title: Stanford_ChipSeq_HepG2_CEBPB_IgG-rab

tag: lab description

value: ChipSeq

tag: cell

tag: cell organism

value: human

value: hepatocellular carcinoma

value: endoderm

value: M

tag: treatment

value: CEBPB

tag: antibody antibodydescription

value: Rabbit polyclonal IgG. Antibody Target:CEBPB

tag: antibody targetdescription

value: epitope mapping at the C-terminus of C/EBP-beta of rat origin

value: Santa Cruz Biotech

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Harvard_ChipSeq_GM12878_ZZZ3_std

status: Public on May 22 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhTfbs

tag: lab

value: Harvard

value: Struhl - Harvard University

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit Polyclonal anti-human ZZZ3, Immunogen:Synthetic peptide coupled to Ovalbumin (Name PI130, sequence CGNNNGRTTDLKQQSTRESW). Antibody Target:ZZZ3

value: ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains.

tag: antibody vendorname

value: Lazlo Tora, Institut de G?n?tique et de Biologie Mol?culaire et Cellulaire

tag: antibody vendorid

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: replicate


title: USC_ChipSeq_HeLa-S3_E2F1_std

value: USC

tag: lab description

value: Farnham - University of Southern California

value: ChipSeq

tag: cell

tag: cell organism

value: human

value: cervical carcinoma

value: cancer

value: ectoderm

tag: treatment

tag: antibody antibodydescription

value: E2F1(KH20 and KH95) is a mouse monoclonal antibody.  The epitope for KH20 has been mapped to amino acids 1-89; KH95 to amino acids 342-386.  Recommended for detection of E2F1 of H and Xn origin by WB and IP. Antibody Target:E2F1

value: E2F1, the original member of the E2F family of transcription factors, was identified as a cellular protein with DNA binding activity associated with the adenovirus E2 gene promoter. E2F1 is cell cycle regulated with very low levels in early G1, then increasing levels as cells move from G1 to S, and highest levels of protein at the G1/S boundary, which is consistent with its role in S-phase entry.

value: Millipore

tag: labversion

value: HeLa cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, precipitated with StaphA and an antibody to E2F1,

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: Stanford_ChipSeq_K562_IFNg30_STAT1_std

tag: lab

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: mesoderm

value: F

value: Interferon gamma treatment - 30 minutes (Snyder)

value: rabbit polyclonal to STAT1 (alpha) p-91 (C-24). Antibody Target:STAT1

tag: antibody targetdescription

value: transcription factor, activated by interferon signalling

value: Santa Cruz Biotech


title: Yale_ChipSeq_HeLa-S3_Brg1_IgG-mus

value: Yale

value: Snyder - Yale University

value: ChipSeq

value: human

value: cervical carcinoma

value: cancer

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Brg-1 (G-7) is a mouse monoclonal antibody raised against amino acids 209-296 mapping near the N-terminus of Brg-1 of human origin. Antibody Target:BRG1

value: Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex.

tag: antibody vendorname

tag: antibody vendorid

tag: control

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: Harvard_ChipSeq_HeLa-S3_BDP1_std

value: Harvard

tag: lab description

value: Struhl - Harvard University

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: ectoderm

value: F

tag: treatment

tag: antibody antibodydescription

value: Rabbit polyclonal - Antiserum 2663 was raised by immunizing rabbits with synthetic peptide CSDRYRIYKAQKLRE (human Bdp1 residues 139?153) coupled to KLH. Antibody Target:BDP1

value: 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB

value: Donated by Dr. RJ White, The Beatson Institute for Cancer Research

value: std

value: Standard input signal for most experiments.

tag: controlid

value: Illumina 2.0, low confidence sequences excluded

tag: replicate


title: Stanford_ChipSeq_H1-hESC_BRCA1_(A300-000A)_IgG-rab

tag: lab

value: Stanford

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: human

tag: cell description

value: embryonic stem cells

tag: cell karyotype

value: normal

value: inner cell mass

value: M

value: No special treatment or protocol applies

value: Rabbit polyclonal recognizing a region between residue 1800 and the C-terminus (residue 1863) of human Breast Cancer Gene 1. Antibody Target:BRCA1

value: Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers.

value: Bethyl Labratories

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_K562_Pol3_std

value: Chromatin IP Sequencing

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

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment description

tag: antibody

value: mouse monoclonal IgG1. Antibody Target:POL3

tag: antibody targetdescription

value: RNA Polymerase III

value: Santa Cruz Biotech

value: std

tag: labversion


title: USC_ChipSeq_GM12878_TR4_std

value: USC

tag: lab description

value: Farnham - University of Southern California

value: ChipSeq

tag: cell

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: Rabbit polyclonal. Antibody Target:TR4

value: (Also:NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus.

tag: antibody vendorname

value: Donated by Dr. J.D.Engel, University of Michigan

tag: antibody vendorid

tag: control

tag: control description

value: Standard input signal for most experiments.

value: Fragmented using Bioruptor, precipitated with StaphA PeakSeq 1.0 (fdr 0.001), samples were 71% and 72% matching in the top 40% overlap analysis.


title: USC_ChipSeq_GM12878_YY1_std

tag: lab

value: Chromatin IP Sequencing

tag: cell organism

value: mesoderm

tag: treatment

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:YY1

value: YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins.

tag: controlid

value: Fragmented using Bioruptor, precipitated with Staph A,

tag: replicate

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: Stanford_ChipSeq_K562_CEBPB_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

tag: cell sex

value: F

tag: treatment description

value: CEBPB

value: Rabbit polyclonal IgG. Antibody Target:CEBPB

value: epitope mapping at the C-terminus of C/EBP-beta of rat origin

value: Santa Cruz Biotech

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_K562_p300_(SC-48343)_IgG-rab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

value: mesoderm

tag: antibody

value: mouse monoclonal raised against amino acids 774-1045 of p300 of human origin. Antibody Target:P300

tag: antibody targetdescription

value: Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein.

