title: TF ChIP-seq from K562 (ENCLB575LDV)

description:
https://www.encodeproject.org/experiments/ENCSR158RYZ/
***************
biological replicate number: 4
technical replicate number: 1
description: eGFP-ZBTB40 ChIP-seq on human K562
experiment encode accession: ENCSR158RYZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR861LKS
encode release date: 2017-12-01
lab: Kevin White, UChicago
library encode accession: ENCLB575LDV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

tag: line

value: cell line

tag: description

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: age

tag: lab

tag: passage number

tag: health state

tag: link

value: ENCBS127TDC at ENCODE; https://www.encodeproject.org/ENCBS127TDC/

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


title: TF ChIP-seq from HepG2 (ENCLB188CJK)

status: Public on Aug 30 2019

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/ENCSR145CXH/
***************
biological replicate number: 2
technical replicate number: 1
description: TARDBP ChIP-seq in HepG2
experiment encode accession: ENCSR145CXH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR352VNP
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB188CJK
size range: 200-400

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 cell line

value: TARDBP

value: TARDBP ChIP-seq in HepG2

value: male

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: ENCBS817KQF at ENCODE; https://www.encodeproject.org/ENCBS817KQF/

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


title: Muscle_NM-003

type: RNA

city: Boston

first: Steven

middle: A

last: Greenberg

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133A Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using GCRMA normalization.

label: biotin

molecule: total RNA

source_name: Necrotizing myopathy_muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen).

tag: disease state

value: Necrotizing myopathy

tag: tissue

value: Muscle


title: Muscle_NL-217

value: Normal


title: TF ChIP-seq from HepG2 (ENCLB421XZZ)

description:
https://www.encodeproject.org/experiments/ENCSR145CXH/
***************
biological replicate number: 1
technical replicate number: 1
description: TARDBP ChIP-seq in HepG2
experiment encode accession: ENCSR145CXH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR352VNP
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB421XZZ
size range: 200-400

value: ENCBS690KCY at ENCODE; https://www.encodeproject.org/ENCBS690KCY/


title: Muscle_NL-218


title: Muscle_NL-133


title: Muscle_NL-128


title: Muscle_NL-186


title: TF ChIP-seq from K562 (ENCLB233ESV)

description:
https://www.encodeproject.org/experiments/ENCSR072VUO/
***************
biological replicate number: 1
technical replicate number: 1
description: SAFB ChIP-seq in K562
experiment encode accession: ENCSR072VUO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR483GYO
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB233ESV
size range: 200-400

source_name: Homo sapiens K562 cell line

value: SAFB

value: SAFB ChIP-seq in K562

value: female

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS271QIL at ENCODE; https://www.encodeproject.org/ENCBS271QIL/


title: Muscle_NL-063


title: Muscle_IBM-223

source_name: Inclusion body myositis_muscle

value: Inclusion body myositis


title: Muscle_NL-045


title: Muscle_IBM-170


title: Muscle_IBM-203


title: Muscle_IBM-251


title: Muscle_NL-176


title: Muscle_IBM-185


title: Muscle_IBM-232


title: Muscle_IBM-173


title: Muscle_IBM-175


title: Muscle_IBM-183


title: Muscle_NL-110


title: Muscle_IBM-237


title: Muscle_IBM-180


title: Muscle_IBM-169


title: Muscle_NL-057


title: Muscle_IBM-167


title: Muscle_NL-050


title: TF ChIP-seq from HepG2 (ENCLB955XZE)

description:
https://www.encodeproject.org/experiments/ENCSR066FXN/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPH1 ChIP-seq in HepG2
experiment encode accession: ENCSR066FXN
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB955XZE
size range: 200-400

value: cell line

value: HNRNPH1 ChIP-seq in HepG2

value: male

value: child

value: 15 year

value: ENCBS781RAA at ENCODE; https://www.encodeproject.org/ENCBS781RAA/


title: Muscle_NL-193

value: Muscle


title: Muscle_IBM-091


title: Muscle_IBM-083


title: TF ChIP-seq from HepG2 (ENCLB254QVF)

description:
https://www.encodeproject.org/experiments/ENCSR031URL/
***************
biological replicate number: 1
technical replicate number: 1
description: XRCC5 ChIP-seq in HepG2
experiment encode accession: ENCSR031URL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB254QVF
size range: 200-400

value: XRCC5 ChIP-seq in HepG2

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: ENCBS423OQV at ENCODE; https://www.encodeproject.org/ENCBS423OQV/

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


title: TF ChIP-seq from HepG2 (ENCLB372FSQ)

description:
https://www.encodeproject.org/experiments/ENCSR066FXN/
***************
biological replicate number: 2
technical replicate number: 1
description: HNRNPH1 ChIP-seq in HepG2
experiment encode accession: ENCSR066FXN
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB372FSQ
size range: 200-400

value: ENCBS516TKV at ENCODE; https://www.encodeproject.org/ENCBS516TKV/


title: Muscle_IBM-112


title: TF ChIP-seq from K562 (ENCLB483SSS)

description:
https://www.encodeproject.org/experiments/ENCSR018MSO/
***************
biological replicate number: 4
technical replicate number: 1
description: eGFP-ZNF148 ChIP-seq on human K562
experiment encode accession: ENCSR018MSO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR745QMZ
encode release date: 2017-12-01
lab: Kevin White, UChicago
library encode accession: ENCLB483SSS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line stably expressing C-terminal eGFP-tagged eGFP-ZNF148

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF148

value: female

value: adult

value: 53 year

value: Kevin White, UChicago

value: ENCBS397IBL at ENCODE; https://www.encodeproject.org/ENCBS397IBL/

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


title: TF ChIP-seq from HepG2 (ENCLB152QYH)

description:
https://www.encodeproject.org/experiments/ENCSR031URL/
***************
biological replicate number: 2
technical replicate number: 1
description: XRCC5 ChIP-seq in HepG2
experiment encode accession: ENCSR031URL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB152QYH
size range: 200-400

value: cell line

value: male

value: child

value: ENCBS628ONB at ENCODE; https://www.encodeproject.org/ENCBS628ONB/


title: TF ChIP-seq from K562 (ENCLB944MMR)

description:
https://www.encodeproject.org/experiments/ENCSR072VUO/
***************
biological replicate number: 2
technical replicate number: 1
description: SAFB ChIP-seq in K562
experiment encode accession: ENCSR072VUO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR483GYO
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB944MMR
size range: 200-400

value: SAFB

value: SAFB ChIP-seq in K562

value: chronic myelogenous leukemia (CML)

value: ENCBS287XKX at ENCODE; https://www.encodeproject.org/ENCBS287XKX/


title: Muscle_IBM-079

value: Inclusion body myositis

value: Muscle


title: Muscle_IBM-001


title: Muscle_IBM-061


title: Muscle_IBM-067


title: Muscle_IBM-027


title: Muscle_DM-258

value: Dermatomyositis


title: Muscle_DM-019


title: Muscle_DM-177


title: Muscle_IBM-038


title: Muscle_DM-058


title: Muscle_IBM-036


title: Muscle_DM-195


title: Muscle_DM-179


title: Muscle_IBM-062


title: Muscle_DM-168


title: Muscle_IBM-007


title: Control ChIP-seq from GM08714 (ENCLB799NCB)

description:
https://www.encodeproject.org/experiments/ENCSR000EUH/
***************
biological replicate number: 1
technical replicate number: 1,2
description: Control ChIP-seq on human GM08714
experiment encode accession: ENCSR000EUH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2012-05-14
lab: Peggy Farnham, USC
library encode accession: ENCLB799NCB
fragmentation methods: see document

source_name: Homo sapiens GM08714 cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e85e27a-1b03-493d-b73f-db4ce2246318/@@download/attachment/wgEncodeSydhHistone.release3.html.pdf, general protocol: https://www.encodeproject.org/documents/0612f0bf-3665-47f8-af5d-09aab3d4ca24/@@download/attachment/wgEncodeSydhTfbs.release3.html.pdf

value: Control

value: B-lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency;dysmorphic facial features, developmental delay, malabsorption, and recurrent infections;see GM08747 Fibroblast;donor subject is a compound heterozygote:one allele has a G>A transition at nucleotide 1807 (1807G>A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B;the second allele has a G>A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G>A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo.

value: female

value: unknown

value: 1 year

value: Peggy Farnham, USC

value: chromosomal abnormalities; ICF syndrome

value: ENCBS182AAA at ENCODE; https://www.encodeproject.org/ENCBS182AAA/

value: Derived from ENCODE donor ENCDO000ABH; https://www.encodeproject.org/ENCDO000ABH/


title: Muscle_DM-004


title: Histone ChIP-seq from GM08714 (ENCLB555ABZ)

description:
https://www.encodeproject.org/experiments/ENCSR000FCL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 GM08714 (ICF) ChIP-Seq
experiment encode accession: ENCSR000FCL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EUH
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-500

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5aaf2e58-de7c-451b-b6d7-747b82278bc3/@@download/attachment/Farnham_TF_ChIP_Library_Protocol_130201.docx.pdf

value: cell line

value: ENCBS478AAA at ENCODE; https://www.encodeproject.org/ENCBS478AAA/


title: Muscle_IBM-020


title: Muscle_DM-009


title: TF ChIP-seq from E14TG2a.4 (ENCLB295HTL)

description:
https://www.encodeproject.org/experiments/ENCSR779CZG/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 NANOG ChIP-seq
experiment encode accession: ENCSR779CZG
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-03-14
lab: Ross Hardison, PennState
library encode accession: ENCLB295HTL
fragmentation methods: see document

organism: Mus musculus

source_name: Mus musculus strain 129/Ola E14TG2a.4 cell line

value: NANOG

value: mouse embryonic stem cell line E14

value: male

value: embryonic

value: 3.5 day

value: Ross Hardison, PennState

value: ENCBS171HGC at ENCODE; https://www.encodeproject.org/ENCBS171HGC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/


title: Histone ChIP-seq from E14TG2a.4 (ENCLB253ATP)

description:
https://www.encodeproject.org/experiments/ENCSR857MYS/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K9me3 ChIP-seq
experiment encode accession: ENCSR857MYS
assay title: Histone ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-10
lab: Ross Hardison, PennState
library encode accession: ENCLB253ATP
fragmentation methods: see document

