title: TF ChIP-seq from HepG2 (ENCLB191WIP)

description:
https://www.encodeproject.org/experiments/ENCSR775EOB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR775EOB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR578XKJ
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB191WIP
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SNAPC2

value: ENCBS124PDF at ENCODE; https://www.encodeproject.org/ENCBS124PDF/


title: TF ChIP-seq from HepG2 (ENCLB634NRH)

status: Public on Apr 30 2023

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR775EOB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR775EOB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR578XKJ
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB634NRH
fragmentation methods: sonication (generic)

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: link

value: ENCBS009EMW at ENCODE; https://www.encodeproject.org/ENCBS009EMW/

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


title: TF ChIP-seq from HepG2 (ENCLB750WPS)

description:
https://www.encodeproject.org/experiments/ENCSR037LQB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR037LQB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB750WPS
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZSCAN25

value: ENCBS323WJT at ENCODE; https://www.encodeproject.org/ENCBS323WJT/


title: TF ChIP-seq from WTC11 (ENCLB665YZF)

description:
https://www.encodeproject.org/experiments/ENCSR579RFH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR579RFH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR678WJT
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB665YZF
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SMAD3

value: adult

value: 30 year

value: ENCBS377MPK at ENCODE; https://www.encodeproject.org/ENCBS377MPK/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from WTC11 (ENCLB285VQZ)

description:
https://www.encodeproject.org/experiments/ENCSR284SMX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR284SMX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB285VQZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens PREB

value: PREB

value: ENCBS926AQQ at ENCODE; https://www.encodeproject.org/ENCBS926AQQ/


title: TF ChIP-seq from WTC11 (ENCLB171RWZ)

description:
https://www.encodeproject.org/experiments/ENCSR583CGO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR583CGO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB171RWZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SP1

value: ENCBS047LAF at ENCODE; https://www.encodeproject.org/ENCBS047LAF/


title: TF ChIP-seq from WTC11 (ENCLB052GCX)

description:
https://www.encodeproject.org/experiments/ENCSR583CGO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR583CGO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB052GCX
fragmentation methods: sonication (generic)

value: cell line

value: ENCBS806IRC at ENCODE; https://www.encodeproject.org/ENCBS806IRC/


title: TF ChIP-seq from WTC11 (ENCLB388CCX)

description:
https://www.encodeproject.org/experiments/ENCSR579RFH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR579RFH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR678WJT
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB388CCX
fragmentation methods: sonication (generic)

value: male

value: ENCBS960OIM at ENCODE; https://www.encodeproject.org/ENCBS960OIM/


title: TF ChIP-seq from HepG2 (ENCLB472KJZ)

description:
https://www.encodeproject.org/experiments/ENCSR039IQA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR039IQA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB472KJZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens BAZ2A

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS901DYD at ENCODE; https://www.encodeproject.org/ENCBS901DYD/


title: TF ChIP-seq from HepG2 (ENCLB071EZP)

description:
https://www.encodeproject.org/experiments/ENCSR037LQB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR037LQB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB071EZP
fragmentation methods: sonication (generic)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS644SVP at ENCODE; https://www.encodeproject.org/ENCBS644SVP/

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


title: TF ChIP-seq from WTC11 (ENCLB578LYN)

description:
https://www.encodeproject.org/experiments/ENCSR284SMX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR284SMX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB578LYN
fragmentation methods: sonication (generic)

value: adult

value: 30 year

value: ENCBS647OQR at ENCODE; https://www.encodeproject.org/ENCBS647OQR/


title: TF ChIP-seq from WTC11 (ENCLB769WVZ)

description:
https://www.encodeproject.org/experiments/ENCSR572DUR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-FOS ChIP-seq on human WTC11
experiment encode accession: ENCSR572DUR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR178OJR
encode release date: 2022-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB769WVZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOS, genetically modified (insertion) using TALEN inserting M. musculus Neurog2

value: FOS

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS264HOU at ENCODE; https://www.encodeproject.org/ENCBS264HOU/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from HepG2 (ENCLB806EMX)

description:
https://www.encodeproject.org/experiments/ENCSR782WWY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR782WWY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR856RWG
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB806EMX
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF546

value: cell line

value: male

value: ENCBS183RFQ at ENCODE; https://www.encodeproject.org/ENCBS183RFQ/


title: TF ChIP-seq from WTC11 (ENCLB095NYG)

description:
https://www.encodeproject.org/experiments/ENCSR034IND/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR034IND
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR678WJT
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB095NYG
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF232

value: ENCBS958IHR at ENCODE; https://www.encodeproject.org/ENCBS958IHR/


title: TF ChIP-seq from WTC11 (ENCLB902LWO)

description:
https://www.encodeproject.org/experiments/ENCSR034IND/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR034IND
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR678WJT
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB902LWO
fragmentation methods: sonication (generic)

value: ENCBS324BDN at ENCODE; https://www.encodeproject.org/ENCBS324BDN/


title: TF ChIP-seq from HepG2 (ENCLB669YAX)

description:
https://www.encodeproject.org/experiments/ENCSR782WWY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR782WWY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR856RWG
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB669YAX
fragmentation methods: sonication (generic)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: ENCBS702OHZ at ENCODE; https://www.encodeproject.org/ENCBS702OHZ/


title: TF ChIP-seq from WTC11 (ENCLB409GKW)

description:
https://www.encodeproject.org/experiments/ENCSR048PPE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR048PPE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR783VJL
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB409GKW
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens STAT6

value: adult

value: 30 year

value: Richard Myers

value: ENCBS250JQW at ENCODE; https://www.encodeproject.org/ENCBS250JQW/


title: TF ChIP-seq from HepG2 (ENCLB988YRB)

description:
https://www.encodeproject.org/experiments/ENCSR765VDK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR765VDK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR578XKJ
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB988YRB
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SMYD3

value: ENCBS778DFE at ENCODE; https://www.encodeproject.org/ENCBS778DFE/

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


title: TF ChIP-seq from WTC11 (ENCLB596YMQ)

description:
https://www.encodeproject.org/experiments/ENCSR032DGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR032DGZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR491BNK
encode release date: 2023-01-10
lab: Richard Myers, HAIB
library encode accession: ENCLB596YMQ
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF281

value: ENCBS244DYF at ENCODE; https://www.encodeproject.org/ENCBS244DYF/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from WTC11 (ENCLB661WBS)

description:
https://www.encodeproject.org/experiments/ENCSR572DUR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-FOS ChIP-seq on human WTC11
experiment encode accession: ENCSR572DUR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR178OJR
encode release date: 2022-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB661WBS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: FOS

value: cell line

value: male

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS749MYI at ENCODE; https://www.encodeproject.org/ENCBS749MYI/


title: TF ChIP-seq from WTC11 (ENCLB293GAY)

description:
https://www.encodeproject.org/experiments/ENCSR032DGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR032DGZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR491BNK
encode release date: 2023-01-10
lab: Richard Myers, HAIB
library encode accession: ENCLB293GAY
fragmentation methods: sonication (generic)

value: ENCBS023HSW at ENCODE; https://www.encodeproject.org/ENCBS023HSW/


title: TF ChIP-seq from HepG2 (ENCLB052ESO)

description:
https://www.encodeproject.org/experiments/ENCSR282ZLP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR282ZLP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR533ASI
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB052ESO
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens JUND

value: JUND

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: ENCBS803JSA at ENCODE; https://www.encodeproject.org/ENCBS803JSA/


title: TF ChIP-seq from HepG2 (ENCLB844OTF)

description:
https://www.encodeproject.org/experiments/ENCSR282ZLP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR282ZLP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR533ASI
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB844OTF
fragmentation methods: sonication (generic)

value: Richard Myers

value: ENCBS325GPO at ENCODE; https://www.encodeproject.org/ENCBS325GPO/


title: TF ChIP-seq from WTC11 (ENCLB881OKZ)

description:
https://www.encodeproject.org/experiments/ENCSR760GZL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR760GZL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR783VJL
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB881OKZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TP53

value: adult

value: 30 year

value: ENCBS742MSK at ENCODE; https://www.encodeproject.org/ENCBS742MSK/


title: TF ChIP-seq from K562 (ENCLB051UCH)

description:
https://www.encodeproject.org/experiments/ENCSR279IMD/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR279IMD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR385DOV
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB051UCH
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HMGXB4

