877ZRR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Memory_CD4_Activated_Day2
experiment encode accession: ENCSR877ZRR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB257TNZ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: ENCBS844TVF at ENCODE; https://www.encodeproject.org/ENCBS844TVF/


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCLB611EQH)

description:
https://www.encodeproject.org/experiments/ENCSR962FFY/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in CD4_Activated_Day7
experiment encode accession: ENCSR962FFY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB611EQH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: CTCF

value: 20 year

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

value: ENCBS860YXJ at ENCODE; https://www.encodeproject.org/ENCBS860YXJ/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCLB265WYE)

description:
https://www.encodeproject.org/experiments/ENCSR446MTI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Naive_CD4_Activated_Day7
experiment encode accession: ENCSR446MTI
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB265WYE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (43 years) activated CD4 positive, naive alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS716JOO at ENCODE; https://www.encodeproject.org/ENCBS716JOO/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from BJ (ENCLB886LNL)

description:
https://www.encodeproject.org/experiments/ENCSR956IXE/
***************
biological replicate number: 3
technical replicate number: 1
description: RNAPII ChIA-PET in BJ
experiment encode accession: ENCSR956IXE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-09-23
lab: Yijun Ruan, JAX
library encode accession: ENCLB886LNL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: BJ

value: cell line

value: male

value: newborn

value: not collected

value: ATCC

value: normal

value: ENCBS189ZMA at ENCODE; https://www.encodeproject.org/ENCBS189ZMA/

value: Derived from ENCODE donor ENCDO000AAG; https://www.encodeproject.org/ENCDO000AAG/


title: ChIA-PET from CD4-positive, alpha-beta memory T cell (ENCLB566GXP)

description:
https://www.encodeproject.org/experiments/ENCSR569TBN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Memory_CD4_Resting
experiment encode accession: ENCSR569TBN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB566GXP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (43 years) CD4-positive, alpha-beta memory T primary cell

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: ENCBS356UPO at ENCODE; https://www.encodeproject.org/ENCBS356UPO/


title: ChIA-PET from CD4-positive, alpha-beta T cell (ENCLB681RUN)

description:
https://www.encodeproject.org/experiments/ENCSR448ZLA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in CD4_Resting
experiment encode accession: ENCSR448ZLA
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB681RUN
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CD4-positive, alpha-beta T cell

value: adult

value: 20 year

value: ENCBS236MDD at ENCODE; https://www.encodeproject.org/ENCBS236MDD/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCLB282YTU)

description:
https://www.encodeproject.org/experiments/ENCSR550JJT/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Naive_CD4_Activated_Day7
experiment encode accession: ENCSR550JJT
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB282YTU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CTCF

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS338LVO at ENCODE; https://www.encodeproject.org/ENCBS338LVO/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCLB744IAF)

description:
https://www.encodeproject.org/experiments/ENCSR408MRB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD8_Activated_Day2
experiment encode accession: ENCSR408MRB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB744IAF
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: male

value: 21 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS051LKA at ENCODE; https://www.encodeproject.org/ENCBS051LKA/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCLB825EVF)

description:
https://www.encodeproject.org/experiments/ENCSR550JJT/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Naive_CD4_Activated_Day7
experiment encode accession: ENCSR550JJT
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB825EVF
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: primary cell

value: ENCBS716JOO at ENCODE; https://www.encodeproject.org/ENCBS716JOO/


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCLB714JTQ)

description:
https://www.encodeproject.org/experiments/ENCSR314TNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in CD4_Activated_Day2
experiment encode accession: ENCSR314TNQ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB714JTQ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: adult

value: 20 year

value: ENCBS923CUW at ENCODE; https://www.encodeproject.org/ENCBS923CUW/


title: ChIA-PET from activated B cell (ENCLB608NXF)

description:
https://www.encodeproject.org/experiments/ENCSR494NNF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in B_Cell_Activated
experiment encode accession: ENCSR494NNF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB608NXF
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (22 years) activated B primary cell treated with 0.5 uM CpG ODN for 24 hours

value: CTCF

value: activated B cell

value: 22 year

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS773GSB at ENCODE; https://www.encodeproject.org/ENCBS773GSB/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: ChIA-PET from CD4-positive naive resting alpha-beta T cell (ENCLB182XVG)

description:
https://www.encodeproject.org/experiments/ENCSR763OCG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in Naive_CD4_Resting
experiment encode accession: ENCSR763OCG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB182XVG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS303DAN at ENCODE; https://www.encodeproject.org/ENCBS303DAN/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from B cell (ENCLB745KSP)

description:
https://www.encodeproject.org/experiments/ENCSR536ZNI/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in B_Cell
experiment encode accession: ENCSR536ZNI
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-15
lab: Yijun Ruan, JAX
library encode accession: ENCLB745KSP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens male adult (22 years) B primary cell

value: B cell

value: male

value: ENCBS371AHM at ENCODE; https://www.encodeproject.org/ENCBS371AHM/


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCLB383QVW)

description:
https://www.encodeproject.org/experiments/ENCSR093CTT/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in CD4_Activated_Day2
experiment encode accession: ENCSR093CTT
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB383QVW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: primary cell

value: adult

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: ChIA-PET from CD8-positive, alpha-beta T cell (ENCLB836ZKG)

description:
https://www.encodeproject.org/experiments/ENCSR180GEY/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD8_Resting
experiment encode accession: ENCSR180GEY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-08-02
lab: Yijun Ruan, JAX
library encode accession: ENCLB836ZKG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CTCF

value: CD8-positive, alpha-beta T cell

value: 21 year

value: ENCBS700QKK at ENCODE; https://www.encodeproject.org/ENCBS700QKK/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCLB701KME)

description:
https://www.encodeproject.org/experiments/ENCSR093CTT/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD4_Activated_Day2
experiment encode accession: ENCSR093CTT
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB701KME
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: 20 year

value: ENCBS840LNC at ENCODE; https://www.encodeproject.org/ENCBS840LNC/


title: ChIA-PET from CD8-positive, alpha-beta T cell (ENCLB552RIC)

description:
https://www.encodeproject.org/experiments/ENCSR185VQH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD8_Resting
experiment encode accession: ENCSR185VQH
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB552RIC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: Yijun Ruan, JAX

value: AllCells


title: ChIA-PET from common myeloid progenitor, CD34-positive (ENCLB581GFO)

description:
https://www.encodeproject.org/experiments/ENCSR421NGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD34_HSC
experiment encode accession: ENCSR421NGZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-08-02
lab: Yijun Ruan, JAX
library encode accession: ENCLB581GFO
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens common myeloid progenitor, CD34-positive primary cell

value: not collected

value: unknown

value: Patrick Gallagher

value: ENCBS114YHK at ENCODE; https://www.encodeproject.org/ENCBS114YHK/

value: Derived from ENCODE donor ENCDO233GAL; https://www.encodeproject.org/ENCDO233GAL/


title: ChIA-PET from CD4-positive, alpha-beta memory T cell (ENCLB389QLR)

description:
https://www.encodeproject.org/experiments/ENCSR106INW/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD4_Resting
experiment encode accession: ENCSR106INW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB389QLR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: male

value: adult

value: 43 year

value: ENCBS356UPO at ENCODE; https://www.encodeproject.org/ENCBS356UPO/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCLB631XUM)

description:
https://www.encodeproject.org/experiments/ENCSR531UMR/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD8_Activated_Day7
experiment encode accession: ENCSR531UMR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB631XUM
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: CTCF

value: 21 year

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

value: ENCBS378MVS at ENCODE; https://www.encodeproject.org/ENCBS378MVS/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ChIA-PET from CD4-positive, alpha-beta T cell (ENCLB368YHC)