tag: antibody vendorname

tag: antibody vendorid


title: Harvard_ChipSeq_HeLa-S3_RPC155_std

tag: lab

value: Harvard

value: Struhl - Harvard University

tag: cell organism

value: cervical carcinoma

value: ectoderm

tag: treatment

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal - Antiserum 1900 was raised by immunizing rabbits with synthetic peptide PKRPLTFDTNEFHIPLVT (residues 1374?1391 of the RPC155 subunit of human pol III) coupled to KLH. Antibody Target:RPC155

value: polymerase (RNA) III (DNA directed) polypeptide A, 155kDa

value: Donated by Dr. RJ White, The Beatson Institute for Cancer Research

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: Harvard_ChipSeq_K562_BRF2_std

tag: datatype

tag: datatype description

tag: cell description

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

value: cancer

value: F

value: Antibody 4295 against Brf2 was raised by immunizing rabbits with keyhole limpet hemocyanin coupled to synthetic peptides VSRSQQRGLRRVRDLC and SDSEIEQYLRTPQEVR, corresponding to human Brf2 residues 66-80 and 385-400, respectively. Antibody Target:BRF2

value: Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB.

tag: controlid

tag: replicate


title: USC_ChipSeq_K562_ZNF274_UCDavis

value: USC

tag: lab description

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell karyotype

tag: cell lineage

value: mesoderm

tag: cell sex

tag: treatment description

value: Mouse polyclonal antibody raised against a partial recombinant ZNF274 (GST-fusion of a.a.420-531 of human ZNF274 protein). Works in IP, WB and ELISA. Antibody Target:ZNF274

value: ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus.

value: ABNOVA

value: UCDavis

value: Input library was prepared at UC Davis.

tag: labversion

value: Fragmented using Bioruptor, precipitated with StaphA

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: Stanford_ChipSeq_K562_GTF2F1_(AB28179)_IgG-rab

tag: lab

value: Stanford

value: Snyder - Stanford University

tag: cell

tag: cell organism

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

value: cancer

value: No special treatment or protocol applies

tag: antibody

value: Rabbit polyclonal to TFIIF - Recombinant full length protein - RAP 74 subunit of TF11F. Antibody Target:GTF2F1

tag: antibody targetdescription

value: RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits:one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_4hr_c-Myc_Harvard_Control

value: Harvard

value: Struhl - Harvard University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: normal

value: ectoderm

value: F

tag: treatment

value: 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl)

value: c-Myc

tag: antibody antibodydescription

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: Santa Cruz Biotech

tag: control

tag: control description

value: input library was prepared at Harvard.


title: Harvard_ChipSeq_GM12878_NF-YA_IgG-mus

tag: lab description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell karyotype

tag: cell lineage

value: mesoderm

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

value: NF-YA

value: Affinity purified rabbit polyclonal raised against amino acids 139-347 of recombinant human NF-YA. Antibody Target:NF-YA

value: NF-YA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif

value: Donated by Dr. R. Mantovani, Universita degli Studi di Milano, Italy

value: missing

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: controlid

tag: replicate


title: USC_ChipSeq_MCF-7_HA-E2F1_UCDavis

tag: lab

value: USC

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: cancer

value: ectoderm

value: F

tag: antibody

value: Mouse Monoclonal antibody HA.11 clone 16B12 was raised against the twelve amino acid peptide CYPYDVPDYASL. This second-generation HA antibody is an excellent substitute for the 12CA5 monoclonal antibody. The HA.11 antibody recognizes the influenza hemagglutinin epitope (YPYDVPDYA) which has been used extensively as a general epitope tag in expression vectors. The extreme specificity of the antibody allows unambiguous identification and quantitative analysis of the tagged protein. The HA.11 antibody recognizes HA epitopes located in the middle of protein sequences as well as at the N- or C-terminus. Antibody Target:HA-E2F1

tag: antibody targetdescription

value: The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus.

value: Covance

value: UCDavis

value: Input library was prepared at UC Davis.

tag: labversion

value: MCF-7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, precipitated with StaphA and an antibody to the  HA tag,

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: Stanford_ChipSeq_GM12878_TNFa_NFKB_IgG-rab

treatment_protocol: TNFa

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: mesoderm

tag: treatment

value: TNFa

value: human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder)

value: NFKB

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:NFKB

value: Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFkB p65 of m, r and h origin by WB, IP, IF and ELISA

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: USC_ChipSeq_HeLa-S3_E2F6_std

value: USC

tag: lab description

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: cervical carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

value: Rabbit polyclonal IgG, epitope corresponding to a.a. 232-281 mapping at the C-terminus of E2F-6 of human origin. Antibody Target:E2F6

value: This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains:a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq).

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: Fragmented using Bioruptor, precipitated with StaphA


title: Yale_ChipSeq_K562_IFNa30_Pol2_std

tag: lab

value: Yale

value: Snyder - Yale University

tag: cell

tag: cell organism

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

value: mesoderm

value: 30 m of Interferon alpha (Snyder)

tag: antibody

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

value: Covance

tag: controlid

value: Illumina 2.0, low confidence sequences excluded

tag: replicate


title: Yale_ChipSeq_K562_IFNa30_STAT1_std

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

tag: cell description

value: cancer

tag: treatment

tag: antibody antibodydescription

value: rabbit polyclonal to STAT1 (alpha) p-91 (C-24). Antibody Target:STAT1

value: transcription factor, activated by interferon signalling

value: Santa Cruz Biotech

tag: labversion


title: Yale_ChipSeq_K562_IFNa30_STAT2_std

tag: lab description

tag: cell karyotype

tag: cell lineage

tag: cell sex

value: F

value: Rabbit polyclonal. Antibody Target:STAT2

value: peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X

tag: antibody vendorname

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.