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS886WXS at ENCODE; https://www.encodeproject.org/ENCBS886WXS/

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


title: TF ChIP-seq from K562 (ENCLB982DGQ)

description:
https://www.encodeproject.org/experiments/ENCSR279IMD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR279IMD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR385DOV
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB982DGQ
fragmentation methods: sonication (generic)

value: ENCBS360BKA at ENCODE; https://www.encodeproject.org/ENCBS360BKA/


title: TF ChIP-seq from WTC11 (ENCLB065ZEV)

description:
https://www.encodeproject.org/experiments/ENCSR760GZL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR760GZL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR783VJL
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB065ZEV
fragmentation methods: sonication (generic)

value: male

value: ENCBS648OTZ at ENCODE; https://www.encodeproject.org/ENCBS648OTZ/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from K562 (ENCLB497VQE)

description:
https://www.encodeproject.org/experiments/ENCSR755CRA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR755CRA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR385DOV, ENCSR615INN
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB497VQE
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZKSCAN8

value: Richard Myers, HAIB

value: ENCBS836GCF at ENCODE; https://www.encodeproject.org/ENCBS836GCF/


title: TF ChIP-seq from HepG2 (ENCLB037DOP)

description:
https://www.encodeproject.org/experiments/ENCSR765VDK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR765VDK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR578XKJ
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB037DOP
fragmentation methods: sonication (generic)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers

value: ENCBS513JWP at ENCODE; https://www.encodeproject.org/ENCBS513JWP/

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


title: TF ChIP-seq from HepG2 (ENCLB094UHH)

description:
https://www.encodeproject.org/experiments/ENCSR031WWM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR031WWM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR315QCW
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB094UHH
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TERF1

value: cell line

value: ENCBS782YQS at ENCODE; https://www.encodeproject.org/ENCBS782YQS/


title: TF ChIP-seq from K562 (ENCLB168UJS)

description:
https://www.encodeproject.org/experiments/ENCSR755CRA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR755CRA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR385DOV, ENCSR615INN
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB168UJS
fragmentation methods: sonication (generic)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS766LQN at ENCODE; https://www.encodeproject.org/ENCBS766LQN/


title: TF ChIP-seq from WTC11 (ENCLB479YJJ)

description:
https://www.encodeproject.org/experiments/ENCSR753PPY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR753PPY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB479YJJ
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TCF7

value: male

value: 30 year

value: ENCBS787MLA at ENCODE; https://www.encodeproject.org/ENCBS787MLA/


title: TF ChIP-seq from K562 (ENCLB226HXB)

description:
https://www.encodeproject.org/experiments/ENCSR269BSA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR269BSA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR516XLO
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB226HXB
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MED1

value: Richard Myers, HAIB

value: ENCBS371OAY at ENCODE; https://www.encodeproject.org/ENCBS371OAY/

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


title: TF ChIP-seq from K562 (ENCLB113ZLH)

description:
https://www.encodeproject.org/experiments/ENCSR269BSA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR269BSA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR516XLO
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB113ZLH
fragmentation methods: sonication (generic)

value: ENCBS217NBD at ENCODE; https://www.encodeproject.org/ENCBS217NBD/


title: TF ChIP-seq from HepG2 (ENCLB884HNI)

description:
https://www.encodeproject.org/experiments/ENCSR569GKR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR569GKR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR315QCW
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB884HNI
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF253

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers

value: ENCBS420JGA at ENCODE; https://www.encodeproject.org/ENCBS420JGA/


title: TF ChIP-seq from K562 (ENCLB961JEK)

description:
https://www.encodeproject.org/experiments/ENCSR568ZXG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR568ZXG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR385DOV
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB961JEK
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ATF3

value: cell line

value: female

value: ENCBS609JRM at ENCODE; https://www.encodeproject.org/ENCBS609JRM/


title: TF ChIP-seq from WTC11 (ENCLB137SJN)

description:
https://www.encodeproject.org/experiments/ENCSR753PPY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR753PPY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB137SJN
fragmentation methods: sonication (generic)

value: adult

value: ENCBS056NAC at ENCODE; https://www.encodeproject.org/ENCBS056NAC/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from HepG2 (ENCLB763IUI)

description:
https://www.encodeproject.org/experiments/ENCSR031WWM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR031WWM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR315QCW
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB763IUI
fragmentation methods: sonication (generic)

value: male

value: ENCBS361ESN at ENCODE; https://www.encodeproject.org/ENCBS361ESN/

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


title: TF ChIP-seq from K562 (ENCLB882FRY)

description:
https://www.encodeproject.org/experiments/ENCSR568ZXG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR568ZXG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR385DOV
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB882FRY
fragmentation methods: sonication (generic)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Richard Myers, HAIB

value: ENCBS508IOO at ENCODE; https://www.encodeproject.org/ENCBS508IOO/


title: TF ChIP-seq from HepG2 (ENCLB116VSH)

description:
https://www.encodeproject.org/experiments/ENCSR569GKR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR569GKR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR315QCW
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB116VSH
fragmentation methods: sonication (generic)

value: hepatocellular carcinoma

value: child

value: ENCBS217PHQ at ENCODE; https://www.encodeproject.org/ENCBS217PHQ/


title: TF ChIP-seq from HepG2 (ENCLB779ZXR)

description:
https://www.encodeproject.org/experiments/ENCSR267TGY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR267TGY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB779ZXR
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ARNT2

value: 15 year

value: Richard Myers

value: ENCBS471TQQ at ENCODE; https://www.encodeproject.org/ENCBS471TQQ/


title: TF ChIP-seq from WTC11 (ENCLB273BID)

description:
https://www.encodeproject.org/experiments/ENCSR029TLS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR029TLS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR730ATD
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB273BID
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ETV6

value: cell line

value: 30 year

value: ENCBS564MHV at ENCODE; https://www.encodeproject.org/ENCBS564MHV/


title: TF ChIP-seq from WTC11 (ENCLB774OSK)

description:
https://www.encodeproject.org/experiments/ENCSR029TLS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR029TLS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR730ATD
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB774OSK
fragmentation methods: sonication (generic)

value: adult

value: ENCBS218PDC at ENCODE; https://www.encodeproject.org/ENCBS218PDC/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from HepG2 (ENCLB157BAX)

description:
https://www.encodeproject.org/experiments/ENCSR267TGY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR267TGY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB157BAX
fragmentation methods: sonication (generic)

value: male

value: ENCBS958BPG at ENCODE; https://www.encodeproject.org/ENCBS958BPG/

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


title: TF ChIP-seq from WTC11 (ENCLB922PGF)

description:
https://www.encodeproject.org/experiments/ENCSR564TIP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR564TIP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR549JGF
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB922PGF
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens CREM

value: CREM

value: Richard Myers, HAIB

value: ENCBS737MIG at ENCODE; https://www.encodeproject.org/ENCBS737MIG/


title: TF ChIP-seq from WTC11 (ENCLB867VXX)

description:
https://www.encodeproject.org/experiments/ENCSR264OKN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR264OKN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB867VXX
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens E2F4

value: ENCBS132OAY at ENCODE; https://www.encodeproject.org/ENCBS132OAY/


title: TF ChIP-seq from glutamatergic neuron (ENCLB372POK)