description:
https://www.encodeproject.org/experiments/ENCSR345UIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD4_Resting
experiment encode accession: ENCSR345UIQ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB368YHC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

value: CD4-positive, alpha-beta T cell

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS267UTU at ENCODE; https://www.encodeproject.org/ENCBS267UTU/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCLB844HGL)

description:
https://www.encodeproject.org/experiments/ENCSR962FFY/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD4_Activated_Day7
experiment encode accession: ENCSR962FFY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB844HGL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: primary cell

value: ENCBS718HAG at ENCODE; https://www.encodeproject.org/ENCBS718HAG/


title: ChIA-PET from CD4-positive, alpha-beta T cell (ENCLB156BUD)

description:
https://www.encodeproject.org/experiments/ENCSR448ZLA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD4_Resting
experiment encode accession: ENCSR448ZLA
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB156BUD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

value: male

value: adult


title: ChIA-PET from CD8-positive, alpha-beta T cell (ENCLB035QSU)

description:
https://www.encodeproject.org/experiments/ENCSR180GEY/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in CD8_Resting
experiment encode accession: ENCSR180GEY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-08-02
lab: Yijun Ruan, JAX
library encode accession: ENCLB035QSU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CD8-positive, alpha-beta T cell

value: ENCBS437GTX at ENCODE; https://www.encodeproject.org/ENCBS437GTX/


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCLB998LQD)

description:
https://www.encodeproject.org/experiments/ENCSR402NAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Naive_CD4_Activated_Day2
experiment encode accession: ENCSR402NAQ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB998LQD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: 43 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS224WCU at ENCODE; https://www.encodeproject.org/ENCBS224WCU/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCLB832WHX)

description:
https://www.encodeproject.org/experiments/ENCSR697ZHG/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD8_Activated_Day2
experiment encode accession: ENCSR697ZHG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB832WHX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: CTCF

value: 30 year

value: ENCBS629LOT at ENCODE; https://www.encodeproject.org/ENCBS629LOT/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCLB031MKT)

description:
https://www.encodeproject.org/experiments/ENCSR291RCO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD4_Activated_Day7
experiment encode accession: ENCSR291RCO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-08-02
lab: Yijun Ruan, JAX
library encode accession: ENCLB031MKT
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS585TLD at ENCODE; https://www.encodeproject.org/ENCBS585TLD/


title: ChIA-PET from common myeloid progenitor, CD34-positive (ENCLB090ZLM)

description:
https://www.encodeproject.org/experiments/ENCSR065MBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD34_HSC
experiment encode accession: ENCSR065MBZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB090ZLM
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: primary cell

value: not collected

value: unknown

value: Patrick Gallagher

value: ENCBS114YHK at ENCODE; https://www.encodeproject.org/ENCBS114YHK/

value: Derived from ENCODE donor ENCDO233GAL; https://www.encodeproject.org/ENCDO233GAL/


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCLB530JEV)

description:
https://www.encodeproject.org/experiments/ENCSR154MAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD4_Activated_Day2
experiment encode accession: ENCSR154MAJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB530JEV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: male

value: adult

value: 43 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS844TVF at ENCODE; https://www.encodeproject.org/ENCBS844TVF/


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCLB128HGW)

description:
https://www.encodeproject.org/experiments/ENCSR159PXF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Memory_CD4_Activated_Day7
experiment encode accession: ENCSR159PXF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB128HGW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from CD4-positive naive resting alpha-beta T cell (ENCLB059DUS)

description:
https://www.encodeproject.org/experiments/ENCSR120LMS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Naive_CD4_Resting
experiment encode accession: ENCSR120LMS
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB059DUS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CTCF

value: ENCBS056PBO at ENCODE; https://www.encodeproject.org/ENCBS056PBO/


title: ChIA-PET from RWPE1 (ENCLB269YIK)

description:
https://www.encodeproject.org/experiments/ENCSR617FPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET with RWPE1 cell
experiment encode accession: ENCSR617FPZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB269YIK
size range: 400-600

source_name: Homo sapiens RWPE1 cell line

value: cell line

value: 54 year

value: Yijun Ruan, JAX

value: ATCC

value: normal

value: ENCBS006RZR at ENCODE; https://www.encodeproject.org/ENCBS006RZR/

value: Derived from ENCODE donor ENCDO000ADM; https://www.encodeproject.org/ENCDO000ADM/


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCLB700QEX)

description:
https://www.encodeproject.org/experiments/ENCSR217TFN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD8_Activated_Day7
experiment encode accession: ENCSR217TFN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB700QEX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: primary cell

value: 21 year

value: AllCells

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

value: ENCBS378MVS at ENCODE; https://www.encodeproject.org/ENCBS378MVS/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ChIA-PET from common myeloid progenitor, CD34-positive (ENCLB511WGT)

description:
https://www.encodeproject.org/experiments/ENCSR421NGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in CD34_HSC
experiment encode accession: ENCSR421NGZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-08-02
lab: Yijun Ruan, JAX
library encode accession: ENCLB511WGT
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: not collected

value: unknown

value: Patrick Gallagher

value: ENCBS635BVK at ENCODE; https://www.encodeproject.org/ENCBS635BVK/

value: Derived from ENCODE donor ENCDO233GAL; https://www.encodeproject.org/ENCDO233GAL/


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCLB646OUJ)

description:
https://www.encodeproject.org/experiments/ENCSR378IUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD8_Activated_Day7
experiment encode accession: ENCSR378IUJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB646OUJ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: CTCF

value: male

value: adult

value: 30 year

value: ENCBS851ZMN at ENCODE; https://www.encodeproject.org/ENCBS851ZMN/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: ChIA-PET from CD4-positive, alpha-beta memory T cell (ENCLB354FDE)

description:
https://www.encodeproject.org/experiments/ENCSR106INW/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD4_Resting
experiment encode accession: ENCSR106INW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB354FDE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: 43 year

value: Yijun Ruan, JAX

value: ENCBS032JGC at ENCODE; https://www.encodeproject.org/ENCBS032JGC/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from CD8-positive, alpha-beta memory T cell (ENCLB398DKV)

description:
https://www.encodeproject.org/experiments/ENCSR187PXW/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD8_Resting
experiment encode accession: ENCSR187PXW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB398DKV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (30 years) CD8-positive, alpha-beta memory T primary cell

value: CD8-positive, alpha-beta memory T cell

value: AllCells

value: ENCBS570HKZ at ENCODE; https://www.encodeproject.org/ENCBS570HKZ/


title: ChIA-PET from activated B cell (ENCLB638WKR)

description:
https://www.encodeproject.org/experiments/ENCSR096ZPB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in B_Cell_Activated
experiment encode accession: ENCSR096ZPB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB638WKR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: activated B cell

value: 22 year

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS773GSB at ENCODE; https://www.encodeproject.org/ENCBS773GSB/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: ChIA-PET from RWPE1 (ENCLB444OAJ)

description:
https://www.encodeproject.org/experiments/ENCSR617FPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET with RWPE1 cell
experiment encode accession: ENCSR617FPZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB444OAJ
size range: 400-600

value: cell line

value: male

value: normal

value: adult

value: 54 year

value: ATCC

value: ENCBS925TMM at ENCODE; https://www.encodeproject.org/ENCBS925TMM/

value: Derived from ENCODE donor ENCDO000ADM; https://www.encodeproject.org/ENCDO000ADM/


title: Unstimulated, differentiated RXRab KO BMDMs rep3

status: Public on Oct 27 2021

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
Single-end
mm_BMDM_RXRKO_VEH_rep3

library_source: transcriptomic

data_processing:
Alignment was performed with TopHat v2.0.7 using default parameters.
Data analysis was performed using Strand NGS software, Version 3.4, Build 230243. © Strand Life Sciences, Bangalore, India
Read counts were calculated based on manufacturer's default parameters.
Normalisation of the read counts was performed with the DEseq method. The normalized counts are log transformed and baselined. This method is based on the paper ‘Differential expression analysis for sequence count data’ by Simon Anders and Wolfgang Huber.
Changes in genes in the pairwise comparisons with FC>=1.5 and p-value<0.05 were considered to be statistically significant. Filtering was performed for genes with normalized expression >=3 in at least one condition.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: WT_RXRKO_RNAseq_Veh_Raw.txt: Tab-delimited text file contains a RAW gene count matrix.
Supplementary_files_format_and_content: WT_RXRKO_RNAseq_Veh_Normalized.txt: Tab-delimited text file contains a DESEQ normalized count matrix.