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d5680f64-80da-4bf1-b79d-dbcf0774a23b/@@download/attachment/HardisonLabChIPseqf.pdf, general protocol: https://www.encodeproject.org/documents/bd84d10f-f22d-4c69-bc0f-6deff87d84c6/@@download/attachment/Cross-linking%20cells%20for%20ChIP-seq.pdf, general protocol: https://www.encodeproject.org/documents/3bafcc94-f4e0-4285-ac91-59963f8a4633/@@download/attachment/SonicationBiorupter.pdf

value: ENCBS705LKU at ENCODE; https://www.encodeproject.org/ENCBS705LKU/


title: Muscle_DM-087

value: Dermatomyositis

value: Muscle


title: Histone ChIP-seq from GM08714 (ENCLB555ABY)

description:
https://www.encodeproject.org/experiments/ENCSR000FCL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 GM08714 (ICF) ChIP-Seq
experiment encode accession: ENCSR000FCL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EUH
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-500

value: B-lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency;dysmorphic facial features, developmental delay, malabsorption, and recurrent infections;see GM08747 Fibroblast;donor subject is a compound heterozygote:one allele has a G>A transition at nucleotide 1807 (1807G>A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B;the second allele has a G>A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G>A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo.

value: female

value: unknown

value: 1 year

value: Peggy Farnham, USC

value: ENCBS477AAA at ENCODE; https://www.encodeproject.org/ENCBS477AAA/


title: TF ChIP-seq from H1 (ENCLB695AAK)

description:
https://www.encodeproject.org/experiments/ENCSR160ZLP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human H1-hESC KDM5A
experiment encode accession: ENCSR160ZLP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2012-03-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AAK
fragmentation methods: see document

source_name: Homo sapiens H1-hESC stem cell male embryo

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f10bdd36-e370-4777-a7f3-83091c115749/@@download/attachment/wgEncodeBroadHistone.html.pdf

value: cell line

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS380OBH at ENCODE; https://www.encodeproject.org/ENCBS380OBH/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: Muscle_DM-030


title: TF ChIP-seq from E14TG2a.4 (ENCLB713DUD)

description:
https://www.encodeproject.org/experiments/ENCSR779CZG/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 NANOG ChIP-seq
experiment encode accession: ENCSR779CZG
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-03-14
lab: Ross Hardison, PennState
library encode accession: ENCLB713DUD
fragmentation methods: see document

value: NANOG

value: mouse embryonic stem cell line E14

value: male

value: embryonic

value: 3.5 day

value: Ross Hardison, PennState


title: Muscle_DM-039

value: Dermatomyositis

value: Muscle


title: TF ChIP-seq from E14TG2a.4 (ENCLB511TWA)

description:
https://www.encodeproject.org/experiments/ENCSR392DGA/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 POU5F1 (OCT4) ChIP-seq
experiment encode accession: ENCSR392DGA
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-03-17
lab: Ross Hardison, PennState
library encode accession: ENCLB511TWA
fragmentation methods: see document

value: unknown

value: ENCBS705LKU at ENCODE; https://www.encodeproject.org/ENCBS705LKU/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/


title: Control ChIP-seq from E14TG2a.4 (ENCLB997DYA)

description:
https://www.encodeproject.org/experiments/ENCSR326ULS/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 Control ChIP-seq
experiment encode accession: ENCSR326ULS
assay title: Control ChIP-seq
assembly: mm9, mm10
encode release date: 2014-02-07
lab: Ross Hardison, PennState
library encode accession: ENCLB997DYA
fragmentation methods: see document

value: Control

value: cell line

value: ENCBS171HGC at ENCODE; https://www.encodeproject.org/ENCBS171HGC/


title: TF ChIP-seq from E14TG2a.4 (ENCLB811KZV)

description:
https://www.encodeproject.org/experiments/ENCSR362VNF/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 CTCF ChIP-seq
experiment encode accession: ENCSR362VNF
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-24
lab: Ross Hardison, PennState
library encode accession: ENCLB811KZV
fragmentation methods: see document

value: CTCF


title: Control ChIP-seq from E14TG2a.4 (ENCLB959PPH)

description:
https://www.encodeproject.org/experiments/ENCSR326ULS/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 Control ChIP-seq
experiment encode accession: ENCSR326ULS
assay title: Control ChIP-seq
assembly: mm9, mm10
encode release date: 2014-02-07
lab: Ross Hardison, PennState
library encode accession: ENCLB959PPH
fragmentation methods: see document


title: TF ChIP-seq from E14TG2a.4 (ENCLB085DZS)

description:
https://www.encodeproject.org/experiments/ENCSR392DGA/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 POU5F1 (OCT4) ChIP-seq
experiment encode accession: ENCSR392DGA
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-03-17
lab: Ross Hardison, PennState
library encode accession: ENCLB085DZS
fragmentation methods: see document


title: TF ChIP-seq from E14TG2a.4 (ENCLB706HXX)

description:
https://www.encodeproject.org/experiments/ENCSR362VNF/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 CTCF ChIP-seq
experiment encode accession: ENCSR362VNF
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-24
lab: Ross Hardison, PennState
library encode accession: ENCLB706HXX
fragmentation methods: see document


title: Histone ChIP-seq from E14TG2a.4 (ENCLB138LTT)

description:
https://www.encodeproject.org/experiments/ENCSR857MYS/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K9me3 ChIP-seq
experiment encode accession: ENCSR857MYS
assay title: Histone ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-10
lab: Ross Hardison, PennState
library encode accession: ENCLB138LTT
fragmentation methods: see document


title: Histone ChIP-seq from E14TG2a.4 (ENCLB819EEW)

description:
https://www.encodeproject.org/experiments/ENCSR212KGS/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K4me3 ChIP-seq
experiment encode accession: ENCSR212KGS
assay title: Histone ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-14
lab: Ross Hardison, PennState
library encode accession: ENCLB819EEW
fragmentation methods: see document


title: TF ChIP-seq from CH12.LX (ENCLB301LJK)

description:
https://www.encodeproject.org/experiments/ENCSR973SOG/
***************
biological replicate number: 1
technical replicate number: 1
description: USF1 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR973SOG
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB301LJK

source_name: Mus musculus strain B10.H-2aH-4bp/Wts CH12.LX immortalized cell line

value: B-cell lymphoma

value: female

value: Michael Snyder, Stanford

value: ENCBS912CAS at ENCODE; https://www.encodeproject.org/ENCBS912CAS/

value: Derived from ENCODE donor ENCDO324YEK; https://www.encodeproject.org/ENCDO324YEK/

value: ENCODE dbxrefs Cellosaurus CVCL_0211; http://web.expasy.org/cellosaurus/CVCL_0211

value: ENCODE dbxrefs CH12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CH12


title: TF ChIP-seq from CH12.LX (ENCLB824HBZ)

description:
https://www.encodeproject.org/experiments/ENCSR973SOG/
***************
biological replicate number: 2
technical replicate number: 1
description: USF1 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR973SOG
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB824HBZ

value: ENCBS076QIH at ENCODE; https://www.encodeproject.org/ENCBS076QIH/


title: TF ChIP-seq from CH12.LX (ENCLB265QCY)

description:
https://www.encodeproject.org/experiments/ENCSR906QEK/
***************
biological replicate number: 1
technical replicate number: 1
description: TCF12 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR906QEK
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB265QCY


title: Histone ChIP-seq from E14TG2a.4 (ENCLB063HEK)

description:
https://www.encodeproject.org/experiments/ENCSR032JUI/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K4me1 ChIP-seq
experiment encode accession: ENCSR032JUI
assay title: Histone ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-10
lab: Ross Hardison, PennState
library encode accession: ENCLB063HEK
fragmentation methods: see document

value: mouse embryonic stem cell line E14

value: male

value: embryonic

value: 3.5 day

value: Ross Hardison, PennState


title: Histone ChIP-seq from E14TG2a.4 (ENCLB326DUQ)

description:
https://www.encodeproject.org/experiments/ENCSR032JUI/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K4me1 ChIP-seq
experiment encode accession: ENCSR032JUI
assay title: Histone ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-10
lab: Ross Hardison, PennState
library encode accession: ENCLB326DUQ
fragmentation methods: see document

value: unknown

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/


title: TF ChIP-seq from CH12.LX (ENCLB822KMQ)

description:
https://www.encodeproject.org/experiments/ENCSR743ZJL/
***************
biological replicate number: 2
technical replicate number: 1
description: IRF4 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR743ZJL
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB822KMQ

value: cell line


title: TF ChIP-seq from ES-E14 (ENCLB548CGH)

description:
https://www.encodeproject.org/experiments/ENCSR531HWD/
***************
biological replicate number: 2
technical replicate number: 1
description: CHD2 ChIP-seq mouse ES-E14 produced by the Snyder lab
experiment encode accession: ENCSR531HWD
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADJ
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB548CGH

source_name: Mus musculus strain 129/Ola ES-E14 stem cell male embryo

value: ENCBS043ENC at ENCODE; https://www.encodeproject.org/ENCBS043ENC/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


title: TF ChIP-seq from MEL cell line (ENCLB769NQF)

description:
https://www.encodeproject.org/experiments/ENCSR705HGT/
***************
biological replicate number: 1
technical replicate number: 1
description: USF1 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR705HGT
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB769NQF

source_name: Mus musculus strain MEL MEL immortalized cell line

value: MEL cell line

value: Leukemia (K562 analog)