description:
https://www.encodeproject.org/experiments/ENCSR749BFL/
***************
biological replicate number: 1
technical replicate number: 1
description: EGR1 ChIP-seq on human WTC11
experiment encode accession: ENCSR749BFL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR548RFU
encode release date: 2022-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB372POK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (30 years) glutamatergic neuron in vitro differentiated cells genetically modified (insertion) using CRISPR targeting H. sapiens EGR1, genetically modified (insertion) using TALEN inserting Mouse Neurog2 originated from WCT11

value: glutamatergic neuron

value: in vitro differentiated cells

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS049FUQ at ENCODE; https://www.encodeproject.org/ENCBS049FUQ/


title: TF ChIP-seq from WTC11 (ENCLB906GCQ)

description:
https://www.encodeproject.org/experiments/ENCSR564TIP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR564TIP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR549JGF
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB906GCQ
fragmentation methods: sonication (generic)

value: cell line

value: 30 year

value: Richard Myers

value: ENCBS156UXS at ENCODE; https://www.encodeproject.org/ENCBS156UXS/


title: TF ChIP-seq from HepG2 (ENCLB193QCC)

description:
https://www.encodeproject.org/experiments/ENCSR263YXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR263YXJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR720MOD
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB193QCC
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF672

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS145UOW at ENCODE; https://www.encodeproject.org/ENCBS145UOW/


title: TF ChIP-seq from WTC11 (ENCLB156HYS)

description:
https://www.encodeproject.org/experiments/ENCSR029OPK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR029OPK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB156HYS
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ESRRA

value: ESRRA

value: male

value: adult

value: ENCBS551RFU at ENCODE; https://www.encodeproject.org/ENCBS551RFU/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from WTC11 (ENCLB109XFD)

description:
https://www.encodeproject.org/experiments/ENCSR264OKN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR264OKN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB109XFD
fragmentation methods: sonication (generic)

value: Richard Myers, HAIB

value: ENCBS479PDF at ENCODE; https://www.encodeproject.org/ENCBS479PDF/


title: TF ChIP-seq from HepG2 (ENCLB022WDD)

description:
https://www.encodeproject.org/experiments/ENCSR263YXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR263YXJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR720MOD
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB022WDD
fragmentation methods: sonication (generic)

value: ENCBS264VFA at ENCODE; https://www.encodeproject.org/ENCBS264VFA/

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


title: TF ChIP-seq from K562 (ENCLB462DIU)

description:
https://www.encodeproject.org/experiments/ENCSR028WJI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR028WJI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615INN
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB462DIU
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TGIF2

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS719MEU at ENCODE; https://www.encodeproject.org/ENCBS719MEU/

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


title: TF ChIP-seq from K562 (ENCLB174AZT)

description:
https://www.encodeproject.org/experiments/ENCSR028WJI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR028WJI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615INN
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB174AZT
fragmentation methods: sonication (generic)

value: Richard Myers

value: ENCBS359JRT at ENCODE; https://www.encodeproject.org/ENCBS359JRT/


title: TF ChIP-seq from glutamatergic neuron (ENCLB770YQZ)

description:
https://www.encodeproject.org/experiments/ENCSR749BFL/
***************
biological replicate number: 2
technical replicate number: 1
description: EGR1 ChIP-seq on human WTC11
experiment encode accession: ENCSR749BFL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR548RFU
encode release date: 2022-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB770YQZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: glutamatergic neuron

value: in vitro differentiated cells

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS875HWO at ENCODE; https://www.encodeproject.org/ENCBS875HWO/


title: TF ChIP-seq from HepG2 (ENCLB886XHL)

description:
https://www.encodeproject.org/experiments/ENCSR747MFU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR747MFU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB886XHL
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens POGK

value: POGK

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: ENCBS996MFE at ENCODE; https://www.encodeproject.org/ENCBS996MFE/


title: TF ChIP-seq from HepG2 (ENCLB561EPW)

description:
https://www.encodeproject.org/experiments/ENCSR747MFU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR747MFU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB561EPW
fragmentation methods: sonication (generic)

value: cell line

value: ENCBS798KMA at ENCODE; https://www.encodeproject.org/ENCBS798KMA/

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


title: TF ChIP-seq from WTC11 (ENCLB666EAM)

description:
https://www.encodeproject.org/experiments/ENCSR261EBV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR261EBV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR491BNK, ENCSR783VJL
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB666EAM
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens AFF4

value: adult

value: Richard Myers

value: ENCBS118TWJ at ENCODE; https://www.encodeproject.org/ENCBS118TWJ/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from WTC11 (ENCLB040HOM)

description:
https://www.encodeproject.org/experiments/ENCSR744RAS/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GRHL2 ChIP-seq on human WTC11
experiment encode accession: ENCSR744RAS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2022-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB040HOM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens GRHL2

value: 30 year

value: Michael Snyder, Stanford

value: ENCBS289EQQ at ENCODE; https://www.encodeproject.org/ENCBS289EQQ/


title: TF ChIP-seq from WTC11 (ENCLB450GPH)

description:
https://www.encodeproject.org/experiments/ENCSR561YGS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR561YGS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2023-01-20
lab: Richard Myers, HAIB
library encode accession: ENCLB450GPH
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens GABPB1

value: ENCBS417DMF at ENCODE; https://www.encodeproject.org/ENCBS417DMF/


title: TF ChIP-seq from WTC11 (ENCLB087TUE)

description:
https://www.encodeproject.org/experiments/ENCSR261EBV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR261EBV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR491BNK, ENCSR783VJL
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB087TUE
fragmentation methods: sonication (generic)

value: male

value: ENCBS792GQU at ENCODE; https://www.encodeproject.org/ENCBS792GQU/


title: TF ChIP-seq from K562 (ENCLB411CJB)

description:
https://www.encodeproject.org/experiments/ENCSR015KAM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR015KAM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615INN
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB411CJB
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens DMTF1

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS128TGE at ENCODE; https://www.encodeproject.org/ENCBS128TGE/

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


title: TF ChIP-seq from HepG2 (ENCLB553FLX)

description:
https://www.encodeproject.org/experiments/ENCSR560HRJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR560HRJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB553FLX
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF136

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: ENCBS225HGS at ENCODE; https://www.encodeproject.org/ENCBS225HGS/


title: TF ChIP-seq from HepG2 (ENCLB481LUR)

description:
https://www.encodeproject.org/experiments/ENCSR553ZJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR553ZJQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR555EMB
encode release date: 2022-09-14
lab: Richard Myers, HAIB
library encode accession: ENCLB481LUR
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF18

value: Richard Myers

value: ENCBS832YMK at ENCODE; https://www.encodeproject.org/ENCBS832YMK/

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


title: TF ChIP-seq from K562 (ENCLB144NVD)

description:
https://www.encodeproject.org/experiments/ENCSR249VFB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR249VFB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR859ZNT
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB144NVD
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB49

value: adult

value: ENCBS870VXU at ENCODE; https://www.encodeproject.org/ENCBS870VXU/


title: TF ChIP-seq from K562 (ENCLB154RUA)

description:
https://www.encodeproject.org/experiments/ENCSR249VFB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR249VFB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR859ZNT
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB154RUA
fragmentation methods: sonication (generic)

value: ENCBS168WHD at ENCODE; https://www.encodeproject.org/ENCBS168WHD/


title: TF ChIP-seq from HepG2 (ENCLB777ZUE)

description:
https://www.encodeproject.org/experiments/ENCSR250LJG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR250LJG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2023-01-10
lab: Richard Myers, HAIB
library encode accession: ENCLB777ZUE
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens GATAD2B

value: male

value: ENCBS278FBM at ENCODE; https://www.encodeproject.org/ENCBS278FBM/


title: TF ChIP-seq from HepG2 (ENCLB239IFT)

description:
https://www.encodeproject.org/experiments/ENCSR560HRJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR560HRJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2022-09-30
lab: Richard Myers, HAIB
library encode accession: ENCLB239IFT
fragmentation methods: sonication (generic)

value: ENCBS861GJN at ENCODE; https://www.encodeproject.org/ENCBS861GJN/


title: TF ChIP-seq from K562 (ENCLB068OOP)

description:
https://www.encodeproject.org/experiments/ENCSR014ARU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR014ARU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR144DXT
encode release date: 2022-09-13
lab: Richard Myers, HAIB
library encode accession: ENCLB068OOP
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ATF2