title: Yale_ChipSeq_K562_IFNa6h_STAT2_std

tag: lab

value: Yale

value: Snyder - Yale University

tag: cell

tag: cell organism

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

value: mesoderm

tag: treatment description

value: Interferon alpha treatment - 6 hours (Snyder)

tag: control

tag: control description


title: USC_ChipSeq_H1-hESC_CtBP2_UCDavis

value: USC

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

value: No special treatment or protocol applies

tag: antibody

value: mouse monoclonal. Antibody Target:CtBP2

tag: antibody targetdescription

value: C-terminal binding protein 2

value: BD Biosciences

value: UCDavis

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: USC_ChipSeq_K562_KAP1_UCDavis

tag: lab description

value: Chromatin IP Sequencing

value: human

tag: cell description

tag: cell karyotype

value: cancer

value: F

tag: treatment

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:KAP1

value: KRAB Associated Protein 1, helps regulate transcriptional repression

value: Abcam


title: Yale_ChipSeq_K562_IFNa6h_STAT1_std

tag: lab

value: Yale

value: Snyder - Yale University

value: ChipSeq

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

tag: cell lineage

value: mesoderm

tag: cell sex

value: Interferon alpha treatment - 6 hours (Snyder)

value: rabbit polyclonal to STAT1 (alpha) p-91 (C-24). Antibody Target:STAT1

value: transcription factor, activated by interferon signalling

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.


title: Yale_ChipSeq_K562_IFNa6h_c-Jun_std

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: treatment description

value: c-Jun

value: Rabbit polyclonal to amino acids 1-79 mapping at the N-terminus of c-Jun p39 of human origin. Antibody Target:c-Jun

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

tag: control

tag: control description

tag: labversion

value: remapped from hg18


title: USC_ChipSeq_PBDE_GATA-1_UCDavis

source_name: PBDE

value: USC

value: Farnham - University of Southern California

tag: datatype

tag: datatype description

value: PBDE

value: peripheral blood-derived erythroblasts

value: M

value: No special treatment or protocol applies

tag: antibody

value: Anti-GATA-1 rabbit polyclonal antibody was generated by using a purified GST fusion to amino acids 1-89 of mouse GATA-1. Antibody Target:GATA1

tag: antibody targetdescription

value: GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells.

value: Donated by Dr. E.H. Bresnick, UW Madison

value: UCDavis

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: USC_ChipSeq_PBDE_Pol2_UCDavis

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: mesoderm

tag: treatment

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance


title: USC_ChipSeq_Raji_Input_UCDavis

source_name: Raji

value: USC

tag: cell

value: Raji

value: human

value: B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID:14086209)

tag: cell karyotype

value: cancer

tag: cell lineage

tag: cell sex

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: USC_ChipSeq_HeLa-S3_ZNF274_UCDavis

value: Farnham - University of Southern California

tag: cell organism

value: cervical carcinoma

value: ectoderm

value: F

tag: treatment description

value: No special treatment or protocol applies

value: Mouse polyclonal antibody raised against a partial recombinant ZNF274 (GST-fusion of a.a.420-531 of human ZNF274 protein). Works in IP, WB and ELISA. Antibody Target:ZNF274

value: ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus.

tag: antibody vendorname

value: ABNOVA

tag: antibody vendorid

tag: control

tag: control description


title: USC_ChipSeq_Raji_Pol2_UCDavis

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mesoderm

value: M

tag: antibody

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

value: UCDavis

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: Yale_ChipSeq_K562_IFNg6h_c-Jun_std

tag: lab

value: Yale

tag: lab description

value: Snyder - Yale University

tag: cell

value: human

tag: cell description

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

value: cancer

tag: treatment

value: Interferon gamma treatment - 6 hours (Snyder)

value: c-Jun

tag: antibody antibodydescription

value: Rabbit polyclonal to amino acids 1-79 mapping at the N-terminus of c-Jun p39 of human origin. Antibody Target:c-Jun

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

value: Santa Cruz Biotech

value: std

value: Standard input signal for most experiments.

tag: labversion

value: remapped from hg18


title: Yale_ChipSeq_K562_IFNa6h_Pol2_std

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

tag: cell karyotype

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment description

value: Interferon alpha treatment - 6 hours (Snyder)

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody vendorname

value: Covance


title: Yale_ChipSeq_K562_IFNg6h_Pol2_std

value: Yale

value: Snyder - Yale University

tag: datatype

tag: datatype description

value: human

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

tag: antibody

value: RNA Polymerase II

tag: antibody vendorid

tag: control

tag: control description


title: USC_ChipSeq_U2OS_SETDB1_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: cell

value: osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID:6081590)

value: cancer

value: No special treatment or protocol applies

value: Rabbit polyclonal. Antibody Target:SETDB1

tag: antibody targetdescription

value: SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure

value: Proteintech Group

value: UCDavis

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: Stanford_ChipSeq_GM19099_TNFa_Input_IgG-rab

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

tag: cell description

value: lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

tag: cell karyotype

value: normal

value: mesoderm

value: F

tag: treatment

value: TNFa

value: human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder)

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_36hr_STAT3_std

value: Harvard

value: Struhl - Harvard University

tag: datatype

tag: datatype description

value: human

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell lineage

value: ectoderm

tag: cell sex

tag: treatment description

value: (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers)

tag: antibody antibodydescription

value: Rabbit polyclonal; epitope mapping at the C-terminus of Stat3 of mouse origin. Antibody Target:STAT3

value: Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis.

tag: antibody vendorname

value: Santa Cruz Biotech

value: std

value: Standard input signal for most experiments.