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel, Balint et al. 2014). Briefly, BMDMs were obtained from bone marrow (BM) precursor cells. Total BM was obtained from mice by flushing femurs and tibiae bone marrow with DMEM. Cells were cultured in DMEM medium containing 20% FBS and 30% conditioned medium of L929 cell line (enriched in CSF-1) for 6 days.

extract_protocol:
Total RNA was isolated with TRIZOL reagent according to the manufacturer’s recommendation (Zymo Research, Direct-zol RNA MiniPrep Plus).
cDNA library for RNA-seq was generated from 100ng total RNA using NEBNext Ultra II RNA Library Prep Kit for Illumina, according to manufacturer’s protocol. Libraries were sequenced on the NextSeq 550, using the NextSeq500/550 High Output Kit v2.5 (75 Cycles). Three biological replicates were sequenced for each condition.

treatment_protocol: Evening of day 5, media was changed to serum-free macrophage media. MFs were activated with Vehicle (DMSO) for 3-hours.

tag: strain/background

tag: genotype/variation

value: RXRafl/flLysMCre RXRb-/-

tag: cell type

value: Bone marrow-derived macrophages

tag: treatment

value: Vehicle (DMSO)


title: ChIA-PET from B cell (ENCLB303DYS)

description:
https://www.encodeproject.org/experiments/ENCSR172WWJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in B_Cell
experiment encode accession: ENCSR172WWJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB303DYS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: B cell

value: primary cell

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS371AHM at ENCODE; https://www.encodeproject.org/ENCBS371AHM/


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCLB958HVH)

description:
https://www.encodeproject.org/experiments/ENCSR291RCO/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD4_Activated_Day7
experiment encode accession: ENCSR291RCO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-08-02
lab: Yijun Ruan, JAX
library encode accession: ENCLB958HVH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CTCF

value: 43 year

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

value: ENCBS558FRJ at ENCODE; https://www.encodeproject.org/ENCBS558FRJ/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ChIA-PET from CD8-positive naive resting alpha-beta T cell (ENCLB058WNE)

description:
https://www.encodeproject.org/experiments/ENCSR064OTE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Naive_CD8_Resting
experiment encode accession: ENCSR064OTE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB058WNE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (30 years) CD8-positive naive resting alpha-beta T primary cell

value: male

value: adult

value: 30 year

value: ENCBS099GFG at ENCODE; https://www.encodeproject.org/ENCBS099GFG/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: Unstimulated, differentiated RXRab KO BMDMs rep2

description:
Single-end
mm_BMDM_RXRKO_VEH_rep2

value: RXRafl/flLysMCre RXRb-/-

value: Bone marrow-derived macrophages


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCLB629AXC)

description:
https://www.encodeproject.org/experiments/ENCSR041UPG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Memory_CD8_Activated_Day2
experiment encode accession: ENCSR041UPG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB629AXC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS629LOT at ENCODE; https://www.encodeproject.org/ENCBS629LOT/


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCLB416SBC)

description:
https://www.encodeproject.org/experiments/ENCSR114KEO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Memory_CD8_Activated_Day7
experiment encode accession: ENCSR114KEO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB416SBC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600
instrument models: Illumina NovaSeq 6000,Illumina MiSeq

value: primary cell

value: Yijun Ruan, JAX

value: ENCBS851ZMN at ENCODE; https://www.encodeproject.org/ENCBS851ZMN/


title: ChIA-PET from CD8-positive, alpha-beta memory T cell (ENCLB560UBX)

description:
https://www.encodeproject.org/experiments/ENCSR149TQU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Memory_CD8_Resting
experiment encode accession: ENCSR149TQU
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB560UBX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: CD8-positive, alpha-beta memory T cell

value: AllCells

value: ENCBS570HKZ at ENCODE; https://www.encodeproject.org/ENCBS570HKZ/


title: Unstimulated, differentiated WT BMDMs rep3

description:
Single-end
mm_BMDM_WT_VEH_rep3

value: WT

value: Vehicle (DMSO)


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCLB590WVA)

description:
https://www.encodeproject.org/experiments/ENCSR154MAJ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Memory_CD4_Activated_Day2
experiment encode accession: ENCSR154MAJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-07-21
lab: Yijun Ruan, JAX
library encode accession: ENCLB590WVA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: CTCF

value: male

value: 43 year

value: ENCBS397TSL at ENCODE; https://www.encodeproject.org/ENCBS397TSL/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: Unstimulated, differentiated WT BMDMs rep2

description:
Single-end
mm_BMDM_WT_VEH_rep2


title: Unstimulated, differentiated WT BMDMs rep1

description:
Single-end
mm_BMDM_WT_VEH_rep1


title: SAMPLE_16.m-TERT-AD-Hippocampal-Neurons-TAM-4

status: Public on Oct 12 2021

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

description: SAMPLE_16.m-TERT-AD-Hippocampal-Neurons-TAM replicate 4

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using STAR software.
The HTSeq-count program was used to generate raw read counts for each gene
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

growth_protocol: Adult mice

extract_protocol:
RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with tamoxifen or vehicle.

tag: strain

tag: tissue

value: Mouse hippocampal neurons

tag: group

value: Treated


title: Day 4 after CTX muscle injury

status: Public on Nov 03 2021

data_processing:
Single cell sequencing reads were processed and aligned to the mouse reference transcriptome (mm10) with the Cell Ranger version 3.1.0 (10x Genomics, Pleasanton, CA). We used CellBender to eliminate technical artifacts.
From the gene expression matrix, the downstream analysis was carried out with R version 4.0.2 (2020-06-22). Quality control, filtering, data clustering and visualization, and the differential expression analysis was carried out using Seurat (v3.2.2) R package (Butler et al., 2018) with some custom modifications to the standard pipeline. Genes expressed in less than 3 cells as well as cells < 1000 UMIs and < 200 genes were removed from the gene expression matrix. In addition, we removed any single-cell with > 5% UMIs mapped to mitochondrial genes, as well as obvious outliers in number of UMIs (cell doublets).
After log-normalizing the data, the expression of each gene was scaled regressing out the number of UMI and the percent mitochondrial gene expressed in each cell. We performed PCA on the gene expression matrix and used the first 30 principal components for clustering and visualization. Unsupervised shared nearest neighbor (SNN) clustering was performed with a resolution of 0.35 and visualization was done using t-distributed stochastic neighbor embedding (t-SNE). We performed a silhouette analysis (R cluster package) to select an optimal SNN resolution parameter, that balanced the number of expected clusters (given known marker expression) with a maximal average silhouette width. Finally, differential expression analysis was achieved using Seurat’s ‘‘FindAllMarkers’’ function using a likelihood ratio test that assumes the data follows a negative binomial distribution and only considering genes with > log2(0.25) fold-change and expressed in at least 40% of cells in the cluster. Feature plots were generated using Nebulosa package.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature barcode matrix generated by cellranger (v3.1.0).