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: TF ChIP-seq from CH12.LX (ENCLB878PLC)

description:
https://www.encodeproject.org/experiments/ENCSR806JZK/
***************
biological replicate number: 1
technical replicate number: 1
description: MEF2A ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR806JZK
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB878PLC

value: B-cell lymphoma

value: female

value: Michael Snyder, Stanford

value: ENCBS912CAS at ENCODE; https://www.encodeproject.org/ENCBS912CAS/

value: Derived from ENCODE donor ENCDO324YEK; https://www.encodeproject.org/ENCDO324YEK/

value: ENCODE dbxrefs Cellosaurus CVCL_0211; http://web.expasy.org/cellosaurus/CVCL_0211

value: ENCODE dbxrefs CH12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CH12


title: TF ChIP-seq from ES-E14 (ENCLB327FWQ)

description:
https://www.encodeproject.org/experiments/ENCSR531HWD/
***************
biological replicate number: 1
technical replicate number: 1
description: CHD2 ChIP-seq mouse ES-E14 produced by the Snyder lab
experiment encode accession: ENCSR531HWD
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADJ
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB327FWQ

value: cell line

value: mouse embryonic stem cell line E14

value: embryonic

value: male

value: unknown

value: ENCBS043ENC at ENCODE; https://www.encodeproject.org/ENCBS043ENC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320


title: TF ChIP-seq from CH12.LX (ENCLB898HTY)

description:
https://www.encodeproject.org/experiments/ENCSR806JZK/
***************
biological replicate number: 2
technical replicate number: 1
description: MEF2A ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR806JZK
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB898HTY

value: ENCBS076QIH at ENCODE; https://www.encodeproject.org/ENCBS076QIH/


title: TF ChIP-seq from CH12.LX (ENCLB271RXW)

description:
https://www.encodeproject.org/experiments/ENCSR743ZJL/
***************
biological replicate number: 1
technical replicate number: 1
description: IRF4 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR743ZJL
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB271RXW


title: TF ChIP-seq from CH12.LX (ENCLB993DJT)

description:
https://www.encodeproject.org/experiments/ENCSR293WTN/
***************
biological replicate number: 2
technical replicate number: 1
description: ELF1 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR293WTN
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB993DJT


title: TF ChIP-seq from MEL cell line (ENCLB207JPP)

description:
https://www.encodeproject.org/experiments/ENCSR349JDH/
***************
biological replicate number: 1
technical replicate number: 1
description: TCF12 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR349JDH
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB207JPP

value: MEL cell line

value: Leukemia (K562 analog)

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: TF ChIP-seq from MEL cell line (ENCLB407HQE)

description:
https://www.encodeproject.org/experiments/ENCSR349JDH/
***************
biological replicate number: 2
technical replicate number: 1
description: TCF12 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR349JDH
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB407HQE

value: cell line


title: single-cell RNAseq

city: Münster

first: Sandra

last: Laurentino

address: Domagkstr. 11

country: Germany

institute: University of Münster

library_source: transcriptomic

data_processing:
Fastq files were generated using cellranger mkfastq
Reads were maped to the human genome (GRCh38) (Cell Ranger v2.1.1)
Primary quality control was performed using Cell Ranger v2.1.1 using default parameters
Filtered barcode matrices were generated using Cell Ranger v2.1.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Feature barcode matrices containing detected cellular barcodes,

source_name: Testicular cells

extract_protocol:
A biopsy was digested using a previously published method (Neuhaus et al., Mol Hum Reprod, 2017) and passed through a 70 μm strainer to obtain a single cell suspension.
The single cell suspension was used to prepare single cell RNA libraries according to the manufacturer's recomendations (10x Genomics Chromium Single Cell Reagent Kit v2). The libraries were paired-end sequenced on a NovaSeq 6000 sequencer (Illumina)

value: testis

tag: syndrome

value: Klinefelter


title: TF ChIP-seq from CH12.LX (ENCLB252TNY)

description:
https://www.encodeproject.org/experiments/ENCSR293WTN/
***************
biological replicate number: 1
technical replicate number: 1
description: ELF1 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR293WTN
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB252TNY

value: B-cell lymphoma

value: female

value: Michael Snyder, Stanford

value: ENCBS912CAS at ENCODE; https://www.encodeproject.org/ENCBS912CAS/

value: Derived from ENCODE donor ENCDO324YEK; https://www.encodeproject.org/ENCDO324YEK/

value: ENCODE dbxrefs Cellosaurus CVCL_0211; http://web.expasy.org/cellosaurus/CVCL_0211

value: ENCODE dbxrefs CH12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CH12


title: TF ChIP-seq from MEL cell line (ENCLB947IFO)

description:
https://www.encodeproject.org/experiments/ENCSR033OWC/
***************
biological replicate number: 1
technical replicate number: 1
description: ELF1 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR033OWC
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB947IFO

value: MEL cell line

value: Leukemia (K562 analog)

value: unknown


title: TF ChIP-seq from MEL cell line (ENCLB832RIH)

description:
https://www.encodeproject.org/experiments/ENCSR033OWC/
***************
biological replicate number: 2
technical replicate number: 1
description: ELF1 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR033OWC
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB832RIH

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/


title: TF ChIP-seq from CH12.LX (ENCLB865WBB)

description:
https://www.encodeproject.org/experiments/ENCSR980YXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: NRF1 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR980YXJ
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB865WBB

value: ENCBS076QIH at ENCODE; https://www.encodeproject.org/ENCBS076QIH/


title: TF ChIP-seq from CH12.LX (ENCLB700JJL)

description:
https://www.encodeproject.org/experiments/ENCSR906QEK/
***************
biological replicate number: 2
technical replicate number: 1
description: TCF12 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR906QEK
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB700JJL

value: cell line


title: Tera-2_RNA

status: Public on Aug 29 2019

city: Prague

first: Jan

last: Stuchly

address: V Uvalu 84

department: Department of Paediatric Hematology/Oncology

country: Czech Republic

institute: Charles University in Prague, 2nd Faculty of Medicne

description:
cell line
deseq_counts_gene_annot.tsv
sample name:
Ntera2012

data_processing:
Variant calling:
alignment bwa mem (0.7.10-r789)
picard-tools FixMateInformation (picard tools version 1.113)
picard-tools SortSam
picard-tools MarkDuplicates
samtools mpileup (version 0.1.19-96b5f2294a)
VarScan.v2.4.0 mpileup2cns, readcounts
SnpSift, snpEff
R pipeline to merge and annotate vcf file to create csv report
Copy-Number Variation:
CNVkit etal/cnvkit docker image was used - version 0.9.1
Gene Expression Analysis:
alignment bowtie2 version 2.2.5
DESeq2 (1.14.1)
Genome_build: Hg19
Supplementary_files_format_and_content: *coding.csv:  annotated variants calls
Supplementary_files_format_and_content: *call.cns: Copy-number variations call
Supplementary_files_format_and_content: deseq_counts_gene_annot.tsv: deseq annotated gene counts

source_name: germ cell tumor cell line

extract_protocol:
DNeasy Mini Kit (Qiagen),  and RecoverAll Total Nucleic Acid Isolation Kit (ThermoFisher Scientific), Rneasy Mini Kit (Qiagen)
SureSelectXT Human All Exon V5+UTR kit (Agilent Technologies) and SureSelectXT RNA Reagent Kit (Agilent Technologies)

tag: cell line

tag: cell type

value: nonseminoma

tag: condition

value: original (cisplatin sensitive)


title: TF ChIP-seq from CH12.LX (ENCLB808UXO)

description:
https://www.encodeproject.org/experiments/ENCSR980YXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: NRF1 ChIP-seq mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR980YXJ
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ERS
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB808UXO

tag: antibody

value: B-cell lymphoma


title: NCCIT_CDDP_RNA

description:
cell line
deseq_counts_gene_annot.tsv
sample name:
NCCIT100

value: NCCIT

value: CDDP-resistant


title: Tera-2_CDDP_RNA

description:
cell line
deseq_counts_gene_annot.tsv
sample name:
Nteracis

value: CDDP-exposed


title: NCCIT_long-term cultured_RNA

description:
cell line
deseq_counts_gene_annot.tsv
sample name:
NCCITnew

value: long-term cultured


title: NCCIT_RNA

description:
cell line
deseq_counts_gene_annot.tsv
sample name:
NCCIT2012


title: Tera-2_CDDP_genomicDNA

description:
cell line
Tera2_output_report__coding.csv
Tera-2_CDDP.call.cns
sample name:
NTERAcis-DNA

data_processing:
Library strategy: DNA-seq
Variant calling:
alignment bwa mem (0.7.10-r789)
picard-tools FixMateInformation (picard tools version 1.113)
picard-tools SortSam
picard-tools MarkDuplicates
samtools mpileup (version 0.1.19-96b5f2294a)
VarScan.v2.4.0 mpileup2cns, readcounts
SnpSift, snpEff
R pipeline to merge and annotate vcf file to create csv report
Copy-Number Variation:
CNVkit etal/cnvkit docker image was used - version 0.9.1
Gene Expression Analysis:
alignment bowtie2 version 2.2.5
DESeq2 (1.14.1)
Genome_build: Hg19
Supplementary_files_format_and_content: *coding.csv:  annotated variants calls
Supplementary_files_format_and_content: *call.cns: Copy-number variations call
Supplementary_files_format_and_content: deseq_counts_gene_annot.tsv: deseq annotated gene counts


title: Histone ChIP-seq from E14TG2a.4 (ENCLB009NHA)

description:
https://www.encodeproject.org/experiments/ENCSR212KGS/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K4me3 ChIP-seq
experiment encode accession: ENCSR212KGS
assay title: Histone ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-14
lab: Ross Hardison, PennState
library encode accession: ENCLB009NHA
fragmentation methods: see document

tag: line

value: mouse embryonic stem cell line E14

value: male

value: embryonic

value: 3.5 day

value: Ross Hardison, PennState

value: ENCBS705LKU at ENCODE; https://www.encodeproject.org/ENCBS705LKU/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/


title: Tera-2_genomicDNA

description:
cell line
Tera2_output_report__coding.csv
Tera-2.call.cns
sample name:
NTERA2012-DNA


title: NCCIT_CDDP_genomicDNA

description:
cell line
NCCIT_output_report__coding.csv
NCCIT_CDDP.call.cns
sample name:
NCCIT-100


title: NCCIT_genomicDNA

description:
cell line
NCCIT_output_report__coding.csv
NCCIT.call.cns
sample name:
NCCIT-2012


title: 449065.1.X_5

status: Public on Aug 15 2019

city: Charlottesville

first: Stephen

middle: Aurelien

last: Hoang

state: Virginia

address: 501 Locust Ave, Suite 301

institute: HemoShear Therapeutics

data_processing:
Transcript-level abundance was quantified using Salmon v0.9.1 (Patro et al. Nature Methods, 2017) against the transcriptome for genome build GRCh37, Ensembl release 75.
Gene-level abundances (counts and transcripts per million) were estimated using Tximport v0.99.8 (Soneson et al. 2015, F1000Research) using the "lengthScaledTPM" argument, and Ensembl transcript-to-Entrez gene ID cross references.
Genome_build: GRCh37
Supplementary_files_format_and_content: csv files contain gene-level counts and transcript per million quantifications generated using tximport.