title: Stanford_ChipSeq_GM18951_TNFa_Input_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment:Epstein-Barr Virus transformed

value: normal

value: mesoderm

value: F

value: TNFa

value: human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder)

tag: antibody

tag: control

tag: control description


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_36hr_Pol2_std

value: Harvard

value: Struhl - Harvard University

tag: cell organism

value: human

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell karyotype

value: ectoderm

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

value: Covance

tag: antibody vendorid

tag: controlid

tag: replicate


title: Stanford_ChipSeq_GM12891_TNFa_Input_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

tag: cell lineage

tag: cell sex

value: M

tag: treatment

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: labversion

value: remapped from hg18


title: Stanford_ChipSeq_GM18526_TNFa_Input_IgG-rab

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment:Epstein-Barr Virus transformed

value: normal

value: mesoderm

value: F

value: TNFa

tag: treatment description

value: human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder)

tag: antibody

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: Stanford_ChipSeq_GM12892_TNFa_Input_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: cell organism

value: human

tag: cell description

tag: cell karyotype

tag: control

tag: control description


title: Stanford_ChipSeq_GM19193_TNFa_Input_IgG-rab

tag: datatype

value: lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: Input

tag: controlid

tag: replicate


title: Stanford_ChipSeq_GM10847_TNFa_Input_IgG-rab

tag: datatype description

value: lymphoblastoid, International HapMap Project, CEPH/Utah, treatment:Epstein-Barr Virus transformed

tag: cell lineage

tag: cell sex

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: IgG-rab


title: Stanford_ChipSeq_GM12878_Input_IgG-rab

value: ChipSeq

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: treatment

value: No special treatment or protocol applies

tag: antibody description

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: USC_ChipSeq_MCF-7_Input_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

value: Chromatin IP Sequencing

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: cancer

value: ectoderm

value: UCDavis

value: Input library was prepared at UC Davis.

tag: labversion

value: MCF7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, crosslinks were reversed at 67*C overnight and Input was Qiagen purified,

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: Stanford_ChipSeq_HepG2_forskolin_Input_std

treatment_protocol: forskolin

value: Stanford

value: Snyder - Stanford University

tag: cell

tag: cell organism

value: human

value: hepatocellular carcinoma

value: endoderm

value: M

value: forskolin

tag: treatment description

value: low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder)

tag: antibody

value: Input

value: std

value: Standard input signal for most experiments.

value: Illumina 2.0, low confidence sequences excluded


title: Harvard_ChipSeq_MCF10A-Er-Src_EtOH_0.01pct_c-Myc_Harvard_Control

value: Harvard

value: Struhl - Harvard University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell karyotype

value: normal

value: ectoderm

value: F

value: 36 h with 0.01% Ethanol (Snyder)

value: c-Myc

tag: antibody antibodydescription

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

tag: antibody targetdescription

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: control description

value: input library was prepared at Harvard.


title: Stanford_ChipSeq_HepG2_insulin_Input_std

treatment_protocol: insulin

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

value: human

value: hepatocellular carcinoma

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment

value: insulin

value: DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder)

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: std

tag: controlid

tag: replicate


title: Stanford_ChipSeq_K562_COREST_(sc-30189)_IgG-rab

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

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

value: mesoderm

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit polyclonal, epitope corresponding to amino acids 246-310 mapping within an internal region of CoREST of human origin recommended for detection of CoREST of mouse, rat and human origin. Antibody Target:COREST (sc30189)

value: Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells.  In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates.

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: USC_ChipSeq_MCF-7_GATA3_(SC-269)_UCDavis

value: USC

value: Farnham - University of Southern California

value: human

tag: cell description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

value: ectoderm

tag: antibody antibodydescription

value: Mouse monoclonal IgG raised against human recombinant GATA-3 (amino acids 1-264). Antibody Target:GATA3

tag: antibody targetdescription

value: This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: UCDavis

value: Input library was prepared at UC Davis.


title: Stanford_ChipSeq_HepG2_Mxi1_(AF4185)_std

value: Stanford

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: hepatocellular carcinoma

tag: cell lineage

value: endoderm

tag: cell sex

value: M

value: Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target:Mxi1

value: Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX

value: R&D Systems

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: Stanford_ChipSeq_A549_BHLHE40_IgG-rab

tag: lab

tag: lab description

value: human

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: cancer

tag: treatment

value: No special treatment or protocol applies

value: Dec-1(S-8) is a mouse monoclonal IgG2b antibody raised against recombinant DEC1 of human origin. Recommended for detection of DEC1 of m and h origin by WB, IP and ELISA. Antibody Target:BHLHE40

value: This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differe

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid

tag: replicate


title: Harvard_ChipSeq_MCF10A-Er-Src_EtOH_0.01pct_c-Fos_Harvard_Control

value: Harvard

value: Struhl - Harvard University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: normal

value: ectoderm

value: F

tag: treatment description

value: 36 h with 0.01% Ethanol (Snyder)

tag: antibody

value: c-Fos

value: Rabbit polyclonal to amino acids 210-335 mapping at the C-terminus of c-Fos of human origin. Antibody Target:c-Fos

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

value: Santa Cruz Biotech

value: input library was prepared at Harvard.


title: USC_ChipSeq_GM12878_IKZF1_(IkN)_(UCLA)_std

value: USC

value: Farnham - University of Southern California

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell karyotype

value: mesoderm

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a recombinant protein encompassing the amino-terminus of the murine IKZF1 protein. Antibody Target:IKZF1

tag: antibody targetdescription

value: IKAROS family zinc finger 1 (Ikaros or IKZF1) is a C2H2 zinc finger transcription factor that is associated with various chromatin-modifying complexes and is suggested to play a role in the development of lymphocytes, B- and T-cells.

tag: antibody vendorname

value: From the laboratory of Stephen Smale, UCLA

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.


title: Harvard_ChipSeq_HeLa-S3_BRF2_std

value: Harvard

value: Struhl - Harvard University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: cervical carcinoma

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

value: Antibody 4295 against Brf2 was raised by immunizing rabbits with keyhole limpet hemocyanin coupled to synthetic peptides VSRSQQRGLRRVRDLC and SDSEIEQYLRTPQEVR, corresponding to human Brf2 residues 66-80 and 385-400, respectively. Antibody Target:BRF2

value: Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB.

value: Donated by Dr. RJ White, The Beatson Institute for Cancer Research

tag: control


title: Stanford_ChipSeq_H1-hESC_JunD_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: human