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS748REQ at ENCODE; https://www.encodeproject.org/ENCBS748REQ/


title: TF ChIP-seq from WTC11 (ENCLB277OYD)

description:
https://www.encodeproject.org/experiments/ENCSR029OPK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR029OPK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB277OYD
fragmentation methods: sonication (generic)

value: ESRRA

value: cell line

value: 30 year

value: ENCBS614PLT at ENCODE; https://www.encodeproject.org/ENCBS614PLT/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from K562 (ENCLB307XXY)

description:
https://www.encodeproject.org/experiments/ENCSR014ARU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR014ARU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR144DXT
encode release date: 2022-09-13
lab: Richard Myers, HAIB
library encode accession: ENCLB307XXY
fragmentation methods: sonication (generic)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS785BSO at ENCODE; https://www.encodeproject.org/ENCBS785BSO/

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


title: TF ChIP-seq from WTC11 (ENCLB131ZBR)

description:
https://www.encodeproject.org/experiments/ENCSR546PDE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR546PDE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB131ZBR
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXP1

value: adult

value: ENCBS749QHS at ENCODE; https://www.encodeproject.org/ENCBS749QHS/


title: TF ChIP-seq from WTC11 (ENCLB507UDO)

description:
https://www.encodeproject.org/experiments/ENCSR248QBT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR248QBT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR421QOH
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB507UDO
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens USF1

value: male

value: ENCBS083HVN at ENCODE; https://www.encodeproject.org/ENCBS083HVN/


title: TF ChIP-seq from K562 (ENCLB270IOR)

description:
https://www.encodeproject.org/experiments/ENCSR015KAM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR015KAM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615INN
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB270IOR
fragmentation methods: sonication (generic)

value: female

value: ENCBS703YSI at ENCODE; https://www.encodeproject.org/ENCBS703YSI/


title: TF ChIP-seq from HepG2 (ENCLB733POP)

description:
https://www.encodeproject.org/experiments/ENCSR250LJG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR250LJG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2023-01-10
lab: Richard Myers, HAIB
library encode accession: ENCLB733POP
fragmentation methods: sonication (generic)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS135JEH at ENCODE; https://www.encodeproject.org/ENCBS135JEH/

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


title: TF ChIP-seq from HepG2 (ENCLB243GFX)

description:
https://www.encodeproject.org/experiments/ENCSR553ZJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR553ZJQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR555EMB
encode release date: 2022-09-14
lab: Richard Myers, HAIB
library encode accession: ENCLB243GFX
fragmentation methods: sonication (generic)

value: cell line

value: ENCBS677JXQ at ENCODE; https://www.encodeproject.org/ENCBS677JXQ/


title: TF ChIP-seq from WTC11 (ENCLB632HSL)

description:
https://www.encodeproject.org/experiments/ENCSR248QBT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR248QBT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR421QOH
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB632HSL
fragmentation methods: sonication (generic)

value: 30 year

value: Richard Myers, HAIB

value: ENCBS703IJJ at ENCODE; https://www.encodeproject.org/ENCBS703IJJ/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from K562 (ENCLB349AJL)

description:
https://www.encodeproject.org/experiments/ENCSR744GHR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR744GHR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR188MIS
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB349AJL
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens E2F5

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Richard Myers

value: ENCBS800XDW at ENCODE; https://www.encodeproject.org/ENCBS800XDW/

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


title: TF ChIP-seq from K562 (ENCLB754KUL)

description:
https://www.encodeproject.org/experiments/ENCSR013UDY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR013UDY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR188MIS
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB754KUL
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TOE1

value: female

value: ENCBS548HNP at ENCODE; https://www.encodeproject.org/ENCBS548HNP/


title: TF ChIP-seq from K562 (ENCLB673SIC)

description:
https://www.encodeproject.org/experiments/ENCSR744GHR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR744GHR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR188MIS
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB673SIC
fragmentation methods: sonication (generic)

value: ENCBS162ROE at ENCODE; https://www.encodeproject.org/ENCBS162ROE/


title: TF ChIP-seq from HepG2 (ENCLB450AQU)

description:
https://www.encodeproject.org/experiments/ENCSR545ADB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR545ADB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB450AQU
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NACC2

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS883NVV at ENCODE; https://www.encodeproject.org/ENCBS883NVV/


title: TF ChIP-seq from HepG2 (ENCLB628ECD)

description:
https://www.encodeproject.org/experiments/ENCSR545ADB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR545ADB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB628ECD
fragmentation methods: sonication (generic)

value: cell line

value: Richard Myers, HAIB

value: ENCBS757ZXF at ENCODE; https://www.encodeproject.org/ENCBS757ZXF/

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


title: TF ChIP-seq from K562 (ENCLB316UXY)

description:
https://www.encodeproject.org/experiments/ENCSR744CXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR744CXJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR144DXT
encode release date: 2022-09-13
lab: Richard Myers, HAIB
library encode accession: ENCLB316UXY
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ELF1

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS473RMH at ENCODE; https://www.encodeproject.org/ENCBS473RMH/


title: TF ChIP-seq from WTC11 (ENCLB539KDU)

description:
https://www.encodeproject.org/experiments/ENCSR546PDE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR546PDE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB539KDU
fragmentation methods: sonication (generic)

value: 30 year

value: Richard Myers

value: ENCBS639CMT at ENCODE; https://www.encodeproject.org/ENCBS639CMT/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from K562 (ENCLB218XNZ)

description:
https://www.encodeproject.org/experiments/ENCSR011WGT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR011WGT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615INN
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB218XNZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens GABPB1

value: female

value: 53 year

value: ENCBS056MOJ at ENCODE; https://www.encodeproject.org/ENCBS056MOJ/

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


title: TF ChIP-seq from WTC11 (ENCLB261DRQ)

description:
https://www.encodeproject.org/experiments/ENCSR561YGS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR561YGS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2023-01-20
lab: Richard Myers, HAIB
library encode accession: ENCLB261DRQ
fragmentation methods: sonication (generic)

value: male

value: ENCBS102CRG at ENCODE; https://www.encodeproject.org/ENCBS102CRG/


title: TF ChIP-seq from WTC11 (ENCLB809IBI)

description:
https://www.encodeproject.org/experiments/ENCSR744RAS/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GRHL2 ChIP-seq on human WTC11
experiment encode accession: ENCSR744RAS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2022-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB809IBI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS966TKS at ENCODE; https://www.encodeproject.org/ENCBS966TKS/


title: TF ChIP-seq from K562 (ENCLB013VTT)

description:
https://www.encodeproject.org/experiments/ENCSR011WGT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR011WGT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615INN
encode release date: 2022-08-23
lab: Richard Myers, HAIB
library encode accession: ENCLB013VTT
fragmentation methods: sonication (generic)

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS864TZK at ENCODE; https://www.encodeproject.org/ENCBS864TZK/


title: TF ChIP-seq from dorsolateral prefrontal cortex (ENCLB390GMI)

description:
https://www.encodeproject.org/experiments/ENCSR384DBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.
experiment encode accession: ENCSR384DBJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR968MKZ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB390GMI
size range: 200-600