source_name: liver biopsy

extract_protocol:
RNA was extracted from cells using a Qiagen RNeasy RNA isolation kit
cDNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation kit

value: liver biopsy

value: F

tag: age at biopsy

tag: lobular inflammation grade

tag: cytological ballooning grade

tag: steatosis grade

tag: nafld activity score

tag: fibrosis stage


title: 449060.1.X_8

tag: Sex


title: 449063.1.X_8


title: 449058.1.X_7


title: 440538.1.X_6

value: M


title: NCCIT_long-term cultured_genomicDNA

description:
cell line
NCCIT_output_report__coding.csv
sample name:
NCCIT-new

value: nonseminoma


title: 440534.1.X_5


title: 440548.1.X_7


title: 440526.1.X_4


title: 440528.1.X_5


title: 440525.1.X_4


title: 440527.1.X_4


title: Hepatic Cirrhosis30-seq

status: Public on Aug 27 2019

city: Hangzhou

first: Wenbiao

last: Chen

address: Zhejiang University, Hangzhou

country: China

institute: Zhejiang University

description: No medication

hyb_protocol: Agilent surehyb is used for hybridization experiments

scan_protocol: Agilent DNA microarray scanner was used for scanning, agilent feature extraction software (v11.0.1.1) was used to collect chip probe signal value, and agilent genespring software was used for chip standardization.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Peripheral lymphocyte

label_protocol: Arraystar RNA flash labeling kit is used for labeling samples

extract_protocol:
peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Hypaque-Ficoll
Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol

value: Peripheral venous blood

tag: disease

value: Hepatic Cirrhosis


title: chronic hepatitis B2-seq

description: No medication

value: chronic hepatitis B


title: HBsAg carriers27-seq

description: No medication

value: HBsAg carriers


title: 440490.1.X_5


title: chronic hepatitis B17-seq

description: No medication


title: HBsAg carriers20-seq

description: No medication


title: Hepatic Cirrhosis32-seq

description: No medication


title: chronic hepatitis B22-seq

description: No medication


title: 440488.1.X_4


title: Hepatic Cirrhosis15-seq

description: No medication


title: 440485.1.X_4


title: 449064.1.X_8


title: 440492.1.X_5


title: 440484.1.X_4


title: HBsAg carriers18-seq

description: No medication


title: 440483.1.X_3


title: 440481.1.X_3


title: 440479.1.X_3


title: 440477.1.X_2


title: 440482.1.X_3


title: 440478.1.X_2


title: 440476.1.X_2


title: 440474.1.X_2


title: 440475.1.X_2


title: 440440.1.X_4


title: 440451.1.X_7


title: 440437.1.X_1


title: 440441.1.X_5


title: 440436.1.X_4


title: 440432.1.X_1


title: 440438.1.X_4


title: 440435.1.X_3


title: 440430.1.X_2


title: 440480.1.X_3


title: 440424.1.X_1


title: 440426.1.X_2


title: 440423.1.X_1


title: 440421.1.X_1


title: TF ChIP-seq from MEL cell line (ENCLB585OQP)

description:
https://www.encodeproject.org/experiments/ENCSR705HGT/
***************
biological replicate number: 2
technical replicate number: 1
description: USF1 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR705HGT
assay title: TF ChIP-seq
assembly: mm9, mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB585OQP

value: MEL cell line

value: cell line

tag: description

value: Leukemia (K562 analog)

tag: biosample encode accession

tag: dev stage

value: unknown

value: not collected

tag: age

tag: health state

tag: lab

value: Bing Ren, UCSD

tag: link

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: 440419.1.X_8

tag: tissue

value: liver biopsy


title: 440418.1.X_8

value: M


title: 440420.1.X_8


title: 440417.1.X_8

value: F


title: 440422.1.X_1


title: 440411.1.X_7


title: 440410.1.X_6


title: 440409.1.X_6


title: 440395.1.X_3


title: 440394.1.X_3


title: 440429.1.X_2


title: 440393.1.X_3


title: 440388.1.X_1


title: 440391.1.X_3


title: 440385.1.X_1


title: 440408.1.X_6


title: 440383.1.X_1


title: 440384.1.X_1


title: 440389.1.X_1


title: 440381.1.X_1


title: 440487.1.X_4


title: 440380.1.X_1


title: 440379.1.X_1


title: 440376.1.X_1


title: 440375.1.X_8


title: 440378.1.X_1


title: 440357.1.X_5


title: 440355.1.X_4


title: 440354.1.X_4


title: 440352.1.X_4


title: 440351.1.X_4


title: 440350.1.X_1


title: 440349.1.X_1


title: 440390.1.X_1


title: E14 ESCs D35 biological replicate 1

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
E14del35kbsum-21kbbin-coarse
E14del35kb-21kbbin-coarse
E14del35kbsum-21kbbin-ooecoarse
E14del35kb-21kbbin-ooecoarse
R_2017_12_06_14_11_27_user_ISA-78-LauraLettice_Del6_061217

data_processing:
The sequencing data was processed through a Torrent 5C data transformation pipeline on Galaxy (https://main.g2.bx.psu.edu/). The data was mapped against a customized reference file with TMAP. The reference file contained a list of all possible contacts between Forward and Reverse 5C primers covering our regions.
The data was then filtered to remove low-quality reads (MAQ quality score of lower than 30), reads aligning more than two nucleotides away from the reference sequence start site, and reads which do not contain HindIII restriction sites.
Before normalizing, interactions between adjacent fragments were removed due to the high noise: signal ratio likely to occur here. Average  read count values over 21kb bins were calculated from the raw sequencing data and 5C data were further processed for visualization. First, the matrices were normalized to sum up to 50,000 reads (excluding the first two diagonals of the matrix). Then adaptive coarsegraining of the matrices was performed to reduce noise using cooltools.numutils.adaptive_ coarsegrain, with the three lowest coverage bins masked and cutoff of 10 reads. Level of coarsegraining for all ES cell matrices was determining using the merged wild type data to ensure identical bin sizes across conditions. For comparison of 5C matrices across conditions, we additionally performed observed/expected normalization by dividing each diagonal of the matrix by its mean. For high resolution, zoomed in, (15kb) heatmaps in Figs. 2 & S2 raw data was used, with comparison zoomed in heatmaps normalised to total read count of compared limb anterior and posterior tissue samples.
Genome_build: mm9
Supplementary_files_format_and_content: This analysis generates a matrix file containing the interaction frequencies. The tar archive "GSE135840_interaction_frequency.tar" contains each interaction frequency for all DNA fragments in 5C experiments in matrix form, without binning and coarsening/normalisation.

source_name: ESCs

growth_protocol: GMEM+ Supplement for ESCs, N2B27 for 7 days for NPCs

extract_protocol:
10-20 million fixed cells were incubated for 15 min on ice in 200 ml of lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP40, supplemented with fresh protease inhibitor cocktail).  Cells were then disrupted on ice with a dounce homogenizer (pestle B; 2 x 20 strokes), cell suspensions transferred to eppendorf tubes and centrifuged 5 min at 2000 g.  Supernatants were removed, the cell pellets washed twice with 100 ml of 1X CutSmart buffer (NEB) and the cell pellet resuspended in 100 ml of 1X CutSmart buffer, and divided into two eppendorf tubes.  1X CutSmart buffer (337 ml) was added to each tube, and the mixture was incubated 10 min at 65°C with 0.1% SDS.  44 ml of 10% Triton X-100 were added before overnight digestion with 400 Units HindIII.  The restriction enzyme was then inactivated by adding 86 ml of 10% SDS, and incubation for 30 min at 65°C.  Samples were then individually diluted into 7.62 ml of ligation mix (750 ml 10% Triton X-100, 750 ml 10X ligation buffer, 80 ml 10 mg/ml of BSA, 80 ml 100 mM ATP and 3000 Cohesive end Units of T4 DNA ligase) and incubated at 16°C for 2 hours. 3C libraries were incubated overnight at 65°C with 50 ml Proteinase K (10 mg/ml), and with an additional 50 ml Proteinase K the following day for 2 hours.  The DNA was purified by one phenol and one phenol-chloroform extraction, and precipitated with 0.1 volume (800 ml) of 3 M NaOAc pH 5.2 and 2.5 volumes of cold EtOH (20 ml).  After at least 1 h at -80°C, the DNA was centrifuged for 25 min at 20,000 g at 4°C, and the pellets washed with cold 70% EtOH. DNA was resuspended in 400 ml of TE pH 8.0, and transferred to eppendorf tubes for another phenol-chloroform extraction and precipitation with 40 ml of 3 M NaOAc pH 5.2 and 1.1 ml of cold EtOH.  DNA was recovered by centrifugation, and washed eight times with cold 70% EtOH.  Pellets were then dissolved in 100 ml TE pH 8.0, and incubated with RNAse A (1 ml at 10 mg/ml) for 15 min at 37°C.
3C libraries were denatured and annealed to 5C primers. 5C oligonucleotide were designed upstream (FORWARD) or downstream (REVERSE) HindIII restriction sites. Annealing was followed by ligation with Taq DNA ligase. Ligated 5C primers were then amplified with the A-key and P1-key primers to generate the 5C libraries. 5C libraries were then prepared for sequencing onto Ion 316™ Chips with an Ion PGM™ Sequencer following either the Ion Xpress™ Template Kit v2.0, and Ion Sequencing Kit v2.0 protocols, or the Ion PGM™ Template OT2 200 Kit, and Ion PGM™ Sequencing 200 Kit v2.0 protocols as recommended by the manufacturer’s instructions (Life TechnologiesTM). Libraries were prepared according to Ion Torrent's instructions

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with glycine (125 mM final concentration), and incubated for 5 min at room temperature followed by 15 min on ice. Cells were centrifuged at 400 g for 10 min at 4°C. Supernatants were removed and cell pellets were flash frozen on dry ice.