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

tag: treatment

value: No special treatment or protocol applies

value: JunD

value: rabbit polyclonal IgG. Antibody Target:JunD

value: The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq)

value: Santa Cruz Biotech

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid


title: Stanford_ChipSeq_HeLa-S3_Znf143_(16618-1-AP)_IgG-rab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: cervical carcinoma

value: cancer

value: ectoderm

value: F

tag: treatment description

value: Rabbit polyclonal against human ZNF143 (amino acids 283-626)-6his fusion protein. Antibody Target:Znf143

value: Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8

value: Proteintech

tag: replicate


title: Stanford_ChipSeq_K562_NF-YA_std

value: Stanford

value: Snyder - Stanford University

value: human

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

tag: cell karyotype

value: mesoderm

tag: antibody

value: NF-YA

tag: antibody antibodydescription

value: Affinity purified rabbit polyclonal raised against amino acids 139-347 of recombinant human NF-YA. Antibody Target:NF-YA

tag: antibody targetdescription

value: NF-YA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif

tag: antibody vendorname

value: Donated by Dr. R. Mantovani, Universita degli Studi di Milano, Italy

value: missing

value: std

value: Standard input signal for most experiments.


title: Stanford_ChipSeq_HeLa-S3_CHD2_(AB68301)_IgG-rab

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: cervical carcinoma

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: No special treatment or protocol applies

value: Rabbit polyclonal to CHD2 Synthetic peptide derived from within residues 1250 - 1350 of Human CHD2. Antibody Target:CHD2

value: CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template.

value: Abcam

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_GM12878_BHLHE40_(NB100-1800)_IgG-mus

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: mesoderm

value: F

tag: treatment

value: Rabbit polyclonal, maps to a region between residues 350 and the C-terminus (residue 412). Antibody Target:BHLHE40

value: This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation.

value: Novus

tag: control

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.


title: Yale_ChipSeq_K562_IFNa30_c-Myc_std

value: Yale

value: Snyder - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

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

value: cancer

tag: treatment description

value: 30 m of Interferon alpha (Snyder)

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: Santa Cruz Biotech

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: Yale_ChipSeq_K562_IFNg6h_Input_std

value: human

tag: cell karyotype

value: mesoderm

value: F

value: Interferon gamma treatment - 6 hours (Snyder)

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: Stanford_ChipSeq_GM12878_Mxi1_(AF4185)_IgG-mus

value: Stanford

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

tag: cell lineage

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target:Mxi1

tag: antibody targetdescription

value: Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX

tag: antibody vendorname

value: R&D Systems

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: replicate


title: USC_ChipSeq_NT2-D1_YY1_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

value: human

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

value: cancer

value: inner cell mass

tag: cell sex

value: M

tag: treatment

value: Rabbit polyclonal. Antibody Target:YY1

value: YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins.

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

value: Fragmented using Bioruptor, precipitated with StaphA

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: Stanford_ChipSeq_GM15510_TNFa_Input_IgG-rab

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment:Epstein-Barr Virus transformed

tag: cell karyotype

value: normal

value: mesoderm

value: U

value: TNFa

tag: treatment description

value: human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder)

tag: antibody

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: USC_ChipSeq_NT2-D1_SUZ12_UCDavis

value: USC

value: Farnham - University of Southern California

tag: datatype

tag: datatype description

value: human

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

value: cancer

tag: cell lineage

value: inner cell mass

value: M

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:SUZ12

tag: antibody targetdescription

value: Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex

tag: antibody vendorname

value: Antibody made by Farnham lab

value: UCDavis

value: Input library was prepared at UC Davis.

value: Fragmented using Bioruptor, precipitated with StaphA

tag: replicate


title: Stanford_ChipSeq_K562_NF-YB_std

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

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

value: mesoderm

tag: cell sex

value: F

tag: treatment

value: NF-YB

value: Affinity purified rabbit polyclonal raised against recombinant full length human NF-YB. Antibody Target:NF-YB

value: NF-YB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif

value: Donated by Dr. R. Mantovani, Universita degli Studi di Milano, Italy

tag: antibody vendorid

value: missing

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: Yale_ChipSeq_K562_XRCC4_std

value: Yale

value: Snyder - Yale University

tag: cell

tag: cell organism

value: human

tag: cell description

tag: cell karyotype

value: cancer

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit polyclonal. Antibody Target:XRCC4

value: Recognizes the XRCC4 protein (X ray cross complementation protein). XRCC4 is a ubiquitous protein reported to have a role in DNA double-stranded break repair and in V(D)J recombination.

value: Abcam

value: Contains incomplete fastq files


title: Yale_ChipSeq_K562_IFNg30_Input_std

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

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

tag: cell lineage

value: mesoderm

value: F

value: Interferon gamma treatment - 30 minutes (Snyder)

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid


title: Yale_ChipSeq_K562_IFNa30_Input_std

tag: lab

value: Yale

tag: lab description

value: 30 m of Interferon alpha (Snyder)

value: std

value: Standard input signal for most experiments.


title: Yale_ChipSeq_K562_IFNa6h_Input_std

value: Snyder - Yale University

value: human

value: cancer

tag: cell sex

tag: treatment

value: Interferon alpha treatment - 6 hours (Snyder)


title: Harvard_ChipSeq_GM12878_SPT20_std

value: Harvard

value: Struhl - Harvard University

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal anti-SPT20 antibody (3006), Immunogen: C-terminal region of mSPT20 (330-531 aa) is cloned in pET28b and over expressed in E. Coli. Protein was purified on Ni-NTA exchange column. Sequence:mSPT20 (330-531 amino acids). Antibody Target:SPT20

tag: antibody targetdescription

value: Also known as FAM48A or P38IP.   It is a component of SAGA complex.  Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail.

tag: antibody vendorname

value: Laszlo Tora

tag: antibody vendorid

value: missing

tag: control

tag: replicate


title: Stanford_ChipSeq_GM18505_TNFa_Input_IgG-rab

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

tag: cell karyotype

value: mesoderm

value: F

value: TNFa

tag: treatment description

value: human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder)