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

value: CTCF

value: dorsolateral prefrontal cortex

value: tissue

value: adult

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS788LTG at ENCODE; https://www.encodeproject.org/ENCBS788LTG/

value: Derived from ENCODE donor ENCDO865EMM; https://www.encodeproject.org/ENCDO865EMM/


title: TF ChIP-seq from K562 (ENCLB523QAF)

description:
https://www.encodeproject.org/experiments/ENCSR013UDY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR013UDY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR188MIS
encode release date: 2022-08-15
lab: Richard Myers, HAIB
library encode accession: ENCLB523QAF
fragmentation methods: sonication (generic)

value: female

value: 53 year

value: Richard Myers

value: ENCBS659JDN at ENCODE; https://www.encodeproject.org/ENCBS659JDN/

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


title: TF ChIP-seq from WTC11 (ENCLB214HXW)

description:
https://www.encodeproject.org/experiments/ENCSR245QUM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR245QUM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2023-01-31
lab: Richard Myers, HAIB
library encode accession: ENCLB214HXW
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NFE2L1

value: cell line

value: male

value: 30 year

value: ENCBS871FXA at ENCODE; https://www.encodeproject.org/ENCBS871FXA/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: RNA from liver from YoungHetRec3

status: Public on Apr 21 2023

city: Boston

first: Jesse

last: Poganik

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

description: Young heterochronic recovery

library_source: transcriptomic

data_processing:
Reads were mapped with STAR (version 2.5.2b) (Dobin et al., 2013)
Reads were  counted via featureCounts (version 1.5) (Liao et al., 2014)
Data was passed through RLD transformation (Love et al., 2014)
Genes with |transformed normalized count| < 1 were filtered out
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol:
RNA was isolated from mouse tissues using the Ambion RNAqueous Total RNA Isolation Kit (Invitrogen). ~25 mg of solid tissue was used as starting material. Concentration of RNA samples was determined using the Qubit RNA HS assay kit (Invitrogen). Total RNA isolated as described above was checked for quality using an Agilent 2100 Bioanalyzer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old or 20-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis. Short-term parabiosis pairs were maintained for 1 month prior to euthanasia and tissue collection.

tag: strain

tag: genotype

value: WT

tag: tissue

value: liver

tag: age (years)

tag: mouseid


title: TF ChIP-seq from HepG2 (ENCLB234WRH)

description:
https://www.encodeproject.org/experiments/ENCSR178SXA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR178SXA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR239QGH
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB234WRH
fragmentation methods: see document

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NCOA2

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: ATCC

value: ENCBS959GFA at ENCODE; https://www.encodeproject.org/ENCBS959GFA/

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


title: RNA from liver from YoungHetRec1

description: Young heterochronic recovery


title: RNA from liver from YoungHetRec2

description: Young heterochronic recovery


title: RNA from liver from YoungHet3

description: Young heterochronic parabiosis


title: TF ChIP-seq from K562 (ENCLB187OCJ)

description:
https://www.encodeproject.org/experiments/ENCSR744CXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR744CXJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR144DXT
encode release date: 2022-09-13
lab: Richard Myers, HAIB
library encode accession: ENCLB187OCJ
fragmentation methods: sonication (generic)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Richard Myers

value: ENCBS544DOA at ENCODE; https://www.encodeproject.org/ENCBS544DOA/


title: RNA from liver from YoungHet2

description: Young heterochronic parabiosis


title: TF ChIP-seq from WTC11 (ENCLB389STL)

description:
https://www.encodeproject.org/experiments/ENCSR245QUM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR245QUM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR428BNQ
encode release date: 2023-01-31
lab: Richard Myers, HAIB
library encode accession: ENCLB389STL
fragmentation methods: sonication (generic)

value: cell line

value: male

value: 30 year

value: ENCBS362GLP at ENCODE; https://www.encodeproject.org/ENCBS362GLP/


title: RNA from liver from YoungIsoRec3

description: Young isochronic recovery

value: WT

value: liver


title: genomic DNA from Liver from YoungIsoRec1

type: genomic

description: Young isochronic recovery

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: For mammalian microarray analysis, raw methylation data were first normalized and beta values were calculated using the SeSAMe R package.

source_name: Liver from YoungIsoRec1

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from whole blood using the DNeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old or 20-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis.