tag: strain

value: E14 ESCs

tag: developmental stage

value: Stem cells


title: E14 ESCs D35 biological replicate 2

description:
E14del35kbsum-21kbbin-coarse
E14del35kbrep-21kbbin-coarse
E14del35kbsum-21kbbin-ooecoarse
E14del35kbrep-21kbbin-ooecoarse
R_2017_12_07_10_37_40_user_ISA-81-LauraLettice_Del18_071217


title: E14 ESCs DCTCF5 biological replicate 1

description:
E14ctcf5sum-21kbbin-coarse
E14ctcf5-21kbbin-coarse
E14ctcf5sum-21kbbin-ooecoarse
E14ctcf5-21kbbin-ooecoarse
R_2016_04_07_10_39_13_user_SN1-404-CTCF_5_5


title: E14 ESCs DCTCF5 biological replicate 2

description:
E14ctcf5sum-21kbbin-coarse
E14ctcf5rep-21kbbin-coarse
E14ctcf5sum-21kbbin-ooecoarse
E14ctcf5rep-21kbbin-ooecoarse
R_2016_04_07_13_58_37_user_SN1-405-CTCF_5_6


title: E14 ESCs DCTCF2 biological replicate 2

description:
E14ctcf2sum-21kbbin-coarse
E14ctcf2rep-21kbbin-coarse
E14ctcf2sum-21kbbin-ooecoarse
E14ctcf2rep-21kbbin-ooecoarse
R_2015_11_13_14_48_45_user_SN1-374-2_7_Tech2_4


title: E14 ESCs DCTCF3 biological replicate 1

description:
E14ctcf3sum-21kbbin-coarse
E14ctcf3-21kbbin-coarse
E14ctcf3sum-21kbbin-ooecoarse
E14ctcf3-21kbbin-ooecoarse
R_2015_09_30_10_50_26_user_SN1-363-CTCF3_1


title: E14 ESCs DCTCF3 biological replicate 2

description:
E14ctcf3sum-21kbbin-coarse
E14ctcf3rep-21kbbin-coarse
E14ctcf3sum-21kbbin-ooecoarse
E14ctcf3rep-21kbbin-ooecoarse
R_2015_09_30_14_11_04_user_SN1-364-CTCF3_3


title: 440377.1.X_1

tag: age at biopsy

tag: lobular inflammation grade


title: E14 ESCs DCTCF4 biological replicate 1

description:
E14ctcf4sum-21kbbin-coarse
E14ctcf4-21kbbin-coarse
E14ctcf4sum-21kbbin-ooecoarse
E14ctcf4-21kbbin-ooecoarse
R_2016_04_06_10_52_19_user_SN1-402-CTCF4_2


title: E14 ESCs DCTCF2 biological replicate 1

description:
E14ctcf2sum-21kbbin-coarse
E14ctcf2-21kbbin-coarse
E14ctcf2sum-21kbbin-ooecoarse
E14ctcf2-21kbbin-ooecoarse
R_2015_10_01_14_01_39_user_SN1-366-CTCF2_7


title: 440353.1.X_4

tag: cytological ballooning grade

tag: steatosis grade


title: E14 ESCs DCTCF1 biological replicate 1

description:
E14ctcf1sum-21kbbin-coarse
E14ctcf1-21kbbin-coarse
E14ctcf1sum-21kbbin-ooecoarse
E14ctcf1-21kbbin-ooecoarse
R_2015_09_10_10_42_26_user_SN1-357-8_CTCF_6


title: E14 ESCs DCTCF1 biological replicate 2

description:
E14ctcf1sum-21kbbin-coarse
E14ctcf1rep-21kbbin-coarse
E14ctcf1sum-21kbbin-ooecoarse
E14ctcf1rep-21kbbin-ooecoarse
R_2016_01_14_11_40_36_user_SN1-388-1_6rpt


title: E14 ESCs wild type biological replicate 1

description:
E14wtsum-21kbbin-coarse
E14wt-21kbbin-coarse
E14wtsum-21kbbin-ooecoarse
E14wt-21kbbin-ooecoarse
R_2015_11_13_11_27_36_user_SN1-373-E14_9


title: E14 ESCs wild type biological replicate 2

description:
E14wtsum-21kbbin-coarse
E14wtrep-21kbbin-coarse
E14wtsum-21kbbin-ooecoarse
E14wtrep-21kbbin-ooecoarse
R_2016_04_06_14_10_29_user_SN1-403-E14_2_rpt


title: E11.5 embryo bodies

description:
E11.5embryobody-21kbbin-coarse
R 2014 10 31 14 24 18 user SN1-284

source_name: Embryonic bodies


title: E11.5 anterior limb buds biological replicate 2

description:
E11.5anteriorlimbsum-21kbbin-coarse
E11.5anteriorlimbrep-21kbbin-coarse
E11.5anteriorlimbsum
E11.5anteriorlimbrep
R 2015 11 12 11 30 38 user SN1-371-Ant2 12

source_name: Embryonic anterior limb buds


title: E11.5 anterior limb buds biological replicate 1

description:
E11.5anteriorlimbsum-21kbbin-coarse
E11.5anteriorlimb-21kbbin-coarse
E11.5anteriorlimbsum
E11.5anteriorlimb
R 2015 09 08 14 36 17 user SN1-354-4 Ant2


title: E11.5 posterior limb buds biological replicate 2

description:
E11.5posteriorlimbsum-21kbbin-coarse
E11.5posteriorlimbrep-21kbbin-coarse
E11.5posteriorlimbsum
E11.5posteriorlimbrep
R_2015_11_12_15_01_00_user_SN1-372-Post2_13

source_name: Embryonic posterior limb buds


title: E11.5 posterior limb buds biological replicate 1

description:
E11.5posteriorlimbsum-21kbbin-coarse
E11.5posteriorlimb-21kbbin-coarse
E11.5posteriorlimbsum
E11.5posteriorlimb
R 2015 09 08 10 54 35 user SN1-353-5 post2


title: E11.5 D700 embryos biological replicate 1 technical replicate 1

description:
E11.5largedelsum-21kbbin-coarse
E11.5largedel-21kbbin-coarse
R 2015 02 24 11 32 11 user SN1-306-gl120 2

source_name: Whole embryos


title: E11.5 D700 embryos biological replicate 1 technical replicate 2

description:
E11.5largedelsum-21kbbin-coarse
E11.5largedel-21kbbin-coarse
R 2015 04 07 09 34 09 user SN1-328-GL120 2 Tech2


title: E11.5 D700 embryos biological replicate 2 technical replicate 2

description:
E11.5largedelsum-21kbbin-coarse
E11.5largedelrep2-21kbbin-coarse
R 2015 07 03 09 27 16 user SN1-345


title: mouse NPC sc-seq chow-3

status: Public on Aug 08 2019

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

data_processing:
Cell ranger (v.2.0.0) was used to QC and generate filtered gene matrices for sample chow1, chow2, NASH1 and NASH2.
Cell ranger (v.3.0.0) was used to QC and generate filtered gene matrices for sample chow3 and NASH3.
Single-cell RNA seq data was processed by Seurat package (v.2.3.4).
The cells with low quality and high mitochondrial content were removed. The potential doublets were removed based on cell-specific marker genes expression.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are the UMI count matrices of cells that passed the filter criteria.

source_name: liver

extract_protocol:
Perfusion collagenase and pronase (0.4mg/ml) from portal vein into mouse liver was performed after euthanasia. Hepatocyte was removed from total cell suspension by gradient centrifugation. The NPCs were suspended in 1ml 2% FBS DMEM at a density of 1e06 cell/ml.
RNA libraries were prepared for sequencing using standard Illumina and 10X genomics Chromium single cell protocols

treatment_protocol: mice were fed on NASH diet (D09100301, Research Diets) for 36 weeks

tag: cell type

value: liver non-parenchymal cells

tag: phenotype

value: control (chow diet)


title: E14 ESCs DCTCF4 biological replicate 2

description:
E14ctcf4sum-21kbbin-coarse
E14ctcf4rep-21kbbin-coarse
E14ctcf4sum-21kbbin-ooecoarse
E14ctcf4rep-21kbbin-ooecoarse
R_2016_04_05_14_11_05_user_SN1-401-CTCF4_1


title: mouse NPC sc-seq NASH-1

value: NASH


title: mouse NPC sc-seq NASH-3


title: mouse NPC sc-seq chow-2


title: mouse NPC sc-seq NASH-2


title: mouse NPC sc-seq chow-1


title: GM19240.ADS385

status: Public on Jul 31 2019

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description:
GM.pp.all.bz2
GM.po.all.bz2

data_processing:
Read pairs from Promoter Capture Hi-C library were independently mapped to human genome hg19 using BWA-mem and manually paired with in house script.
Unmapped, non-uniquely mapped, and PCR duplicates were removed.
Trans-chromosomal read pairs and putative self-ligated products (<15kb read pairs) were removed.
Off-target reads were removed when both read pairs did not match to capture probe sequences.
Genome_build: Hg19
Supplementary_files_format_and_content: *.po and *.pp provide interaction frequencies for promoter-promoter interactions or promoter-other interactions, respectively.  We combined multiple donors or replicates according to cell/tissue types.

source_name: Human Lymphoblasts

extract_protocol:
Promoter Capture Hi-C library was constructed by performing a target enrichment protocol (enriching target promoter-centered proximity ligation fragments from Hi-C library using capture RNA probes). Briefly, we incubated 500ng Hi-C library 24h at 65 °C within a humidified hybridization chamber with 2.5ug human Cot-1 DNA (Life Technologies), 2.5ug salmon sperm DNA (Life Technologies), and p5/p7 blocking oligos with hybridization buffer mix (10X SSPE, 10mM EDTA, 10X Denhardts solution, and 0.26% SDS) and 500ng RNA probes. RNA:DNA hybrids were enriched using 50ul T1 streptavidin beads (Invitrogen) with 30min incubation at RT. Next, bead-bound hybrids were washed by a 15min incubation in wash buffer1 (1X SSC and 0.1% SDS) with frequent vortexing, and then washed three times with 500ul of pre-warmed (65 °C) wash buffer2 (0.1X SSC and 0.1% SDS), and resuspended in nuclease-free water. The resulting capture Hi-C libraries were amplified while bound to the T1 beads, and purified using AMPure XP beads, followed by sequencing.
Promoter Capture Hi-C library sequencing procedures were carried out as previously described according to Illumina HiSeq2500 or HiSeq4000 protocols with minor modifications (Illumina, San Diego, CA).
Capture Hi-C

value: Lymphoblasts


title: GM12878.ADS185

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS158

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM19240.ADS168

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM19240.ADS177

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM19240.ADS157

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS195

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM19240.ADS223

description:
GM.pp.all.bz2
GM.po.all.bz2


title: E11.5 D700 embryos biological replicate 2 technical replicate 1

description:
E11.5largedelsum-21kbbin-coarse
E11.5largedelrep2-21kbbin-coarse
R 2015 04 07 13 23 06 user SN1-329-GL120 3 Tech1


title: GM12878.ADS178

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS169

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM19240.ADS222

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM19240.ADS123

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS82

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS122

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS131

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM19240.ADS119

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS88

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS80

description:
GM.pp.all.bz2
GM.po.all.bz2


title: GM12878.ADS121

description:
GM.pp.all.bz2
GM.po.all.bz2


title: Gata4.d2.FVF.Gata.r2

status: Public on Jul 26 2019

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

description: ES cells were seeded without feedeers in gelatin-coated plates and grown for 48h in ES standard medium (LIF/serum) supplemented with 40ng/ml doxycycline.