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: Harvard_ChipSeq_MCF10A-Er-Src_EtOH_0.01pct_4hr_Input_std

tag: lab

value: Harvard

value: Struhl - Harvard University

tag: datatype

tag: datatype description

value: human

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: normal

tag: cell lineage

value: ectoderm

value: 4 h with 0.01% Ethanol (Snyder)

tag: antibody

tag: antibody description

value: std

value: Standard input signal for most experiments.

tag: controlid


title: Yale_ChipSeq_GM12878_Input_std

value: Yale

tag: lab description

value: Snyder - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: mesoderm

tag: cell sex

value: F

tag: treatment

value: No special treatment or protocol applies


title: Harvard_ChipSeq_GM12878_GCN5_std

value: Harvard

tag: cell

tag: antibody antibodydescription

value: Rabbit polyclonal anti-GCN5 antibody (2676), Immunogen :synthetic peptide coupled to Ovalbumin (sequence-MAEPSQAPTPAPAAQPRPLC). Antibody Target:GCN5

tag: antibody targetdescription

value: KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4

tag: antibody vendorname

value: Laszlo Tora

tag: antibody vendorid

value: Missing

tag: control

tag: replicate


title: Yale_ChipSeq_K562_c-Jun_std

tag: lab

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: cancer

tag: treatment description

value: c-Jun

value: Rabbit polyclonal to amino acids 1-79 mapping at the N-terminus of c-Jun p39 of human origin. Antibody Target:c-Jun

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

value: Santa Cruz Biotech

tag: control description


title: Harvard_ChipSeq_HeLa-S3_ZZZ3_std

value: Struhl - Harvard University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: cervical carcinoma

tag: cell lineage

value: ectoderm

tag: antibody

value: Rabbit Polyclonal anti-human ZZZ3, Immunogen:Synthetic peptide coupled to Ovalbumin (Name PI130, sequence CGNNNGRTTDLKQQSTRESW). Antibody Target:ZZZ3

value: ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains.

value: Lazlo Tora, Institut de G?n?tique et de Biologie Mol?culaire et Cellulaire

value: std

value: Standard input signal for most experiments.

tag: controlid


title: Harvard_ChipSeq_HeLa-S3_NF-YB_IgG-rab

value: Harvard

tag: lab description

tag: cell

value: human

tag: cell sex

value: F

tag: treatment

value: No special treatment or protocol applies

value: NF-YB

tag: antibody antibodydescription

value: Affinity purified rabbit polyclonal raised against recombinant full length human NF-YB. Antibody Target:NF-YB

value: NF-YB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif

value: Donated by Dr. R. Mantovani, Universita degli Studi di Milano, Italy

value: missing

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Yale_ChipSeq_GM12878_c-Fos_std

value: Yale

value: Snyder - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: mesoderm

value: c-Fos

value: Rabbit polyclonal to amino acids 210-335 mapping at the C-terminus of c-Fos of human origin. Antibody Target:c-Fos

tag: antibody targetdescription

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: replicate


title: USC_ChipSeq_HCT-116_Pol2_UCDavis

tag: lab

value: USC

value: Farnham - University of Southern California

tag: cell organism

value: human

tag: cell description

value: colorectal carcinoma (PMID:7214343)

tag: cell karyotype

value: cancer

value: endoderm

value: M

tag: treatment description

value: No special treatment or protocol applies

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: UCDavis

value: Input library was prepared at UC Davis.

tag: labversion

value: Fragmented using Bioruptor, precipitated with protein A agarose beads, PeakSeq 1.0 (fdr 0.001) Illumina 2.0, low confidence sequences excluded


title: USC_ChipSeq_NT2-D1_Input_UCDavis

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell lineage

value: inner cell mass

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control description

tag: controlid


title: Stanford_ChipSeq_HepG2_Max_IgG-rab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: cell

value: human

value: hepatocellular carcinoma

tag: cell sex

tag: treatment

value: Max

tag: antibody antibodydescription

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target:Max

tag: antibody targetdescription

value: The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq).

tag: antibody vendorname

value: Santa Cruz Biotech

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_K562_CTCF_(SC-15914)_IgG-rab

tag: lab

tag: cell organism

tag: cell description

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

tag: cell karyotype

value: cancer

value: mesoderm

value: F

value: No special treatment or protocol applies

value: Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target:CTCF

value: Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.

tag: antibody vendorid

tag: control

tag: replicate


title: Stanford_ChipSeq_K562_Pol2(phosphoS2)_IgG-rab

value: Stanford

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell lineage

tag: treatment description

tag: antibody

value: Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target:POL2S2

value: RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain.

value: Abcam


title: Stanford_ChipSeq_K562_p300_IgG-rab

tag: lab description

value: Snyder - Stanford University

tag: cell

value: human

tag: cell sex

value: Rabbit Polyclonal. Antibody Target:P300

tag: control description

tag: controlid


title: Stanford_ChipSeq_IMR90_CTCF_(SC-15914)_IgG-rab

tag: lab

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: normal

value: endoderm

tag: treatment

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

value: Santa Cruz Biotech

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_36hr_E2F4_Harvard_Control

value: Harvard

value: Struhl - Harvard University

tag: cell organism

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell karyotype

value: ectoderm

value: F

value: (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers)

value: rabbit polyclonal. Antibody Target:E2F4

value: mapping at the C-terminus of E2F4 of human origin

tag: antibody vendorid

tag: control

value: input library was prepared at Harvard.