tag: mouse strain

value: C57BL/6 WT

value: Female

tag: mouse id

value: Liver


title: RNA from liver from YoungHet1

description: Young heterochronic parabiosis


title: RNA from liver from YoungIsoRec2

description: Young isochronic recovery


title: RNA from liver from YoungIsoRec1

description: Young isochronic recovery


title: genomic DNA from Heart from YoungIsoRec2

description: Young isochronic recovery

source_name: Heart from YoungIsoRec2

value: Heart


title: genomic DNA from Heart from YoungIsoRec1

description: Young isochronic recovery

source_name: Heart from YoungIsoRec1


title: genomic DNA from Heart from YoungIsoRec4

description: Young isochronic recovery

source_name: Heart from YoungIsoRec4


title: genomic DNA from Liver from YoungIsoRec2

description: Young isochronic recovery

source_name: Liver from YoungIsoRec2


title: genomic DNA from Heart from YoungIso7

description: Young isochronic parabiosis

source_name: Heart from YoungIso7


title: genomic DNA from Heart from YoungIsoRec3

description: Young isochronic recovery

source_name: Heart from YoungIsoRec3


title: RNA from liver from YoungIso1

description: Young isochronic parabiosis


title: RNA from liver from YoungIso6

description: Young isochronic parabiosis


title: genomic DNA from Liver from YoungIso6

description: Young isochronic parabiosis

source_name: Liver from YoungIso6


title: genomic DNA from Kidney from YoungIso5

description: Young isochronic parabiosis

source_name: Kidney from YoungIso5

value: Kidney


title: genomic DNA from Liver from YoungIsoRec5

description: Young isochronic recovery

source_name: Liver from YoungIsoRec5


title: genomic DNA from Fat from YoungIso5

description: Young isochronic parabiosis

source_name: Fat from YoungIso5

value: Fat


title: RNA from liver from YoungIso2

description: Young isochronic parabiosis


title: genomic DNA from Liver from YoungIso5

description: Young isochronic parabiosis

source_name: Liver from YoungIso5


title: genomic DNA from Kidney from YoungIso4

description: Young isochronic parabiosis

source_name: Kidney from YoungIso4


title: genomic DNA from Brain from YoungIso3

description: Young isochronic parabiosis

source_name: Brain from YoungIso3

value: Brain


title: genomic DNA from Brain from YoungIso5

description: Young isochronic parabiosis

source_name: Brain from YoungIso5


title: genomic DNA from Liver from YoungIsoRec3

description: Young isochronic recovery

source_name: Liver from YoungIsoRec3


title: genomic DNA from Fat from YoungIso3

description: Young isochronic parabiosis

source_name: Fat from YoungIso3


title: genomic DNA from Kidney from YoungIso3

description: Young isochronic parabiosis

source_name: Kidney from YoungIso3


title: genomic DNA from Liver from YoungIsoRec4

description: Young isochronic recovery

source_name: Liver from YoungIsoRec4


title: genomic DNA from Liver from YoungIso4

description: Young isochronic parabiosis

source_name: Liver from YoungIso4


title: genomic DNA from Fat from YoungIso4

description: Young isochronic parabiosis

source_name: Fat from YoungIso4


title: genomic DNA from Brain from YoungIso4

description: Young isochronic parabiosis

source_name: Brain from YoungIso4


title: genomic DNA from Brain from YoungIso2

description: Young isochronic parabiosis

source_name: Brain from YoungIso2


title: genomic DNA from Fat from YoungIso2

description: Young isochronic parabiosis

source_name: Fat from YoungIso2


title: genomic DNA from Liver from YoungIso3

description: Young isochronic parabiosis

source_name: Liver from YoungIso3


title: genomic DNA from Fat from YoungIso1

description: Young isochronic parabiosis

source_name: Fat from YoungIso1


title: genomic DNA from Kidney from YoungHetRec4

description: Young heterochronic recovery

source_name: Kidney from YoungHetRec4


title: genomic DNA from Brain from YoungHetRec4

description: Young heterochronic recovery

source_name: Brain from YoungHetRec4


title: genomic DNA from Liver from YoungHetRec5

description: Young heterochronic recovery

source_name: Liver from YoungHetRec5


title: genomic DNA from Fat from YoungHetRec5

description: Young heterochronic recovery

source_name: Fat from YoungHetRec5


title: genomic DNA from Brain from YoungHetRec5

description: Young heterochronic recovery

source_name: Brain from YoungHetRec5


title: genomic DNA from Kidney from YoungIso1

description: Young isochronic parabiosis

source_name: Kidney from YoungIso1


title: genomic DNA from Kidney from YoungHetRec5

description: Young heterochronic recovery

source_name: Kidney from YoungHetRec5


title: genomic DNA from Kidney from YoungIso2

description: Young isochronic parabiosis

source_name: Kidney from YoungIso2


title: genomic DNA from Fat from YoungHetRec4

description: Young heterochronic recovery

source_name: Fat from YoungHetRec4


title: genomic DNA from Brain from YoungIso1

description: Young isochronic parabiosis

source_name: Brain from YoungIso1


title: genomic DNA from Heart from YoungHetRec4

description: Young heterochronic recovery

source_name: Heart from YoungHetRec4


title: genomic DNA from Brain from YoungHetRec3

description: Young heterochronic recovery

source_name: Brain from YoungHetRec3


title: genomic DNA from Heart from YoungHetRec5

description: Young heterochronic recovery

source_name: Heart from YoungHetRec5


title: genomic DNA from Kidney from YoungHetRec3

description: Young heterochronic recovery

source_name: Kidney from YoungHetRec3


title: genomic DNA from Heart from YoungIso2

description: Young isochronic parabiosis

source_name: Heart from YoungIso2


title: genomic DNA from Heart from YoungHetRec3

description: Young heterochronic recovery

source_name: Heart from YoungHetRec3


title: genomic DNA from Liver from YoungHetRec3

description: Young heterochronic recovery

source_name: Liver from YoungHetRec3


title: genomic DNA from Liver from YoungHetRec4

description: Young heterochronic recovery

source_name: Liver from YoungHetRec4


title: genomic DNA from Brain from YoungHetRec2

description: Young heterochronic recovery

source_name: Brain from YoungHetRec2


title: genomic DNA from Kidney from YoungHetRec2

description: Young heterochronic recovery

source_name: Kidney from YoungHetRec2


title: genomic DNA from Liver from YoungIso1

description: Young isochronic parabiosis

source_name: Liver from YoungIso1


title: genomic DNA from Liver from YoungHetRec2

description: Young heterochronic recovery

source_name: Liver from YoungHetRec2


title: genomic DNA from Fat from YoungHetRec3

description: Young heterochronic recovery

source_name: Fat from YoungHetRec3


title: genomic DNA from Heart from YoungHetRec1

description: Young heterochronic recovery

source_name: Heart from YoungHetRec1


title: genomic DNA from Kidney from YoungHetRec1

description: Young heterochronic recovery

source_name: Kidney from YoungHetRec1


title: genomic DNA from Fat from YoungHetRec2

description: Young heterochronic recovery

source_name: Fat from YoungHetRec2


title: genomic DNA from Fat from YoungHetRec1

description: Young heterochronic recovery

source_name: Fat from YoungHetRec1


title: genomic DNA from Heart from YoungHetRec2

description: Young heterochronic recovery

source_name: Heart from YoungHetRec2


title: genomic DNA from Liver from YoungHetRec1

description: Young heterochronic recovery

source_name: Liver from YoungHetRec1


title: genomic DNA from Heart from YoungHet5

description: Young heterochronic parabiosis

source_name: Heart from YoungHet5


title: genomic DNA from Brain from YoungHet5

description: Young heterochronic parabiosis

source_name: Brain from YoungHet5


title: genomic DNA from Kidney from YoungHet5

description: Young heterochronic parabiosis

source_name: Kidney from YoungHet5


title: genomic DNA from Brain from YoungHetRec1

description: Young heterochronic recovery

source_name: Brain from YoungHetRec1


title: genomic DNA from Liver from YoungHet5

description: Young heterochronic parabiosis

source_name: Liver from YoungHet5


title: genomic DNA from Heart from YoungHet4

description: Young heterochronic parabiosis

source_name: Heart from YoungHet4


title: genomic DNA from Fat from YoungHet4

description: Young heterochronic parabiosis

source_name: Fat from YoungHet4


title: genomic DNA from Brain from YoungHet3

description: Young heterochronic parabiosis

source_name: Brain from YoungHet3


title: genomic DNA from Liver from YoungHet4

description: Young heterochronic parabiosis

source_name: Liver from YoungHet4


title: genomic DNA from Kidney from YoungHet4

description: Young heterochronic parabiosis

source_name: Kidney from YoungHet4


title: genomic DNA from Fat from YoungHet3

description: Young heterochronic parabiosis

source_name: Fat from YoungHet3


title: genomic DNA from Fat from YoungHet5

description: Young heterochronic parabiosis

source_name: Fat from YoungHet5


title: genomic DNA from Kidney from YoungHet3

description: Young heterochronic parabiosis

source_name: Kidney from YoungHet3


title: H9, MSL3KD RNA-seq Rep2

status: Public on Apr 13 2023

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

data_processing:
The reads were processed and mapped using Lexogen Bluebee pipeline. The mapped data obtained as bam files were further used for extracting uniquely mapped reads and subjected to merging, sorting and indexing. The sorted bam files were converted to bigwigs via deepTools (version 3.5.1) bamCoverage tool with --skipNAs  ?normalizeUsing  RPKM --smoothLength 60  --centerReads options. Noramlised signal for Control (Scr) over MSL3KD was generated using bigwigCompare tool with options --skipZeroOverZero --binSize 20 with default noramlisation (log2 ratio).
Assembly: hg38
Supplementary files format and content: bigwig containing signal for RNAseq
H9_CT_merge_old_new.bw comprises data for H9, Scr RNA-seq Rep1-Rep4
H9_MSL3_sh1_merge_old_new.bw comprises data for H9, MSL3KD RNA-seq Rep1-Rep4
H9_CT_logFC_MSL3_merge_unq.bw contains the normalised signal as log2-ratio of H9_CT_merge_old_new.bw over H9_MSL3_sh1_merge_old_new.bw

growth_protocol: H9 hPSC (Control and MSL3 KD) lines were grown on geltrex coated plates (ThermoFisher Scientific, A1413302) in mTeSR™ Plus medium (StemCell Technologies, #100-0276) supplemented with 100 U/ml penicillin-streptomycin (Gibco, 15140122) and passaged every 3-4 days with ReLeSR™ (StemCell Technologies, 100-0484) according to manufacturer’s protocols. All the cell lines were tested for Mycoplasma contamination using EZ-PCR Kit (Geneflow, K1-0210).

extract_protocol:
RNA was isolated from RNeasy Plus Mini Kit (Qiagen, Cat. No. / ID: 74134 ), we spiked in equal amounts of The External RNA Controls Consortium (ERCC) Spike-in RNA Variant Control Sets (SIRV set 3, Lexogen) and 500 ng of RNA was used for depletion of rRNA using RiboCOP kit (Lexogen).
RNAseq library preparation using CORALL Total RNA-Seq Library Prep Kit (Lexogen). Libraries were sequenced as 150 bp paired-end reads using Novaseq 6000.