source_name: muscle

extract_protocol: After tissue digestion and bead selection, CD45+ single-cell sorted suspensions were washed and resuspended in 0.04% BSA in PBS at a concentration of at least 400 cells/μL. Cells were counted manually with a hemocytometer to determine their concentration. Single-cell RNA-sequencing libraries were then prepared using the Chromium Single Cell 3’ reagent kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the manufacturer’s protocol. Briefly, the cells were diluted into the Chromium Single Cell A Chip as to yield a recovery of ~10,000 single-cell transcriptomes with < 5% doublet rate. Following the library preparation, the libraries were sequenced on the NovaSeq 6000 sequencer (Illumina, San Diego, CA) to produce about 450 million reads per library and on average a minimum of 40,000 reads per single cell.

treatment_protocol: Mice (8-12 weeks-old male) were anaesthetized with isoflurane (adjusted flow rate or concentration to 1,5%) and 50 µl of 10uM cardiotoxin (EMD Millipore, 217503-1MG) was injected in the tibialis anterior (TA) muscle. Mice were brought out of anesthesia and monitored until they were euthanized and processed at various time points. Muscles were recovered for flow cytometry analysis at day 1 to day 4 post-injury or for muscle histology at day 8 to day 21 post-injury.

value: CTX-induced acute sterile muscle injury


title: SAMPLE_15.m-TERT-AD-Hippocampal-Neurons-TAM-3

description: SAMPLE_15.m-TERT-AD-Hippocampal-Neurons-TAM replicate 3


title: SAMPLE_13.m-TERT-AD-Hippocampal-Neurons-TAM-1

description: SAMPLE_13.m-TERT-AD-Hippocampal-Neurons-TAM replicate 1


title: SAMPLE_11.m-TERT-AD-Hippocampal-Neurons-CTL-3

description: SAMPLE_11.m-TERT-AD-Hippocampal-Neurons-CTL replicate 3

value: Control


title: SAMPLE_12.m-TERT-AD-Hippocampal-Neurons-CTL-4

description: SAMPLE_12.m-TERT-AD-Hippocampal-Neurons-CTL replicate 4


title: SAMPLE_10.m-TERT-AD-Hippocampal-Neurons-CTL-2

description: SAMPLE_10.m-TERT-AD-Hippocampal-Neurons-CTL replicate 2


title: SAMPLE_08.m-TERT-AD-Cortical-Neurons-TAM-4

description: SAMPLE_08.m-TERT-AD-Cortical-Neurons-TAM replicate 4

value: Mouse cortical neurons


title: SAMPLE_14.m-TERT-AD-Hippocampal-Neurons-TAM-2

description: SAMPLE_14.m-TERT-AD-Hippocampal-Neurons-TAM replicate 2


title: SAMPLE_09.m-TERT-AD-Hippocampal-Neurons-CTL-1

description: SAMPLE_09.m-TERT-AD-Hippocampal-Neurons-CTL replicate 1


title: Unstimulated, differentiated RXRab KO BMDMs rep1

description:
Single-end
mm_BMDM_RXRKO_VEH_rep1

value: RXRafl/flLysMCre RXRb-/-

value: Bone marrow-derived macrophages


title: ChIA-PET from activated CD8-positive, naive alpha-beta T cell (ENCLB267XHH)

description:
https://www.encodeproject.org/experiments/ENCSR114QCL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Naive_CD8_Activated_Day7
experiment encode accession: ENCSR114QCL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-10-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB267XHH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens male adult (30 years) activated CD8-positive, naive alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

tag: antibody

value: primary cell

value: adult

value: 30 year

value: Yijun Ruan, JAX

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

value: ENCBS003RIO at ENCODE; https://www.encodeproject.org/ENCBS003RIO/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: SAMPLE_06.m-TERT-AD-Cortical-Neurons-TAM-2

description: SAMPLE_06.m-TERT-AD-Cortical-Neurons-TAM replicate 2


title: SAMPLE_07.m-TERT-AD-Cortical-Neurons-TAM-3

description: SAMPLE_07.m-TERT-AD-Cortical-Neurons-TAM replicate 3


title: SAMPLE_05.m-TERT-AD-Cortical-Neurons-TAM-1

description: SAMPLE_05.m-TERT-AD-Cortical-Neurons-TAM replicate 1


title: SAMPLE_03.m-TERT-AD-Cortical-Neurons-CTL-3

description: SAMPLE_03.m-TERT-AD-Cortical-Neurons-CTL replicate 3


title: SAMPLE_02.m-TERT-AD-Cortical-Neurons-CTL-2

description: SAMPLE_02.m-TERT-AD-Cortical-Neurons-CTL replicate 2


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 18 rep 3 (S243)

status: Public on Sep 14 2021

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

data_processing:
pre-processing: Filtered and trimmed with fastp (v0.20.1, default settings).
pre-processing: Reads mapping to rRNA were removed using Bbmap. Command line used: bbsplit.sh minratio=0.56 minhits=1 maxindel=16000
Filtered reads were mapped to gencode vm22 transcriptome using Salmon (v0.14.1)
Differential expression (gene): Import with tximeta, summarizeToGene with countsFromAbundance=lengthScaledTPM. Analyse with tidybulk: (i) scale for sequencing depth (2) keep abundant genes (3) calculate differential expression using DEseq2.
Differential expression (transcript) : Import with tximeta. Analyse with tidybulk: (i) scale for sequencing depth (2) keep abundant genes (3) calculate differential expression using DEseq2.
Alternative splicing: Trimmed and rRNA removed reads were mapped with STAR (v2.7.6a) to the mouse mm10 genome using parameters "--twopassMode Basic  --outFilterIntronMotifs RemoveNoncanonical" [Dobin 2013, PMID: 23104886].
Alternative splicing: Alternative splicing analysis was then performed using PSI-Sigma (v1.9j)  [Lin 2019, PMID:31135034] using "nreads=5" or "nreads=10".
Genome_build: mm10
Supplementary_files_format_and_content: *.quant.sf : Salmon mapping raw output.
Supplementary_files_format_and_content: *.IR.out.tab : Alternative splicing PSI-sigma IR output files.
Supplementary_files_format_and_content: *.SJ.out.tab : Alternative splicing STAR SJ output files.
Supplementary_files_format_and_content: gene.counts.csv : Salmon quantification (gene level)
Supplementary_files_format_and_content: transcript.counts.csv : Salmon quantification (transcript level)
Supplementary_files_format_and_content: SRSF2_GMCSF_gene_expression.xlsx : Gene and transcript differential expression
Supplementary_files_format_and_content: SRSF2_GMCSF_PSIsigma_alternative_splicing_analysis.annot.xlsx : PSI-sigma analysis output

source_name: Hoxb8 imortalised GM-CSF cell line

growth_protocol: Hoxb8 immortalised cell lines - Bone marrow cells were collected from three R26-CreERT2 Srsf2P95H/+ and three R26-CreERT2 Srsf2+/+ mice and stimulated for 48 hours in complete IMDM (20% FBS, 1% Penicillin/Streptomycin, 1% glutamine) supplemented with recombinant mouse stem cell factor (rmSCF, 50ng/mL)(Peprotech), recombinant mouse interleukin 3 (rmIL-3, 10ng/mL) (Peprotech) and recombinant human interleukin 6 (rhIL-6, 10ng/mL)(Amgen). After stimulation, 1x106 cells were spin-infected with Hoxb8 retrovirus {Wang, 2006 #23} and polybrene at 1,100g for 90 minutes. After 48 hours, the non-adherent cells were passaged into complete IMDM (10% FBS, 1% Penicillin/Streptomycin, 1% glutamine) with rmSCF, rmIL-3, rhIL-6 and 1% granulocyte-macrophage colony-stimulating factor (GM-CSF) conditioned medium (from BHK-HM5 cell conditioned medium). After 1 to 2 passages, cells were cultured in complete IMDM with 1% GM-CSF only. The cells were fully immortalised after four weeks and were GM-CSF dependent.