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_12hr_STAT3_Harvard_Control

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

tag: cell lineage

tag: treatment description

value: 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl)

value: Rabbit polyclonal; epitope mapping at the C-terminus of Stat3 of mouse origin. Antibody Target:STAT3

value: Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis.

tag: replicate


title: Stanford_ChipSeq_HeLa-S3_Max_IgG-rab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: cell

value: cervical carcinoma

value: cancer

tag: cell sex

value: No special treatment or protocol applies

tag: antibody

value: Max

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target:Max

value: The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq).

value: Santa Cruz Biotech

value: IgG-rab

tag: control description


title: Stanford_ChipSeq_IMR90_MafK_(ab50322)_IgG-rab

tag: lab

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: normal

value: endoderm

value: F

tag: treatment

tag: antibody antibodydescription

value: Rabbit polyclonal. Raised against synthetic peptide:TTNPKPNKALKVKKEA conjugated to KLH by a C-terminal Cysteine residue linker, corresponding to amino acids 2-17 of Human MAFK. Antibody Target:MafK

tag: antibody targetdescription

value: NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites.

value: Abcam

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid


title: Yale_ChipSeq_K562_IFNa6h_c-Myc_std

value: Yale

value: Snyder - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: mesoderm

value: Interferon alpha treatment - 6 hours (Snyder)

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

tag: antibody vendorname

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_12hr_c-Fos_Harvard_Control

value: Harvard

value: Struhl - Harvard University

tag: datatype

tag: datatype description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: normal

tag: cell lineage

value: ectoderm

value: F

tag: treatment description

value: 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl)

value: c-Fos

value: Rabbit polyclonal to amino acids 210-335 mapping at the C-terminus of c-Fos of human origin. Antibody Target:c-Fos

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

value: Santa Cruz Biotech

tag: control

value: input library was prepared at Harvard.

tag: replicate


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_4hr_c-Fos_Harvard_Control

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

tag: cell sex

value: 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl)

tag: antibody

tag: control description


title: Yale_ChipSeq_K562_c-Myc_std

value: Yale

value: Snyder - Yale University

tag: cell organism

tag: cell description

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

value: cancer

value: mesoderm

tag: treatment

value: No special treatment or protocol applies

value: c-Myc

tag: antibody antibodydescription

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

tag: antibody targetdescription

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: std

value: Standard input signal for most experiments.

tag: controlid


title: Stanford_ChipSeq_HUVEC_Pol2_std

source_name: HUVEC

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

value: HUVEC

value: umbilical vein endothelial cells

tag: cell karyotype

value: normal

value: U

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid


title: Harvard_ChipSeq_MCF10A-Er-Src_4OHTAM_1uM_36hr_c-Fos_Harvard_Control

tag: lab

value: Harvard

value: Struhl - Harvard University

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell lineage

value: ectoderm

value: F

tag: treatment description

value: (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers)

value: c-Fos

value: Rabbit polyclonal to amino acids 210-335 mapping at the C-terminus of c-Fos of human origin. Antibody Target:c-Fos

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

value: Santa Cruz Biotech

tag: control

value: input library was prepared at Harvard.

tag: replicate


title: Harvard_ChipSeq_K562_GTF2B_std

tag: lab description

tag: cell

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

value: cancer

value: mesoderm

tag: cell sex

value: No special treatment or protocol applies

tag: antibody

value: rabbit polyclonal IgG, 200 ?g/ml. epitope mapping near the C-terminus of TFIIB of human origin. Antibody Target:GTF2B

value: DNA- binding general transcription factor

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labversion

value: remapped from hg18


title: Yale_ChipSeq_K562_NF-E2_std

value: Yale

value: Snyder - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

tag: treatment

tag: antibody antibodydescription

value: Rabbit polyclonal, epitope mapping at the C-terminus of NF-E2 of mouse origin and recommended for detection of protein of rat, mouse and human origin. Antibody Target:NF-E2

tag: antibody targetdescription

value: Nuclear factor, erythroid-derived 2

tag: controlid


title: Harvard_ChipSeq_K562_ATF3_std

tag: lab

value: Harvard

value: Struhl - Harvard University

tag: datatype

tag: datatype description

tag: cell karyotype

value: F

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of ATF3 of human origin. Antibody Target:ATF3

value: Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid


title: Stanford_ChipSeq_GM10847_Pol2_IgG-mus

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: cell

value: lymphoblastoid, International HapMap Project, CEPH/Utah, treatment:Epstein-Barr Virus transformed

value: normal

tag: cell lineage

value: mesoderm

tag: treatment description

value: No special treatment or protocol applies

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: control

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

value: remapped from hg18, Data paired with GM10847_IgG_Control.

tag: replicate


title: Stanford_ChipSeq_K562_IFNg30_Pol2_std

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

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

value: cancer

tag: cell sex

value: Interferon gamma treatment - 30 minutes (Snyder)

tag: antibody

value: std

tag: control description

value: Standard input signal for most experiments.


title: Stanford_ChipSeq_GM12891_Input_IgG-mus

tag: lab

value: Stanford

value: Snyder - Stanford University

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: normal

value: M

tag: treatment

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid


title: Stanford_ChipSeq_HeLa-S3_Pol2(phosphoS2)_IgG-rab

tag: datatype

tag: datatype description

value: cervical carcinoma

tag: cell karyotype

value: ectoderm

value: F

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target:POL2S2

tag: antibody targetdescription

value: RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain.

tag: antibody vendorname

value: Abcam

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_K562_COREST_(ab24166)_IgG-rab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

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

value: cancer

tag: cell lineage

value: mesoderm

tag: treatment description

value: Synthetic peptide conjugated to KLH derived from within residues 400 to the C-terminus of Human CoREST.   Note:This antibody has since been discontinued.  Full product information is attached as part of validation document. Antibody Target:COREST_(ab24166)

value: Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells.  In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates.

tag: antibody vendorid

tag: control


title: Stanford_ChipSeq_HeLa-S3_SMC3_(ab9263)_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: cell organism

tag: cell description

value: cervical carcinoma

tag: cell sex

tag: antibody

value: Rabbit polyclonal raised against synthetic peptide representing a portion within the last 100 amino acids of the human Structural Maintenance of Chromosomes-3 conjugated to KLH. Antibody Target:SMC3

value: Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex.  The cohesin complex is required for the cohesion of sister chromatids after DNA replication.

tag: control description

tag: replicate


title: Stanford_ChipSeq_H1-hESC_Input_IgG-rab

tag: lab

tag: datatype

tag: datatype description

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

tag: treatment

value: No special treatment or protocol applies

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid


title: Yale_ChipSeq_HeLa-S3_Pol2_std

value: Yale

tag: lab description

value: Snyder - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

tag: cell karyotype

value: ectoderm

value: F

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

value: std

value: Standard input signal for most experiments.