data_processing:
reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

source_name: ES cells

extract_protocol:
1-2 million FACS-sorted cross-linked cells (1% formaldehyde, 10min RT) were lysed in 100 ul Buffer-B-0.3 (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0,3%SDS, 1x protease inhibitors -Roche) and sonicated in a microtube (Covaris; 520045) using a Covaris S220 device until most of the DNA fragments were 200-500 base pairs long (settings: temperature 4°C, duty cycle 2%, peak incident power 105 Watts, cycles per burst 200). After shearing, lysates were centrifuged 10min, 4°C, 12000g and supernatant diluted with 1 volume of Dilution Buffer (1mM EGTA 300 mM NaCl, 2% Triton x-100, 0.2% sodium deoxycholate, 1x protease inhibitors-Roche). Sonicated chromatin was then incubated 4h at 4°C on a rotating wheel with 6 ug of antibody conjugated to 20 µl of magnetic beads  (Dynabeads, Life Technology). Beads were washed four times with Buffer-A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors) and once with Buffer-C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (20mg/ml) for 1 hour at 55°C and 8 hours at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 hour at 55°C. Finally, DNA was purified with SPRI AMPure XP beads (Beckman Coulter) (sample-to-beads ratio 1:2). Purified DNA was used as input for library preparation.
MicroPlex Library Preparation Kit v2 (Diagenode, cat. C05010012)

tag: cell line

value: doxycycline (Dox) inducible Foxa2-Venus, Gata4-tBFP ES cell line (T134)

tag: genotype

value: TetON-Foxa2-Venus; TetON-Gata4-tBFP

tag: facs sorting markers

value: Venus-positive/tBFP-positive

tag: chip antibody

value: anti-Gata4 (R&D Systems; AF2606)


title: GM12878.ADS81

description:
GM.pp.all.bz2
GM.po.all.bz2


title: Gata4.d2.FVF.Gata.r1


title: GM19240.ADS83

description:
GM.pp.all.bz2
GM.po.all.bz2


title: Foxa2.d2.FVF.Gata.r1

value: anti-Foxa2 (SantaCruz; sc6554x)


title: Foxa2.d2.FVF.Gata.r2


title: Foxa2.d1.FVFp.r2

description: ES cells were seeded without feedeers in gelatin-coated plates and grown for 24h in ES standard medium (LIF/serum) supplemented wiht 40ng/ml doxycycline.

value: doxycycline (Dox) inducible Foxa2-Venus ES cell line (T128)

value: Venus-positive


title: PTU_NCORdeltaID_rep2_RNA

status: Public on Jul 01 2019

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
RPKM_RNA_WT_PTU_T3_NCORdeltaID_PTU.txt
This sample has runs from 2 instrument models: Illumina HiSeq 1500 and Illumina NovaSeq 6000.

data_processing:
RNA-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression, H3K27Ac and H3K9Ac were analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
H3K27Ac and H3K9Ac domains were indentified using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text file with RPKM

extract_protocol:
Approximately 5 mg of liver tissue were homogenized using Ultra-Thorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) in EconoSpin columns (Epoc Life) according to manufacturerâ€™s instructions.
Total RNA (1000 ng) was prepared for sequencing using polyA enrichment followed by fragmentation and random priming for cDNA synthesis according to the manufacturer's (NEB) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina.

value: liver

value: L-NCORdeltaID

tag: treatment

value: PTU


title: PTU_NCORdeltaID_rep4_RNA


title: PTU_NCORdeltaID_rep3_RNA


title: Foxa2.d1.FVFp.r1


title: PTU_T3_WT_rep3_RNA

value: WT


title: PTU_T3_WT_rep4_RNA


title: PTU_T3_WT_rep2_RNA


title: Foxa2.d4.FVFp.r2

description: ES cells were seeded without feedeers in gelatin-coated plates and grown for 96h in ES standard medium (LIF/serum) supplemented wiht 40ng/ml doxycycline.


title: PTU_WT_rep1_RNA


title: PTU_WT_rep2_RNA


title: PTU_WT_rep3_RNA


title: PTU_T3_WT_rep1_RNA


title: Foxa2.d4.FVFp.r1


title: PTU_WT_rep4_RNA


title: 440529.1.X_5

value: liver biopsy

tag: Sex

value: M

tag: nafld activity score

tag: fibrosis stage


title: Fibroblasts 24 hr Control biological rep1

status: Public on Jun 30 2019

city: Richmond

first: Bryan

last: Zeitler

state: California

address: 501 Canal Blvd.

institute: Sangamo Therapeutics

description: Gene expression data from HD fibroblasts treated with Control for 24 hours

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on PrimeView Human Gene Expression Arrays. Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: PrimeView Human Gene Expression Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Robust Multi-array Average (RMA) was used to normalize the raw signal from each probe set.  Fold-change analysis was performed using Transcriptome Analysis Console 4.0 (Affymetrix) with “Analysis Type – Expression (Gene)” and “Summarization – RMA” options selected.

source_name: HD fibroblasts Control 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for 3’ IVT PLUS kits.

growth_protocol: HD fibroblast line GM02151 (CAG18/45) was obtained from the Coriell Cell Repository and maintained in complete MEM with 20% FBS.

extract_protocol: After 24 hrs, cells were washed 1X with PBS, then processed for total RNA extraction (High Pure, Roche).

treatment_protocol: 100 ng in vitro-transcribed mRNA encoding the ZFP-TFs was transfected into 1.5e5 GM02151 HD fibroblasts using an Amaxa shuttle, setting CA-137, solution P2, (Lonza).

tag: dose

value: 100 ng mRNA

value: control


title: Fibroblasts 24 hr ZFPC biological rep1

description: Gene expression data from HD fibroblasts treated with ZFPC for 24 hours

source_name: HD fibroblasts ZFPC 24 hours

value: ZFPC 24 hours


title: Fibroblasts 24 hr ZFPC biological rep6


title: MeCP2 OE 11x ATAC-seq 3

status: Public on Jun 27 2019

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

description:
Tn5 transposed chromatin
h_MeCP2_OE_E6_113

data_processing:
Pre-process reads with Trimmomatic version 0.32 ILLUMINACLIP:nextera.fa:2:40:15 MINLEN:25
Align to genome with bwa v0.7.5a-r405
Filter for unique primary alignments with Samtools 1.3.1
Remove duplicate reads with Picard v1.107
Remove mitochondrial reads and blacklisted regions with bedtools 2.27
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files of aligned reads

source_name: LUHMES-derived neurons

growth_protocol: LUHMES cells were cultured and differentiated according to published protocol (Shah et al., 2016).

extract_protocol:
Neurons were scraped from the plate and nuclei were isolated using hypotonic buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3mM MgCl2, 0.1% [v/v] Igepal CA-630) and counted. 50,000 nuclei were resuspended in 50 µl transposition reaction mix containing 2.5 µl Nextera Tn5 Transposase and 2x TD Nextera reaction buffer. The reaction was incubated for 30 min at 37 ºC.
DNA was purified by either MinElute PCR kit (Qiagen) or Agencourt AMPure XP (Beckman Coulter) beads and PCR amplified with NEBNext High Fidelity reaction mix (NEB) to generate a sequencing library.

treatment_protocol: Cells were modified using CRISPR system for KO and infected with lentiviruses carrying MeCP2 for OE.

tag: div

value: Day 9

tag: passage

value: LUHMES

value: LUHMES-derived neurons

value: MeCP2 OE 11x


title: Fibroblasts 24 hr Control biological rep3


title: Fibroblasts 24 hr ZFPB biological rep5

description: Gene expression data from HD fibroblasts treated with ZFPB for 24 hours

source_name: HD fibroblasts ZFPB 24 hours

value: ZFPB 24 hours


title: MeCP2 OE 11x ATAC-seq 4

description:
Tn5 transposed chromatin
h_MeCP2_OE_E6_115


title: Fibroblasts 24 hr ZFPB biological rep6


title: Fibroblasts 24 hr ZFPC biological rep4


title: Fibroblasts 24 hr ZFPC biological rep3


title: Fibroblasts 24 hr ZFPB biological rep3


title: Fibroblasts 24 hr Control biological rep6


title: Fibroblasts 24 hr ZFPC biological rep5


title: Fibroblasts 24 hr Control biological rep2


title: Fibroblasts 24 hr ZFPB biological rep4


title: Fibroblasts 24 hr ZFPA biological rep4

description: Gene expression data from HD fibroblasts treated with ZFPA for 24 hours

source_name: HD fibroblasts ZFPA 24 hours

value: ZFPA 24 hours


title: Fibroblasts 24 hr ZFPA biological rep2


title: 440382.1.X_1

tag: tissue

tag: age at biopsy


title: Fibroblasts 24 hr ZFPA biological rep1


title: Fibroblasts 24 hr ZFPC biological rep2


title: Fibroblasts 24 hr ZFPA biological rep5


title: Fibroblasts 24 hr ZFPB biological rep1


title: Fibroblasts 24 hr Control biological rep5


title: Input

status: Public on Jun 24 2019

city: North Chicago

first: Weihang

last: Chai

state: Illinois

address: 3333 N Green Bay Rd, IRP 257

department: Center for Genetic Diseases

institute: Rosalind Franklin University of Medicine and Sciences, Chicago Medical School

data_processing:
DNA was sequenced using Illumina HiSeq 2500
Reads aligned to hg38 using Bowtie2 in paired-end mode with default setttings
Samtools was used to remove reads below q40 and remove PCR duplicates
Peak calling was performed using MACS2 using the settings: --broad –no-model --broad-cutoff 10e-3 -p, and shift size determined using gel quantification from library quality control
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files are BED 6+4 files containing peak position, relative enrichment, and p- and q- values; Bedgraph files contain tags per (x) bp bin

source_name: Lymphoblastoid

growth_protocol: Cells were passaged in RPMI1640 (LifeTechnologies) supplemented with 2 mM L0glutamine and 15% fetal bovine serum