extract_protocol:
Genomic DNA was extracted from the cell pellets using the Gentra Puregene kit (Qiagen). The extracted DNA was quantified on a Nanodrop spectrophotometer.
DNA libraries were generated by PCR amplification of the integrated sgRNA constructs (as described in https://portals.broadinstitute.org/gpp/public/resources/protocols).
CRISPR screen. In total, 24 libraries were generated and sequenced on the Illumina HiSeq X Ten platform (150bp paired end reads) by Novogene (China).

treatment_protocol: At the start of the screen, 130x106 Cas9 cells from each of the cell lines (n=3 independently derived cell lines per genotype) were infected with the Brie CRISPR knockout pooled library (Mouse Brie CRISPR knockout pooled library was a gift from David Root and John Doench (Addgene #73633)) {Doench, 2016 #24}. The number of cells to infect was calculated by multiplying 78,637 (the number of guides in the library) by 500 (representing the desired number of cells for each guide at the start of the experiment), divided by 0.3 (multiplicity of infection; MOI). The 130x106 cells were separated into four Nunc™ cell culture T75 flasks and in each spin-infection flask, 35x106 cells were mixed with 122µL of concentrated lentivirus containing the Brie library and 35µL of polybrene (8µg/mL)(Sigma-Aldrich) in 35mL of IMDM-Cas9 media. The infection mix was then spun at 1,100g for 90 minutes and the cells were re-incubated immediately after the spin-infection. Approximately 4 hours later, the mixture was transferred into two T-175 flasks (Falcon) with the addition of 65mL of IMDM-Cas9 media and cells were re-incubated. After 48 hours, cells were counted and diluted to 8x105 cells/mL before adding puromycin (0.5µg/mL)(Merck). After 4 days of puromycin selection, the puromycin and blasticidin were washed out and the cells were cultured in IMDM with 10%FBS, 1% GM-CSF and 400nM 4-hydroxy tamoxifen (Merck Millipore). This timepoint is labelled day 0 of the screen. The tamoxifen was removed from the cells after 4 days and cells were then passaged at 2x105/mL every 2 days or 1x105/mL for a 3-day interval for a total of 14 days. A minimum of 40x106 cells was maintained during each split. On day 0, day 4, day 11 and day 18 of the screen, pellets of 40x106 cells were collected for gDNA isolation and library preparation.

tag: strain background

tag: cell line

value: imortalised GM-CSF cell line

tag: srsf2 genotype

tag: day

tag: sampleID

tag: replicate


title: scRNA.Day1

status: Public on Sep 17 2021

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

data_processing:
The raw sequencing data were pre- processed (demultiplexed cellular barcodes, read alignment, and generation of gene count matrix) using Cell Ranger Single Cell Software Suite provided by 10x Genomics. Detailed QC metrics were generated and evaluated. Genes detected in <0.1% of total sequenced cells and cells where < 200 genes had nonzero counts were filtered out and not included in the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: matrix counts

source_name: Ex vivo samples from pancreas

extract_protocol: Pancreata were harvested from C57BL/6J wild-type mice at different time points before and after acute inflammation and digested to obtain single cell suspension. After depletion of CD45-positive cells, primary cells derived from 3 pancreata were mixed for each time point, and 10,000 cells were captured followed by library preparation using 10X Chromium single cell 3’ V3 chemistry according to manufacturer’s protocol. Libraries were then multiplexed and sequenced on a single lane of NovaSeq6000 S2‐100 flow cell (Illumina).

value: Primary pancreatic epithelial cells

tag: growth protocol

value: Ex vivo samples, no need to grow

tag: time point

value: Harvest at 1 day after treatment

value: Caerulein


title: SAMPLE_01.m-TERT-AD-Cortical-Neurons-CTL-1

description: SAMPLE_01.m-TERT-AD-Cortical-Neurons-CTL replicate 1


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 18 rep 2 (S83)


title: scRNA.Day28

value: Harvest at 28 days after treatment


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 4 rep 3 (S243)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 0 rep 3 (S243)


title: scRNA.CTRL

value: Untreated


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 0 rep 2 (S83)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 11 rep 2 (S83)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 18 rep 1 (S81)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 11 rep 1 (S81)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 4 rep 1 (S81)


title: scRNA.Day7

value: Harvest at 7 days after treatment


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 11 rep 3 (S281)

value: WT


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 0 rep 3 (S281)


title: SAMPLE_04.m-TERT-AD-Cortical-Neurons-CTL-4

description: SAMPLE_04.m-TERT-AD-Cortical-Neurons-CTL replicate 4

value: Mouse cortical neurons

value: Control


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 4 rep 2 (S145)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 18 rep 2 (S145)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 18 rep 3 (S281)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 0 rep 1 (S81)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 18 rep 1 (S144)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 0 rep 2 (S145)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 11 rep 2 (S145)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 11 rep 3 (S243)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 0 rep 1 (S144)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 11 rep 1 (S144)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 4 rep 1 (S144)


title: Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2P95H/+ rep 2 (S83)

extract_protocol:
RNA was isolated from Hoxb8 immortalised R26-CreERT2 Srsf2P95H/+ and R26-CreERT2 Srsf2+/+ cells (n=3 per genotype) at 7 days post tamoxifen treatment. RNA was ribosome depleted.
Library preparation using (Kapa Stranded RNA-Seq Library Kit; Kapa Biosystems).
Sequenced at 150bp PE reads on the Illumina HiSeq X Ten platform by Novogene (China).

value: R26-CreERT2 Srsf2P95H/+

tag: tamixofen

value: yes


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, Srsf2P95H/+  Day 4 rep 2 (S83)


title: Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2P95H/+ rep 3 (S243)


title: Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ rep 3 (S281)

value: R26-CreERT2 Srsf2+/+


title: Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ rep 2 (S145)


title: Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ rep 1 (S144)


title: CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 4 rep 3 (S281)


title: Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2P95H/+ rep 1 (S81)


title: 5 week old osteoblast replicate 3

status: Public on Aug 25 2021

type: RNA

hyb_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

data_processing:
The normalization and differential expression steps were performed using GenePattern [http://www.ncbi.nlm.nih.gov/pubmed/16642009]. All samples were background corrected, and quantile normalised using GenePattern/NormalizeAffymetrix3prime (v.2.1). We used the Ensembl transcript annotation (v20.0) CDF from Dai [http://www.ncbi.nlm.nih.gov/pubmed/16284200].
Filtering: In order to set a threshold for detected genes and remove genes below the detection threshold, we used an expression threshold of 100. This generated a list of 13,880 transcripts (10,238 gene symbols), which showed expression above background in at least  3/3 of one subtype (w5 OB, w8 OB, w5 OP or w8 OP). See w5w8_OB_OP_FiltANY.gct.
Differential expression: Differentially expressed genes were determined using the GenePattern/LimmaGP module (v20.0) using the most informative probe [http://www.ncbi.nlm.nih.gov/pubmed/25605792]. For each comparison we created a separate GCT file containing only those transcripts detected in at least 3/3 samples for at least one of the two subtypes. Differential expression results in ODF format.
Annotation of transcripts: We used biomaRt [Durinck et al 2009, http://www.ncbi.nlm.nih.gov/pubmed/19617889] to annotate the resulting differential expression tables with additional information (chromosome name and position, band, description). Annotationed differential expression results in excel format.