tag: cell line

tag: cell type

value: Human embryonic

tag: treatment

value: MSL3 KD


title: H9, Scr RNA-seq Rep1

value: scr KD


title: H9, MSL3KD RNA-seq Rep1


title: Female, HUVEC, AngII, 3

status: Public on Mar 31 2023

city: College Park

first: Alisa

last: Morss Clyne

state: MD

address: 8278 Paint Branch Dr.

institute: University of Maryland

data_processing:
usegalaxy.org version 22.05.rc1
Quality assessment using FASTQC (all passed)
Trimmomatic on paired-end reads to remove low-quality bases and adaptor sequences
HISAT2 on paired-end reads to align them
FeatureCounts to align HISAT2 data to human (hg38) genome
EdgeR to compare gene expression in AngII vs. No Treatment for each sex
Assembly: hg38
Supplementary files format and content: tab-deliminated text files containing FeatureCounts for each sample

source_name: HUVEC

growth_protocol: Male and female HUVEC were maintained in EGM-2 (Lonza) and used from passage 4-9.

extract_protocol:
RNA was extracted using a phenol/chloroform extraction
Library constructed by Novogene USA (Sacramento, CA)

treatment_protocol: Confluent male and female HUVEC were treated with either 1 uL/mL H2O as a vehicle control or 1 uM AngII for 24 hours in EGM-2.

value: HUVEC

tag: cell sex

value: 1 uM AngII


title: genomic DNA from Liver from YoungHet3

description: Young heterochronic parabiosis

source_name: Liver from YoungHet3

tag: Sex


title: Male, HUVEC, No Treatment, 3

value: Male

value: No Treatment


title: Female, HUVEC, AngII, 1


title: Male, HUVEC, No Treatment, 2


title: Female, HUVEC, AngII, 2


title: genomic DNA from Heart from YoungHet3

description: Young heterochronic parabiosis

source_name: Heart from YoungHet3


title: genomic DNA from Kidney from YoungHet1

description: Young heterochronic parabiosis

source_name: Kidney from YoungHet1


title: genomic DNA from Brain from YoungHet4

description: Young heterochronic parabiosis

source_name: Brain from YoungHet4


title: Male, HUVEC, No Treatment, 1


title: genomic DNA from Liver from YoungHet2

description: Young heterochronic parabiosis

source_name: Liver from YoungHet2


title: genomic DNA from Heart from YoungHet2

description: Young heterochronic parabiosis

source_name: Heart from YoungHet2


title: genomic DNA from Heart from YoungHet1

description: Young heterochronic parabiosis

source_name: Heart from YoungHet1


title: genomic DNA from Kidney from YoungHet2

description: Young heterochronic parabiosis

source_name: Kidney from YoungHet2


title: genomic DNA from Brain from YoungHet2

description: Young heterochronic parabiosis

source_name: Brain from YoungHet2


title: genomic DNA from Brain from YoungHet1

description: Young heterochronic parabiosis

source_name: Brain from YoungHet1


title: genomic DNA from Fat from YoungHet1

description: Young heterochronic parabiosis

source_name: Fat from YoungHet1


title: genomic DNA from Liver from YoungHet1

description: Young heterochronic parabiosis

source_name: Liver from YoungHet1


title: H9, Scr RNA-seq Rep2


title: HF13W

city: New Haven

first: Valentina

last: Greco

state: CT

address: 333 Cedar Street NSB 388

department: Genetics

institute: Yale University

library_source: transcriptomic single cell

data_processing:
Cell Ranger software was used to generate the FASTQ files from the samples using the cellranger mkfastq command. Cell Ranger compatible reference including GFP and tdTomato transcripts information was created using the cellranger mkgtf and cellranger mkref commands. The final counts matrices were obtained by running cellranger count pipeline on the FASTQ files.
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: H5 file contains the feature-barcode matrix. FASTQ files contain the reads from library sequencing.

molecule: polyA RNA

source_name: HRASG12V/+ full wounded

growth_protocol: Mice were housed together with sex-matched littermates and fed ad libitum. All animal experiments were performed in accordance with the local legislation.

extract_protocol:
After the sacrifice of wild-type and HrasG12V/+-mosaic models at 6 days post-tamoxifen injection (3 days post-wound induction), the uninjured and injured ears of each mouse were cut in small pieces with a punch biopsy of 8 mm in diameter (the wound was kept at the center the 8 mm biopsy to mostly isolate cells involved in injury-repair). The ear epidermis was dissociated from the dermis and incubated in 0.25 % Trypsin at 37°C for 30 minutes. The epidermal preparation was placed in a 70 μm cell strainer, smashed with a piston and rinsed three times with PBS + 0.04% BSA. The flow-through was subsequently filtered through a 40 μm cell strainer, spun-down and resuspended in 300-400 μl of PBS + 0.04% BSA. The viability of the cell suspension was determined using trypan blue.
Cellular suspensions were counted and diluted to a final concentration of 1200 cells/μl in PBS/0.04% BSA and then loaded on a Chromium Controller to generate single-cell gel bead emulsions, targeting 3′. Libraries were sequenced on the Illumina Novaseq 6000 system in the following configuration: 28, 10, 10, 90 (read1, i7 index, i5 index, read2)

treatment_protocol: Mice were treated 6 days prior to sacrifice i.p. with 100ug of Tamoxifen dissolved in corn oil

value: Mouse ear punch

value: K14CreER; LSL-HrasG12V/+; LSL-tdTomato; K14H2B-GFP

value: skin

tag: background

tag: wounding

value: 4mm wound at P22

value: 2mg Tamoxifen ip at P19

value: postnatal day 25 (P25)


title: HF2W

tag: age


title: HF2U

source_name: HRASG12V/+ full uninjured

tag: source

value: uninjured


title: HFU


title: WTFW

source_name: Wild-type full wounded

value: K14CreER; LSL-tdTomato; K14H2B-GFP


title: WTF6U

source_name: Wild-type full uninjured


title: WTF8U


title: WTF8W


title: WTF6W


title: HF12W


title: WTFU


title: HM12W

data_processing:
Cell Ranger software was used to generate the FASTQ files from the samples using the cellranger mkfastq command. Cell Ranger compatible reference including GFP and tdTomato transcripts information was created using the cellranger mkgtf and cellranger mkref commands. The final counts matrices were obtained by running cellranger count pipeline on the FASTQ files.
Genome_build: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary_files_format_and_content: H5 file contains the feature-barcode matrix. FASTQ files contain the reads from library sequencing.

source_name: HRASG12V/+ mosaic wounded

extract_protocol:
After the sacrifice of wild-type and HrasG12V/+-mosaic models at 6 days post-tamoxifen injection (3 days post-wound induction), the uninjured and injured ears of each mouse were cut in small pieces with a punch biopsy of 8 mm in diameter (the wound was kept at the center the 8 mm biopsy to mostly isolate cells involved in injury-repair). The ear epidermis was dissociated from the dermis and incubated in 0.25 % Trypsin at 37°C for 30 minutes. The epidermal preparation was placed in a 70 μm cell strainer, smashed with a piston and rinsed three times with PBS + 0.04% BSA. The flow-through was subsequently filtered through a 40 μm cell strainer, spun-down and resuspended in 300-400 μl of PBS + 0.04% BSA. The viability of the cell suspension was determined using trypan blue.
Cellular suspensions were counted and diluted to a final concentration of 1200 cells/μl in PBS/0.04% BSA and then loaded on a Chromium Controller to generate single-cell gel bead emulsions, targeting 3′. Libraries were sequenced on the Illumina Novaseq 6000 system in the following configuration: 28, 10, 10, 90 (read1, i7 index, i5 index, read2)
3' single-cell RNA-seq (10x Genomics)