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 15 min, and crosslinking was stopped with glycine. Cells were then lysed and whole cell lysates were sonicated to obtain DNA fragment sizes <500bp. gamma-H2AX antibody was then used to isolate DNA bound to gamma-H2AX.
Libraries were prepared according to Illumina's TruSeq® ChIP Sample Preparation Guide (Part# 15023092 Rev. B) . Briefly, ChIP-enriched DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA fragments with sizes of 250-300 bp were selected on 2% agarose gels and were PCR amplified with Illumina primers for 18 cycles. The libraries were captured on an Illumina flow cell for cluster generation and sequenced on HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Cells were treated for 24 hrs with 2 mM HU, 0.1 μg/mL APH, or 200 μM MMS

tag: cell

value: Human B-lyphocytes


title: MMS2

value: methyl methanesulfonate

value: g-H2AX (Active Motif, 39118)


title: Fibroblasts 24 hr ZFPA biological rep3


title: Fibroblasts 24 hr ZFPA biological rep6


title: Fibroblasts 24 hr ZFPB biological rep2


title: MMS1


title: HU2

value: hydroxyurea


title: APH 2

value: aphidicolin


title: HU1


title: APH 1


title: PTU_NCORdeltaID_rep1_RNA

value: liver

value: L-NCORdeltaID

value: PTU


title: Untreated 1

value: untreated


title: Untreated 2


title: Lung Day4

status: Public on Jun 17 2019

city: Buffalo

first: Jian

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

data_processing:
Basecalling was performed with bcl2fastq version 2.17.1.14
Mapping to genome with TopHat (v2.1.1) with default parameters
Expression level was quantified as RPKM using Cufflink(v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM value for each sample

molecule: polyA RNA

growth_protocol: Primary human fibroblasts AG04451 and AG04452 (both from Coriell) were cultured in DMEM containing 10% FBS and 2mM L-glutamine. For the generation of induced dopaminergic neurons, fibroblasts were plated at 5x103/cm2 and infected 1 day later for 16h with lentiviruses of FUW-tetO-LoxP-cDNA (ASCL1, NURR1, LMX1A, miR124) and pLKO/p53shRNA(MOI 10 for pLKO/p53shRNA, MOI 20 for all others) in the presence of 8 μg/ml polybrene. Cells were then washed three time with DMEM/F12 to remove remaining serum and cultured in DMEM/F12 for 24h to arrest cell cycle. Then medium was changed to neural induction medium (DMEM/F12, 1x N2, 1x B27, 1xNEAA, 5 μM dorsomorphin,  2 μM purmorphamine and 10 μM SB431542, 3 μM CHIR99021, 0.2mM vitamin C, 10 μM Y27632, 0.5mM dcAMP, 20 ng/ml GDNF, 20 ng/ml BDNF, 1 ng/ml TGFb3 and 1 μg/ml doxycycline). The medium was changed every other day for the duration of the culture period.

extract_protocol:
Total RNA Extraction with TRIZOL Reagent and Purification with QIAGEN. RNeasy Mini Kit(cat # 74104).
cDNA libraries were prepared using the TrueSeq RNA Sample Preparation Kit (Illumina)

value: Lung fibroblasts

tag: time point

value: Day 4

value: transdifferentiation to dopaminergic neuron induced by ANLmp


title: Lung Day2

tag: cell type

value: Day 2


title: Lung Day1

value: Day 1


title: Skin Day3

value: Skin fibroblasts

value: Day 3


title: N_3

city: shanghai

first: xiaopeng

last: hu

address: dongchuan road 800

institute: shanghai jiaotong university

description: Competing endogenous RNA expression data

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Cat# 5188-5242; Agilent Technologies) in a Hybridization Oven (Cat# G2545A; Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Slides were scanned by an Agilent Microarray Scanner (Cat# G2565CA; Agilent Technologies) with default settings (dye channel: green; scan resolution = 3 µm; PMT: 100%, 20 bit).

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent Technologies). Raw data were normalized by the quantile algorithm of limma package in R.

source_name: normal human

label_protocol: RNA was amplified and labeled by a Low Input Quick Amp WT Labeling Kit (Cat# 5190-2943; Agilent Technologies) following the manufacturer’s instructions.

extract_protocol: Total RNA of placenta tissue was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

tag: condition

value: normal

value: placenta

tag: age


title: Skin Day2

tag: cell line


title: Skin Day4


title: Skin Day1


title: Lung Day3


title: NET-CAGE_GM12878_8M_biologicalRep2

status: Public on Jun 10 2019

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

country: Japan

institute: RIKEN, Yokohama

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_GCT

data_processing:
Library strategy: RNA-seq (CAGE)
For all our datasets we performed the following steps, (i) split reads by barcode, (ii) trimmed reads to remove barcode sequences and (iii) removed reads aligned to rRNA sequences (Human: GenBank U13369.1; Mouse: GenBank BK000964.3). These steps were performed using MOIRAI (Hasegawa et al., 2014) for human cell line data and using Trimmomatic v 0.36 (Bolger et al., 2014) and MOIRAI (Hasegawa et al., 2014) for mouse tissue data. For all CAGE based data and mouse RNA-seq data, sequences with base ‘N’ were also removed.
Non rRNA reads were mapped hg19 genome and human reference gene model Gencode v27lift37 comprehensive using  STAR v 2.5.0a with the following parameters for indexing: --runThreadN 12 --runMode genomeGenerate --genomeDir genome.fa --sjdbGTFfile Gencodeannotation.gtf and the following parameters for mapping: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --out FilterMultimapNmax 1 --readFilesCommand zcat.
Transcription start sites for CAGE based data were identified using bedtools v 2.2.25 (Quinlan and Hall, 2010) as described here: http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment
Genome_build: Human: hg19 and Mouse:mm9
Supplementary_files_format_and_content: Bed 6 file for trasncription start sites. Scores represent aggregated tags with same starting position.

source_name: Blood

growth_protocol: MCF-7, HeLa-S3 and HepG2 cells were cultured at 37 ˚C under 5% CO2 in DMEM with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS. GM12878 and K562 cells were cultured at 37 ˚C under 5% CO2 in RPMI 1640 with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS.

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Approximately 1.0 × 107 cells were used for total and nascent RNA fractionation. Culture medium was transferred to a conical centrifuge tube and centrifuged at 800 G for 5 minutes at 4 ˚C. The supernatant was removed and the cell pellets were washed with 5 mL of ice-cold D-PBS. To lyse cells, 1,000 μL of Buffer A (Nuclei ez lysis buffer (Sigma-Aldrich), 25 μM alpha-amanitin (FUJIFILM Wako Pure Chemical), 1× cOmplete Protease Inhibitor solution (Sigma-Aldrich) and 20 units of SUPERase IN RNase Inhibitor (Thermo Fisher Scientific)) was added to the cell pellets and resuspended by gentle vortex. 100 μL of the cell lysate was sampled and mixed with 700 μL of QIAzol for total RNA extraction. The remaining lysate was set on ice for 10 minutes. Then the lysate was centrifuged at 800 G for 5 minutes at 4 ˚C. The pellets were washed once with 600 μL of Buffer A.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

treatment_protocol: For the time course experiment, MCF-7 cells were serum-starved for 16 hours, and heregulin beta-1 was added to the medium at a final concentration of 10 nM. Cells were harvested at 0 (no treatment), 15, 30, 45, 60, 120, 180 and 360 minutes in triplicates.

value: GM12878 cell line

tag: urea treatment

value: 8 M

tag: molecule subtype

value: Nascent RNA


title: NET-CAGE_GM12878_4M_biologicalRep2

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_GCG

value: 4 M


title: N_2


title: CAGE_GM12878_biologicalRep1

value: Total RNA


title: NET-CAGE_GM12878_1M_biologicalRep2

value: 1 M


title: NET-CAGE_GM12878_2M_biologicalRep3

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_ACC

value: 2 M


title: NET-CAGE_GM12878_6M_biologicalRep1

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_ATG

value: 6 M


title: NET-CAGE_GM12878_4M_biologicalRep1

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_AGT


title: SPE_3

source_name: severe preeclampsia patient

value: severe preeclampsia


title: NET-CAGE_GM12878_2M_biologicalRep4

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_CAC


title: NET-CAGE_GM12878_0.5M_biologicalRep2


title: SPE_1


title: NET-CAGE_GM12878_0.5M_biologicalRep1


title: NET-CAGE_GM12878_1M_biologicalRep1


title: NET-CAGE_GM12878_2M_biologicalRep1


title: CAGE_GM12878_biologicalRep2


title: N_1


title: SPE_2


title: GM12878-GM18502 MIXTURE

status: Public on Jun 09 2019

city: Austin

first: Daniel

middle: Camilo

last: Osorio

state: TX

address: 1601 Trinity St

institute: The University of Texas at Austin

data_processing:
Mapping of reads to transcripts and cells
Quality Control
Cell cycle phase and population assignment
Genome_build: hg38
Supplementary_files_format_and_content: QC files include common quality control measures for scRNA-Seq including UMI count per cell and percentage of mitochondrial transcripts. Barcodes, Genes and Matrix files are the output of the 10X pipeline.

source_name: LCL cell line

growth_protocol: GM12878 and GM18502 were purchased from the Coriell Institute for Medical Research. Cells were cultured in the Roswell Park Memorial Institute (RPMI) Medium 1640 supplemented with 2mM L-glutamine and 20% of non-inactivated fetal bovine serum in T25 tissue culture flasks. Flasks with 20 mL medium were incubated on upright position at 37°C under 5% carbon dioxide. Cell cultures were split every three days for maintenance.