label: biotin

source_name: WT Osteoblasts from 5 week old mice

growth_protocol: Isolated directly from mice - no in vitro growth conditions used

treatment_protocol: No treatment involved, all animals were untreated WT C57BL6 animals

tag: time

value: 5 week old

tag: genetic background

tag: Sex

value: Female


title: 5 week old Progenitor replicate 2

scan_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

source_name: WT Osteo-progenitors from 5 week old mice


title: 8 week old osteoblast replicate 1

source_name: WT Osteoblasts from 8 week old mice

label_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

value: 8 week old

value: Male


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFR-+ replicate 4

data_processing:
The normalization and differential expression steps were performed using GenePattern [http://www.ncbi.nlm.nih.gov/pubmed/16642009]. All samples were background corrected, and quantile normalised using GenePattern/NormalizeAffymetrix3prime (v.2.1). We used the Ensembl transcript annotation (v20.0) CDF from Dai [http://www.ncbi.nlm.nih.gov/pubmed/16284200].
Filtering: In order to set a threshold for detected genes and remove genes below the detection threshold, we used an expression threshold of 100. This generated a list of 12,440 transcripts (9,131 gene symbols), which showed expression above background in at least 3/4 of one subtype (A, AB, B, DN, SL). See OB_subtypes.100.FiltANY.gct.
Differential expression: Differentially expressed genes were determined using the GenePattern/LimmaGP module (v20.0, 4) using the most informative probe [http://www.ncbi.nlm.nih.gov/pubmed/25605792]. For each comparison we created a separate GCT file containing only those transcripts detected in at least ¾ of samples for at least one of the two subtypes. Differential expression results in ODF format.
Annotation of transcripts: We used biomaRt [Durinck et al 2009, http://www.ncbi.nlm.nih.gov/pubmed/19617889] to annotate the resulting differential expression tables with additional information (chromosome name and position, band, description). Annotationed differential expression results in excel format.

source_name: WT DN from 8 week old mice

extract_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

value: DN


title: 8 week old Progenitor replicate 1

source_name: WT Osteo-progenitors from 8 week old mice


title: 5 week old Progenitor replicate 3


title: 8 week old Lin-, CD31-, Sca-1lo, CD51+ PDGFRa- PDGFR-+ replicate 4

source_name: WT SL from 8 week old mice

value: SL


title: 8 week old Lin-, CD31-, Sca-1-, CD51+, PDGFRa+, PDGFRb- replicate 3

source_name: WT A from 8 week old mice

value: A


title: 5 week old Progenitor replicate 1


title: 8 week old Lin-, CD31-, Sca-1lo, CD51+ PDGFRa- PDGFR-+ replicate 3


title: 5 week old osteoblast replicate 1


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFRb+ replicate 4

source_name: WT B from 8 week old mice

value: B


title: 8 week old osteoblast replicate 2


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa+ PDGFRb+ replicate 4

source_name: WT AB from 8 week old mice

value: AB


title: 8 week old Lin-, CD31-, Sca-1-, CD51+, PDGFRa+, PDGFRb- replicate 4


title: 8 week old osteoblast replicate 3


title: 8 week old Lin-, CD31-, Sca-1lo, CD51+ PDGFRa- PDGFR-+ replicate 2


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFRb+ replicate 3


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa+ PDGFRb+ replicate 3


title: 8 week old Progenitor replicate 3


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFR-+ replicate 3


title: 8 week old Progenitor replicate 2


title: 8 week old Lin-, CD31-, Sca-1lo, CD51+ PDGFRa- PDGFR-+ replicate 1


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFRb+ replicate 2


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFRb+ replicate 1


title: 5 week old osteoblast replicate 2


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa+ PDGFRb+ replicate 2


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFR-+ replicate 2


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa- PDGFR-+ replicate 1


title: 8 week old Lin-, CD31-, Sca-1-, CD51+, PDGFRa+, PDGFRb- replicate 2


title: ChIA-PET from K562 (ENCLB587PEE)

status: Public on Jun 15 2021

description:
https://www.encodeproject.org/experiments/ENCSR597AKG/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in K562
experiment encode accession: ENCSR597AKG
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR606GRT
encode release date: 2021-03-12
lab: Yijun Ruan, JAX
library encode accession: ENCLB587PEE
size range: 300-600

source_name: Homo sapiens K562 cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/480f9184-07a5-4e57-bc33-ca6f675a1f97/@@download/attachment/ChIA-PET%20protocol%20for%20ENCODE4_Final.pdf
extraction method: SDS

value: CTCF

tag: line

value: cell line

tag: description

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises

tag: biosample encode accession

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Yijun Ruan, JAX

tag: source

value: ATCC

tag: link

value: ENCBS353IVQ at ENCODE; https://www.encodeproject.org/ENCBS353IVQ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIA-PET from K562 (ENCLB135RUF)

description:
https://www.encodeproject.org/experiments/ENCSR880DSH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in K562
experiment encode accession: ENCSR880DSH
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR606GRT
encode release date: 2021-02-26
lab: Yijun Ruan, JAX
library encode accession: ENCLB135RUF
size range: 300-600

tag: antibody

value: ENCBS868NPQ at ENCODE; https://www.encodeproject.org/ENCBS868NPQ/


title: ChIA-PET from HepG2 (ENCLB203LSE)

description:
https://www.encodeproject.org/experiments/ENCSR411IVB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET with HepG2 cell
experiment encode accession: ENCSR411IVB
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR152QMD
encode release date: 2021-03-12
lab: Yijun Ruan, JAX
library encode accession: ENCLB203LSE
size range: 300-600

source_name: Homo sapiens HepG2 cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS402OYQ at ENCODE; https://www.encodeproject.org/ENCBS402OYQ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ChIA-PET from AG04449 (ENCLB872ZUK)

description:
https://www.encodeproject.org/experiments/ENCSR720WRW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in AG04449
experiment encode accession: ENCSR720WRW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-18
lab: Yijun Ruan, JAX
library encode accession: ENCLB872ZUK
size range: 400-600
instrument models: Illumina MiSeq,Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens AG04449 cell line

value: cell line

value: fetal buttock/thigh fibroblast

value: apparently healthy

value: embryonic

value: 12 week

value: Coriell

value: ENCBS499QBB at ENCODE; https://www.encodeproject.org/ENCBS499QBB/

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


title: ChIA-PET from HepG2 (ENCLB460XMS)

description:
https://www.encodeproject.org/experiments/ENCSR411IVB/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET with HepG2 cell
experiment encode accession: ENCSR411IVB
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR152QMD
encode release date: 2021-03-12
lab: Yijun Ruan, JAX
library encode accession: ENCLB460XMS
size range: 300-600

value: CTCF

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS709FBU at ENCODE; https://www.encodeproject.org/ENCBS709FBU/


title: ChIA-PET from A549 (ENCLB427HJM)

description:
https://www.encodeproject.org/experiments/ENCSR911ZMB/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in A549
experiment encode accession: ENCSR911ZMB
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR414IDX
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB427HJM
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens A549 cell line

value: human epithelial cell line derived from a lung carcinoma tissue. The cells are adherent in culture. The karyotype is hypotriploid male with a modal chromosome number of 12. There are numerous chromosome abnormalities and marker chromosomes.

value: male

value: adult

value: 58 year

value: ENCBS744PGM at ENCODE; https://www.encodeproject.org/ENCBS744PGM/

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


title: ChIA-PET from HepG2 (ENCLB203QLI)

description:
https://www.encodeproject.org/experiments/ENCSR789ZIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET with HepG2 cell
experiment encode accession: ENCSR789ZIJ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR152QMD
encode release date: 2020-12-18
lab: Yijun Ruan, JAX
library encode accession: ENCLB203QLI
size range: 300-600

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS402OYQ at ENCODE; https://www.encodeproject.org/ENCBS402OYQ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ChIA-PET from GM10248 (ENCLB227NGL)

description:
https://www.encodeproject.org/experiments/ENCSR627XQX/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET with GM10248 cell
experiment encode accession: ENCSR627XQX
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB227NGL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens GM10248 cell line

value: B-Lymphocyte; Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12).