value: 100ug Tamoxifen ip at P19


title: HM5U

source_name: HRASG12V/+ mosaic uninjured


title: HM5W


title: HMW


title: HF12U


title: WTM13U

source_name: Wild-type mosaic uninjured


title: WTM11W

source_name: Wild-type mosaic wounded


title: HMU


title: WTM3W


title: WTM3U


title: NB4-LDB1

status: Public on Mar 29 2023

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

country: China

institute: Children’s Hospital of Soochow University

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.4)
Peaks were identified using MACS3 (v3.0)
Assembly: hg38
Supplementary files format and content: peak text files
Library strategy: CUT-TAG

extract_protocol: HyperactiveUniversalCUT&TagAssayKitfor Illumina (Vazyme #TD903)

tag: chip antibody

tag: treat

value: LDB1 overexpression


title: DAY40

city: San Diego

first: Thomas

last: Riffelmacher

state: California

address: Athena Circle drive

institute: La Jolla Institute for Immunology

description:
scRNA sequencing
MAIT.raw.counts.csv
MAIT.normalized.counts.csv
MAIT.metadata.csv

data_processing:
Libraries were mapped with Cell Ranger’s count pipeline for mm10.
Multiple libraries were aggregated with the aggr pipeline
Aggregated data were then imported into the R environment where Seurat(2.1.0) was used to filter and find clusters.
Cells with less than 200 genes and more than 2,500 genes were discarded. Cells with more than 5% UMIs coming from mitochondrial genes were filtered out. Genes expressed in less than 3 cells were ignored.
Assembly: mm10
Supplementary files format and content: Count Files

source_name: lung

extract_protocol:
Cells were sorted by flow cytometry into a low retention 1.5 mL collection tubes, containing 500 μL of a solution of PBS:FBS (1:1) supplemented with RNase inhibitor (1:100). After sorting, ice-cold PBS was added to make up to a volume of 1400 μl, spun down and single-cell libraries prepared as per the manufacturer’s instructions (10x Genomics). Samples were processed using 10X v2 chemistry as per the manufacturer’s recommendations; 11 and 12 cycles were used for cDNA amplification and library preparation, respectively.
Single-cell libraries prepared as per the manufacturer’s instructions (10x Genomics).
Samples were processed using 10X v3 chemistry, as per the manufacturer’s recommendations.

treatment_protocol: BRD509 1x10e6 retropharyngeal or BRD509 1x10e6 retropharyngeal followed by 3e6 Streptococcus pneumonia infection.

value: lung

value: MAIT

tag: strain

value: BRD509 infection


title: NB4-IgG

value: IgG

value: untreated


title: HM12U

tag: genotype

tag: tissue


title: H10SP

value: 10h Streptococcus pneumonia infection


title: DAY40H10SP

value: 40 Day BRD509 infection followed by 10h Streptococcus pneumonia infection


title: Uninfected

value: Untreated


title: Kidney allograft, borderline rejection

status: Public on Mar 28 2023

first: Jamil

middle: R

last: Azzi

address: 221 Longwood ave

department: Transplantation Research Center

institute: Brigham and Women's Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1
empty drops were removed using dropletUtils package
Doublets were removed using doubletfinder package
Cells with nFeature_RNA > 3500, nFeature_RNA > 4000, nFeature_RNA > 6000, for non-rejecting, TCMR and borderline, respectively. Cells with percent.mt < 20 were kept.
The three samples were integrated and the resolution of 0.3 was used for the clustering of cells
Assembly: Hg38
Supplementary files format and content: barcodes_raw_borderline_rejection.tsv, barcodes_raw_non_rejecting.tsv,barcodes_raw_TCMR.tsv contain the barcodes for each sample
Supplementary files format and content: matrix_raw_borderline_rejection.mtx, matrix_raw_non_rejecting.mtx, matrix_raw_TCMR.mtx contain sparse matrix for each sample
Library strategy: snRNA-seq

molecule: nuclear RNA

source_name: Kidney allograft

extract_protocol:
Frozen kidney biopsy specimens were obtained after appropriate patient consent and in accordance with Partners Healthcare IRB and institutional guidelines. After first removing the surrounding optimal cutting temperature (OCT) embedding medium with PBS, a previously published protocol using salt Tris-based buffers was used to isolate single nuclei. 8,000 single nuclei were then loaded into each channel of the Chromium single cell 3’ chip (v3; 10x Genomics, Pleasanton, USA).
Single nuclei were partitioned into gel bead-in-emulsions (GEMs) and incubated to generate barcoded cDNA by reverse transcription. Barcoded cDNA was then amplified by PCR prior to library construction. Fragmentation, sample index, and adaptor ligation, and PCR were used to generate libraries of paired-end constructs according to the manufacturer’s recommendations (10x Genomics, Pleasanton, USA). Libraries were pooled and sequenced using the Illumina HiSeq X system (San Diego, USA).
single nuclei RNA sequencing (snRNA seq)

value: Kidney allograft


title: Kidney allograft, T-cell mediated rejection

description: 10x Genomics


title: Y_pellet_rep1

status: Public on Mar 17 2023

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Library strategy: DNA-Seq
Illumina sequencing reads (~54 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with cutadapt/3.0 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned with bowtie/2-2.4.2 using the end-to-end option to the GRCm38/mm10 genome assembly
Sam output files were then filtered to retain alignments with a minimum mapping quality of 2 using samtools/1.9. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM (reads per kilobase per million mapped reads) normalized bigWig files. Input reads were subtracted from the different salt fractions and pellet with bigwigCompare.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; Scores represent the coverage on the genome location

source_name: mouse liver

extract_protocol:
Nuclei was released from frozen tissue by douncing in TM2 buffer (10 mM Tris HCl, pH 7.4, 2 mM MgCl2 supplemented with 1X Halt protease and phosphatase inhibitor and 0.5 mM PMSF), pelleted by centrifugation and washed once to remove debris. The washed pellet was resuspended in TM2 buffer with 1 mM CaCl2 and 12000U of MNase (New England Biolabs), incubated at 23°C for 15 minutes and the reactions stopped by addition of 0.5 mM EGTA. Approximately 30% was saved for analysis (“0”) and the rest was pelleted by centrifugation. The supernatant was removed and saved as “Supernatant” fraction after clearing. The nuclei were washed once with TM2 buffer and then resuspended in 70 µl Triton buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 2 mM EGTA, 0.1% Triton X-100 supplemented with 1X Halt protease and phosphatase inhibitor and 0.5 mM PMSF) and evenly divided. The first aliquot was saved as “Input” while the second was used for sequential salt extraction by using Triton buffer with either 67.5, 150, 250 or 350 mM NaCl. Each extraction was done by incubating the resuspended pellet at 4°C for 2 hours. After each extraction, the nuclei were pelleted by centrifugation and the supernatant saved as “67.5”, “150”, “250” or “350” mM fraction. Finally, the remainder pellet which corresponds to ~5–10% of chromatin, was resuspended in 35 µl of TNE buffer (10 mM Tris–HCl pH 7.4, 200 mM NaCl, 1 mM EDTA supplemented with 1X Halt protease and phosphatase inhibitor) and labeled as “Pellet” fraction. DNA was purified from each of these fractions using DNA clean and concentrator columns (Zymo Research).
Purified DNA (~10 ng) was used to make libraries using the NEBNext Ultra II kit (New England Biolabs).

treatment_protocol: Old as treated group

value: liver

tag: salt concentration

value: pellet

tag: group

value: young


title: Y_250_rep1


title: Y_350_rep1


title: Y_0_rep1


title: WTM13W

value: Mouse ear punch

value: skin

value: 4mm wound at P22

value: postnatal day 25 (P25)


title: Y_Input_rep1

value: Input


title: Y_150_rep1


title: O_0_rep2

value: old


title: O_pellet_rep2


title: Y_67_rep1


title: O_Input_rep2


title: O_150_rep2


title: WTM11U

value: K14CreER; LSL-tdTomato; K14H2B-GFP

value: uninjured

value: 100ug Tamoxifen ip at P19


title: O_350_rep2