extract_protocol:
Single-cell sample preparation was conducted according to Sample Preparation Demonstrated Protocol provided by 10X Genomics as follows: 1 mL of cell suspensions from each cell line (day 4, stable phase) was pelleted in Eppendorf tubes by centrifugation (400g, 5min). The supernatant was discarded, and the cells pellet was then resuspended in 1X PBS with 0.04% BSA, followed by two washing procedures by centrifugation (150g, 3min). After the second wash, cells were resuspended in ~500 uL 1X PBS with 0.04% BSA followed by gently pipetting mix 10-15 times.
Libraries were prepared using the Chromium Controller (10X Genomics, CA) in conjunction with the single-cell 3’ v2 kit. Briefly, the cell suspensions were diluted in nuclease-free water according to manufacturer instructions to achieve a targeted cell count of 5,000 for each cell line. The cDNA synthesis, barcoding and library preparation were then carried out according to the manufacturer's instructions. Libraries were sequenced in the North Texas Genome Center facilities on a Novaseq 6000 sequencer (Illumina, San Diego).

value: LCL


title: NET-CAGE_GM12878_8M_biologicalRep1

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_ACG


title: GM12878


title: NET-CAGE_GM12878_2M_biologicalRep2


title: GM18502


title: VEH 3

status: Public on May 26 2019

city: Urbana

first: Zeynep

last: Madak-Erdogan

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

data_processing:
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.36). Next, the reads were mapped to the Homo sapiens reference genome from Ensembl database and aligned using the STAR alignment tool (Version 2.5.3). After this, the read counts were generated from SUBREAD (Version 1.5.2) and featured counts were outputted for statistical analysis in R. Quality control and normalization was conducted in R using edgeR (Version 3.20.9).
Statistical Analysis and DEGs: Statistical analysis was conducted in R using limma (Version 3.34.9). Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >1.5 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: count files

source_name: mammary cells

growth_protocol: BT474 were cultured in ATCC recommended Hybri-care medium with 10% inactivated FBS, sodium bicarbonate and antibiotics. MDA-MB-134 cells were cultured in Leibovitz’s medium with 20% FBS (HyClone), and 100 g/ml penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies) according to manufacturer protocol and cleaned using QIAGEN clean-up kit. RNA quality was assessed using bioanalyzer.
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

treatment_protocol: BT474 cells were treated with Veh (0.5% EtOH), 10-7 M 4-OH Tamoxifen (Sigma, St. Louis, MO), 10-7 M Selinexor (SXR) (Selleckchem, Houston, TX) or 4-OH Tamoxifen and SXR combination for 24 hours.

tag: treatment

value: Veh (0.5% EtOH)


title: Selinexor 1

value: 10-7 M Selinexor (SXR)


title: VEH 2


title: VEH 1


title: Selinexor 2


title: Selinexor 3


title: 4-OH Tamoxifen+SXR 3

value: 4-OH Tamoxifen and SXR


title: 4-OH Tamoxifen+SXR 2


title: 4-OH Tamoxifen+SXR 1


title: 4-OH Tamoxifen 2

value: 10-7 M 4-OH Tamoxifen (Sigma, St. Louis, MO)


title: R1_4sU_Seq_MYC_ON_Plus_Strand

status: Public on Mar 27 2019

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

description: nascent RNA

data_processing:
Library strategy: 4sU Seq
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
genome build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: U2OS cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using miRNeasy columns and biotinylated. This was followed by pulldown using streptavidin-MyOne beads and elution
NEB Ultra/Ultra Directional RNA Seq

treatment_protocol: Dox - 12-16 hours (when dox is added)/48 hours

tag: sirna

value: siMYC+Dox

tag: antibody


title: 4-OH Tamoxifen 1


title: R1_4sU_Seq_MYC_ON_Minus_Strand

description: nascent RNA


title: tumor_bearing_mouse_1 [mouse_t_1_4]

status: Public on Apr 09 2019

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description: Analyses in the publication (Zilionis et al. 2019) use t_1_4 library counts (GSM3635312_mouse_t_1_4_raw_counts.tsv.gz) generated from one sequencing run (SRR8646225). Additional reads were obtained for the library t_1_4 [SRR10097590] and are made available on SRA for completeness.

data_processing:
All  processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops). The following steps are provided as an overview on the internal workings of inDrops.py. FASTQ files and processing steps are provided for mouse only.
inDrops.py first filters reads  for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 12 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > 600; ii) mitochondrial gene content <15.  Counts were total counts normalized as described in methods, and combined into a single genes x cells normalized filtered matrix per species. Putative cell doublets were identified using Scrublet (Wolock et al., 2018) and removed from further analysis. The resulting count matrixes are provided as mouse_counts_normalized_15939x28205.mtx and human_counts_normalized_54773x41861.mtx
Genome_build: GRCm38/91 (mouse) and GRCh38/81 (human)
Supplementary_files_format_and_content: human_counts_normalized_54773x41861.mtx contains filtered normalized counts from human samples.  human_cell_metadata_54773x25.tsv contains per-cell meta data for human samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_human_41861.tsv contains the list of human gene names.  mouse_counts_normalized_15939x28205.mtx contains filtered normalized counts from mouse samples.  mouse_cell_metadata_15939x12.tsv contains per-cell meta data for mouse samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_mouse_28205.tsv contains the list of mouse gene names.  human_*_raw_counts.tsv.gz contain unfiltered raw counts from human samples prior to normalization; one file per sequencing library.  mouse_*_raw_counts.tsv.gz contain unfiltered raw counts from mouse samples prior to normalization; one file per sequencing library.

source_name: lung tumor

extract_protocol:
Single cell suspensions were obtained from lung tissue of C57BL/6 male mice which were perfused with PBS. Small tissue pieces were generated from perfused lungs using scissors and digested (RPMI containing 0.2 mg/ml collagenase type I, Worthington Biochemical Corporation) for 15min at 37°C while shaking (700rpm). Digested lung tissue was gently meshed through 70µM cell strainers using a plunger. Single cell suspensions were then stained with a fluorescent conjugated antibody specific to CD45 (clone 30-F11, Biolegend) for 45min at 4°C. The cells were washed with staining buffer (PBS containing 0.5% BSA and 2 mM EDTA) and CD45+ live cells were sorted on a FACS Aria cell sorter (BD) into FBS containing tubes which were kept on ice until the cells were further processed for scRNASeq. 7-aminoactinomycin (7AAD, Sigma) positivity was used to exclude dead cells.
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols.

treatment_protocol: Murine KP1.9 lung adenocarcinoma tumor cells were injected into C57BL/6 male mice intravenously (2.5x105 cells in 100µl PBS) to develop orthotopic tumors in the lung. The tumor cell line was derived from lung tumor nodules of a C57BL/6 KrasLSL-G12D/WT;p53Flox/Flox (KP) mouse and was kindly provided by Dr. Zippelius (University Hospital Basel, Switzerland). Mice were analyzed for tumor phenotypes 4 weeks post-tumor initiation.

tag: strain

tag: gender

value: M

tag: treatment received prior to surgery (1= treated; 0=untreated)

tag: tumor cell line injected

value: KP1.9 lung adenocarcinoma tumor cells from lung tumor nodules of a C57BL/6 KrasLSL-G12D/WT;p53Flox/Flox male mouse

tag: age at injection of tumor cell line (weeks)

tag: purification

value: RBC-depletion; CD45+ cells

tag: age at sacrifice (weeks)


title: R1_4sU_Seq_MYC_OFF_Minus_Strand

description: nascent RNA

value: siMYC+EtOH


title: vp16_srf

status: Public on Mar 14 2019

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

data_processing:
Sequencer: Illumina HiSeq 2500 (SND00104). Basecalling pipeline: HiSeq Control Software 2.2.58; Gerald version 1.8
Run:
RNAseq: Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequenced reads were mapped to the mouse genome (build GRCm38/mm10) using STAR (v2.5.0c). SAM/BAM files were further processed using SAMTOOLS v1.3. Read count quantifications were obtained using HTSeq (v0.6.1). Further data process was performed with custom scripts in the R programming language (https://cran.r-project.org/). Normalization of read counts and differential expression analysis between genotypes was carried out using DESeq2 R package from Bioconductor v3.2 (BiocInstaller 1.20.3). GO analysis was performed with Panther (Huaiyu Mi et al., 2013)
ChIPseq: Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Libraries were trimmed from adapters and low quality bases using Trimmomatic v0.36 (Bolger et al., 2014), and mapped to reference genome (Ensembl GRCm38) using Bowtie2 v2.3.2 (Langmead et al., 2009). Data was further processed using samtools (v1.5) (Li et al., 2009) and bedtools (v2.26.0) (Quinlan and Hall, 2010). Peak calling was performed using MACS2 (v2.1.1) (Zhang et al., 2008). SeqMINER (Ye et al 2011) was used to generate the k-means clustering data and the merged ChIP-seq profiles. Further analyses were performed with custom scripts in the R programming language (https://cran.r-project.org/). GO analysis was performed with the R bioconductor package ChIPpeakAnno v3.8.9. Data from Kim et al 2010 were lifted over from mm9 to mm10 using the R package rtracklayer.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl gene identifiers (ENSMUSG) and raw counts; bigwig files

extract_protocol:
RNA-seq: Total RNA from cortical cultures was extracted with TRI reagent (Sigma-Aldrich) and digested with DNase I (QIAGEN®). RNA samples were extracted and re-precipitated using acid phenol-chloroform and ethanol.   .
ChIP-seq: Primary hippocampal neurons were obtained from E17 embryos. Cultured neurons were infected with syn-VP16-SRF/Syn-GFP viral vector at DIV3. After 7 days post-infection neurons were collected and genomic DNA from 5 × 10^6 hippocampal neurons was fragmented by sonication and immunoprecipitated with anti-VP16 antibody (Santa Cruz, sc-7545) as previously described (Scandaglia et al., 2015). Immunoprecipitated DNA was resuspended in 40 μL of water
Single-End stranded Chip and RNA libraries were prepared for sequencing using standard Illumina protocols (HiSeq Sequencing v4 Chemistry), with read length 50 and application Truseq Stranded mRNA.  Service provided by CRG.

tag: strain/background

value: ICR

tag: tissue

value: Primary neurons

tag: chip antibody

tag: flowcell

tag: index

value: GTTTCGGA