value: clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12)\n

value: unknown

value: 32 year

value: Coriell

value: ENCBS610TWD at ENCODE; https://www.encodeproject.org/ENCBS610TWD/

value: Derived from ENCODE donor ENCDO000ABI; https://www.encodeproject.org/ENCDO000ABI/


title: ChIA-PET from GM10248 (ENCLB879LRU)

description:
https://www.encodeproject.org/experiments/ENCSR627XQX/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET with GM10248 cell
experiment encode accession: ENCSR627XQX
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB879LRU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: male

value: Yijun Ruan, JAX

value: ENCBS664VXF at ENCODE; https://www.encodeproject.org/ENCBS664VXF/


title: ChIA-PET from A549 (ENCLB227SBJ)

description:
https://www.encodeproject.org/experiments/ENCSR911ZMB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in A549
experiment encode accession: ENCSR911ZMB
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR414IDX
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB227SBJ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: human epithelial cell line derived from a lung carcinoma tissue. The cells are adherent in culture. The karyotype is hypotriploid male with a modal chromosome number of 12. There are numerous chromosome abnormalities and marker chromosomes.

value: adult

value: 58 year

value: ATCC

value: ENCBS085MQM at ENCODE; https://www.encodeproject.org/ENCBS085MQM/

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


title: ChIA-PET from HEK293 (ENCLB238DBN)

description:
https://www.encodeproject.org/experiments/ENCSR934CYB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HEK293
experiment encode accession: ENCSR934CYB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB238DBN
size range: 300-600

source_name: Homo sapiens HEK293 cell line

value: Embryonic kidney cells contain Adenovirus 5 DNA

value: female

value: embryonic

value: not collected

value: ENCBS010SUH at ENCODE; https://www.encodeproject.org/ENCBS010SUH/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIA-PET from HEK293T (ENCLB802NWR)

description:
https://www.encodeproject.org/experiments/ENCSR676KCF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HEK293T
experiment encode accession: ENCSR676KCF
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR128PFN
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB802NWR
size range: 350-600

source_name: Homo sapiens HEK293T cell line

value: CTCF

value: embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line

value: unknown

value: Thermo Fisher

value: ENCBS581PVT at ENCODE; https://www.encodeproject.org/ENCBS581PVT/


title: ChIA-PET from AG04449 (ENCLB480RUC)

description:
https://www.encodeproject.org/experiments/ENCSR580MNR/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in AG04449
experiment encode accession: ENCSR580MNR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB480RUC
size range: 350-600

value: cell line

value: fetal buttock/thigh fibroblast

value: male

value: apparently healthy

value: 12 week

value: Yijun Ruan, JAX

value: Coriell

value: ENCBS794PMH at ENCODE; https://www.encodeproject.org/ENCBS794PMH/

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


title: ChIA-PET from K562 (ENCLB363ZMS)

description:
https://www.encodeproject.org/experiments/ENCSR880DSH/
***************
biological replicate number: 3
technical replicate number: 1
description: RNAPII ChIA-PET in K562
experiment encode accession: ENCSR880DSH
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR606GRT
encode release date: 2021-02-26
lab: Yijun Ruan, JAX
library encode accession: ENCLB363ZMS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-650

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS078KXL at ENCODE; https://www.encodeproject.org/ENCBS078KXL/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIA-PET from MCF 10A (ENCLB911AJL)

description:
https://www.encodeproject.org/experiments/ENCSR499JGQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET with MCF10A cell
experiment encode accession: ENCSR499JGQ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR775RVY
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB911AJL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-650

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: The MCF 10A cell line is a non-tumorigenic epithelial cell line. The cells are positive for epithelial sialomucins, cytokeratins and milk fat globule antigen.

value: fibrocystic disease

value: 36 year

value: ENCBS406JSW at ENCODE; https://www.encodeproject.org/ENCBS406JSW/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: 8 week old Lin-, CD31-, Sca-1- CD51+ PDGFRa+ PDGFRb+ replicate 1

value: AB

value: 8 week old

value: Male


title: 8 week old Lin-, CD31-, Sca-1-, CD51+, PDGFRa+, PDGFRb- replicate 1

value: A


title: ChIA-PET from HEK293T (ENCLB360NZX)

description:
https://www.encodeproject.org/experiments/ENCSR773XVD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HEK293T
experiment encode accession: ENCSR773XVD
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR128PFN
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB360NZX
size range: 350-600

value: cell line

value: embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line

value: female

value: unknown

value: embryonic

value: not collected

value: Yijun Ruan, JAX

value: Thermo Fisher

value: ENCBS581PVT at ENCODE; https://www.encodeproject.org/ENCBS581PVT/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIA-PET from HepG2 (ENCLB751HSL)

description:
https://www.encodeproject.org/experiments/ENCSR857MYZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET with HepG2 cell
experiment encode accession: ENCSR857MYZ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR152QMD
encode release date: 2020-12-30
lab: Yijun Ruan, JAX
library encode accession: ENCLB751HSL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS581YWD at ENCODE; https://www.encodeproject.org/ENCBS581YWD/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ChIA-PET from HepG2 (ENCLB091KZA)

description:
https://www.encodeproject.org/experiments/ENCSR857MYZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET with HepG2 cell
experiment encode accession: ENCSR857MYZ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR152QMD
encode release date: 2020-12-30
lab: Yijun Ruan, JAX
library encode accession: ENCLB091KZA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: cell line

value: ENCBS000CSQ at ENCODE; https://www.encodeproject.org/ENCBS000CSQ/


title: ChIA-PET from K562 (ENCLB728NYL)

description:
https://www.encodeproject.org/experiments/ENCSR597AKG/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in K562
experiment encode accession: ENCSR597AKG
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR606GRT
encode release date: 2021-03-12
lab: Yijun Ruan, JAX
library encode accession: ENCLB728NYL
size range: 300-600

value: CTCF

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS868NPQ at ENCODE; https://www.encodeproject.org/ENCBS868NPQ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIA-PET from GM10248 (ENCLB188GRR)

description:
https://www.encodeproject.org/experiments/ENCSR825RKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET with GM10248 cell
experiment encode accession: ENCSR825RKJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-18
lab: Yijun Ruan, JAX
library encode accession: ENCLB188GRR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-650

value: B-Lymphocyte; Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12).

value: male

value: clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12)\n

value: unknown

value: 32 year

value: Yijun Ruan, JAX

value: Coriell

value: ENCBS610TWD at ENCODE; https://www.encodeproject.org/ENCBS610TWD/

value: Derived from ENCODE donor ENCDO000ABI; https://www.encodeproject.org/ENCDO000ABI/


title: ChIA-PET from HEK293 (ENCLB885AAO)

description:
https://www.encodeproject.org/experiments/ENCSR934CYB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HEK293
experiment encode accession: ENCSR934CYB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB885AAO
size range: 300-600

value: cell line

value: Embryonic kidney cells contain Adenovirus 5 DNA

value: embryonic

value: not collected

value: ATCC

value: ENCBS329AQW at ENCODE; https://www.encodeproject.org/ENCBS329AQW/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIA-PET from HEK293 (ENCLB445AQQ)

description:
https://www.encodeproject.org/experiments/ENCSR410UHV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HEK293
experiment encode accession: ENCSR410UHV
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB445AQQ
size range: 350-600

value: CTCF

value: female

value: ENCBS010SUH at ENCODE; https://www.encodeproject.org/ENCBS010SUH/


title: ChIA-PET from GM10248 (ENCLB032LAN)

description:
https://www.encodeproject.org/experiments/ENCSR825RKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET with GM10248 cell
experiment encode accession: ENCSR825RKJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-18
lab: Yijun Ruan, JAX
library encode accession: ENCLB032LAN
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-650

value: B-Lymphocyte; Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12).

value: male

value: clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12)\n

value: ENCBS664VXF at ENCODE; https://www.encodeproject.org/ENCBS664VXF/


title: ChIA-PET from MCF 10A (ENCLB944VUV)

description:
https://www.encodeproject.org/experiments/ENCSR499JGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET with MCF10A cell
experiment encode accession: ENCSR499JGQ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR775RVY
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB944VUV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: MCF 10A

value: The MCF 10A cell line is a non-tumorigenic epithelial cell line. The cells are positive for epithelial sialomucins, cytokeratins and milk fat globule antigen.

value: fibrocystic disease

value: adult

value: 36 year

value: Yijun Ruan, JAX

value: ENCBS283FQS at ENCODE; https://www.encodeproject.org/ENCBS283FQS/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: ChIA-PET from SK-N-SH (ENCLB984WWM)

description:
https://www.encodeproject.org/experiments/ENCSR514HBO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in SK-N-SH
experiment encode accession: ENCSR514HBO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB984WWM
size range: 300-600

source_name: Homo sapiens SK-N-SH cell line

value: SK-N-SH

value: cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: ATCC

value: ENCBS210ZQV at ENCODE; https://www.encodeproject.org/ENCBS210ZQV/

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


title: ChIA-PET from HEK293 (ENCLB014FZN)

description:
https://www.encodeproject.org/experiments/ENCSR410UHV/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HEK293
experiment encode accession: ENCSR410UHV
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB014FZN
size range: 350-600

value: CTCF

value: Embryonic kidney cells contain Adenovirus 5 DNA

value: female

value: unknown

value: embryonic

value: not collected

value: ENCBS329AQW at ENCODE; https://www.encodeproject.org/ENCBS329AQW/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIA-PET from BJ (ENCLB993AEN)

description:
https://www.encodeproject.org/experiments/ENCSR573PZV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in BJ
experiment encode accession: ENCSR573PZV
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-26
lab: Yijun Ruan, JAX
library encode accession: ENCLB993AEN
size range: 350-600

source_name: Homo sapiens BJ cell line

value: BJ

value: skin fibroblast, The line was established from skin taken from normal foreskin. - ATCC.

value: male

value: normal

value: newborn

value: Yijun Ruan, JAX

value: ENCBS425ZJX at ENCODE; https://www.encodeproject.org/ENCBS425ZJX/

value: Derived from ENCODE donor ENCDO000AAG; https://www.encodeproject.org/ENCDO000AAG/


title: ChIA-PET from AG04449 (ENCLB462BII)

description:
https://www.encodeproject.org/experiments/ENCSR580MNR/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in AG04449
experiment encode accession: ENCSR580MNR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB462BII
size range: 350-600

value: cell line

value: fetal buttock/thigh fibroblast

value: apparently healthy

value: 12 week

value: Coriell

value: ENCBS499QBB at ENCODE; https://www.encodeproject.org/ENCBS499QBB/

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


title: ChIA-PET from K562 (ENCLB299VCX)

description:
https://www.encodeproject.org/experiments/ENCSR880DSH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in K562
experiment encode accession: ENCSR880DSH
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR606GRT
encode release date: 2021-02-26
lab: Yijun Ruan, JAX
library encode accession: ENCLB299VCX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-650

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS353IVQ at ENCODE; https://www.encodeproject.org/ENCBS353IVQ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIA-PET from AG04450 (ENCLB138TLQ)

description:
https://www.encodeproject.org/experiments/ENCSR514BNX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in AG04450
experiment encode accession: ENCSR514BNX
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-02-23
lab: Yijun Ruan, JAX
library encode accession: ENCLB138TLQ
size range: 350-600

source_name: Homo sapiens AG04450 cell line

value: male

value: embryonic

value: Yijun Ruan, JAX

value: ENCBS097WVO at ENCODE; https://www.encodeproject.org/ENCBS097WVO/


title: ChIA-PET from HEK293T (ENCLB200COE)

description:
https://www.encodeproject.org/experiments/ENCSR773XVD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HEK293T
experiment encode accession: ENCSR773XVD
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR128PFN
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB200COE
size range: 350-600

value: cell line

value: embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line

value: unknown

value: not collected

value: Thermo Fisher

value: ENCBS936QXM at ENCODE; https://www.encodeproject.org/ENCBS936QXM/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIA-PET from AG04449 (ENCLB758LDH)

description:
https://www.encodeproject.org/experiments/ENCSR720WRW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in AG04449
experiment encode accession: ENCSR720WRW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-18
lab: Yijun Ruan, JAX
library encode accession: ENCLB758LDH
size range: 350-600

value: fetal buttock/thigh fibroblast

value: apparently healthy

value: 12 week

value: Coriell

value: ENCBS794PMH at ENCODE; https://www.encodeproject.org/ENCBS794PMH/

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


title: ChIA-PET from HEK293T (ENCLB058KBT)

description:
https://www.encodeproject.org/experiments/ENCSR676KCF/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HEK293T
experiment encode accession: ENCSR676KCF
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR128PFN
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB058KBT
size range: 350-600

value: CTCF

value: female


title: ChIA-PET from endothelial cell of umbilical vein (ENCLB678FKH)

description:
https://www.encodeproject.org/experiments/ENCSR404FPI/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HUVEC
experiment encode accession: ENCSR404FPI
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR049NDZ
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB678FKH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

value: newborn

value: Yijun Ruan, JAX

value: Lonza

value: ENCBS046NPX at ENCODE; https://www.encodeproject.org/ENCBS046NPX/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: ChIA-PET from MCF-7 (ENCLB978GEE)

description:
https://www.encodeproject.org/experiments/ENCSR200VHL/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in MCF7
experiment encode accession: ENCSR200VHL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB978GEE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens MCF-7 cell line

value: cell line

value: Breast cancer derived from metastatic site. The MCF7 line retains several characteristics of differentiated mammary epithelium including ability to process estradiol via cytoplasmic estrogen receptors and the capability of forming domes. The cells express the WNT7B oncogene.

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: ATCC

value: ENCBS734CYW at ENCODE; https://www.encodeproject.org/ENCBS734CYW/

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


title: ChIA-PET from IMR-90 (ENCLB068URF)

description:
https://www.encodeproject.org/experiments/ENCSR076TTY/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET with IMR90 cell
experiment encode accession: ENCSR076TTY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB068URF
size range: 300-600

source_name: Homo sapiens IMR-90 cell line

value: CTCF

value: fetal lung fibroblasts

value: unknown

value: embryonic

value: 16 week

value: ENCBS844OYT at ENCODE; https://www.encodeproject.org/ENCBS844OYT/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: ChIA-PET from IMR-90 (ENCLB702AGZ)

description:
https://www.encodeproject.org/experiments/ENCSR076TTY/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET with IMR90 cell
experiment encode accession: ENCSR076TTY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB702AGZ
size range: 300-600

value: female

value: Yijun Ruan, JAX

value: ENCBS080CCO at ENCODE; https://www.encodeproject.org/ENCBS080CCO/


title: ChIA-PET from MCF 10A (ENCLB208HPT)

description:
https://www.encodeproject.org/experiments/ENCSR403ZYJ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET with MCF10A cell
experiment encode accession: ENCSR403ZYJ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR775RVY
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB208HPT
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: MCF 10A

value: cell line

value: The MCF 10A cell line is a non-tumorigenic epithelial cell line. The cells are positive for epithelial sialomucins, cytokeratins and milk fat globule antigen.

value: fibrocystic disease

value: 36 year

value: ENCBS406JSW at ENCODE; https://www.encodeproject.org/ENCBS406JSW/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/