title: Stanford_ChipSeq_H1-hESC_USF2_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: cell organism

tag: cell description

value: embryonic stem cells

value: normal

tag: cell lineage

value: inner cell mass

tag: treatment description

value: Mouse monoclonal. Immunogen corresponds to amino acids 1-101 of Human USF2. Antibody Target:USF2

value: Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3').

value: abcam

tag: antibody vendorid

tag: control

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_GM12878_Pol2_IgG-mus

tag: lab

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: mesoderm

tag: cell sex

value: No special treatment or protocol applies

tag: antibody

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded. Data paired with GM12878_IgG_Control.

tag: replicate


title: Stanford_ChipSeq_GM12878_BRCA1_(A300-000A)_IgG-mus

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype description

tag: cell

tag: cell karyotype

value: F

tag: treatment

value: Rabbit polyclonal recognizing a region between residue 1800 and the C-terminus (residue 1863) of human Breast Cancer Gene 1. Antibody Target:BRCA1

value: Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers.

value: Bethyl Labratories

tag: controlid


title: Stanford_ChipSeq_H1-hESC_RFX5_(200-401-194)_IgG-rab

tag: cell organism

tag: cell description

value: embryonic stem cells

value: normal

tag: cell lineage

value: inner cell mass

value: M

tag: antibody antibodydescription

value: Rabbit polyclonal against RFX5 peptide corresponding to a region at amino acids 320 to 494 of the human protein conjugated to Keyhole Limpet Hemocyanin. Antibody Target:RFX5

tag: antibody targetdescription

value: Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters

tag: antibody vendorname

value: Rockland Immunochemicals

value: IgG-rab


title: Stanford_ChipSeq_H1-hESC_Rad21_IgG-rab

tag: lab

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

value: Rabbit polyclonal. Antibody Target:RAD21

value: Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14

value: Abcam

tag: antibody vendorid

tag: control

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_GM12878_EBF1_(SC-137065)_std

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: mesoderm

value: F

tag: antibody

value: Mouse monoclonal IgG, raised against a.a. 1-300 mapping at the N-terminus of EBF of human origin. Antibody Target:EBF1

value: Early B-cell factor 1.  Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity).

value: Santa Cruz Biotech

value: std

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: Stanford_ChipSeq_GM12878_CHD2_(AB68301)_IgG-mus

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell karyotype

value: normal

tag: treatment

value: Rabbit polyclonal to CHD2 Synthetic peptide derived from within residues 1250 - 1350 of Human CHD2. Antibody Target:CHD2

value: CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template.

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: controlid


title: USC_ChipSeq_K562_GATA-2_UCDavis

value: USC

value: Farnham - University of Southern California

value: human

tag: cell description

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

value: cancer

tag: cell lineage

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:GATA2

tag: antibody targetdescription

value: GATA binding protein 2

tag: antibody vendorname

value: Donated by Dr. E.H. Bresnick, UW Madison

value: UCDavis

value: Input library was prepared at UC Davis.

tag: labversion

value: Fragmented using Bioruptor, precipitated with StaphA

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: USC_ChipSeq_K562_TR4_UCDavis

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: mesoderm

tag: cell sex

value: F

tag: treatment description

value: Rabbit polyclonal. Antibody Target:TR4

value: (Also:NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus.

value: Donated by Dr. J.D.Engel, University of Michigan

tag: antibody vendorid

tag: control

value: Fragmented using Bioruptor, precipitated with protein A agarose beads,


title: Harvard_ChipSeq_K562_NELFe_std

value: Harvard

value: Struhl - Harvard University

tag: datatype description

tag: cell

tag: cell organism

value: human

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

tag: cell karyotype

value: cancer

tag: antibody

value: NELFe

value: NELFe (RDBP). Antibody Target:NELFe

value: NELFe (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation.

value: Santa Cruz Biotech

value: std

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: Harvard_ChipSeq_K562_SIRT6_std

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

tag: cell lineage

value: mesoderm

tag: treatment

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:SIRT6

tag: antibody targetdescription

value: A synthetic peptide made to an internal region of the human SIRT6 protein

tag: antibody vendorname

value: Abcam

tag: controlid

value: fragmented with both a probe sonicator and a Misonix sonicator, and precipitated with protein A sepharose beads


title: USC_ChipSeq_HeLa-S3_AP-2gamma_std

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: human

value: cervical carcinoma

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: Rabbit polyclonal - AP-2Y (H-77) is a rabbit polyclonal antibody raised against amino acids 145-221 mapping with in an internal region of AP-2Y of human origin. Antibody Target:AP-2gamma

value: Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes.  AP-2 factors bind to the consensus sequence 5'-GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development.  They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC.

tag: labversion

value: Fragmented using Bioruptor, precipitated with StaphA

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: USC_ChipSeq_K562_YY1_UCDavis

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

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

tag: cell karyotype

value: cancer

tag: antibody

value: Rabbit polyclonal. Antibody Target:YY1

value: YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins.

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

value: UCDavis

value: Input library was prepared at UC Davis.

value: Fragmented using Bioruptor, precipitated with protein G magnetic beads,


title: Harvard_ChipSeq_K562_RPC155_std

value: Harvard

value: Struhl - Harvard University

value: human

tag: cell description

tag: cell lineage

value: mesoderm

tag: treatment

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal - Antiserum 1900 was raised by immunizing rabbits with synthetic peptide PKRPLTFDTNEFHIPLVT (residues 1374?1391 of the RPC155 subunit of human pol III) coupled to KLH. Antibody Target:RPC155

tag: antibody targetdescription

value: polymerase (RNA) III (DNA directed) polypeptide A, 155kDa

value: Donated by Dr. RJ White, The Beatson Institute for Cancer Research

value: std

tag: control description

value: Standard input signal for most experiments.

value: Illumina 2.0, low confidence sequences excluded, fragmented with both a probe sonicator and a Misonix sonicator, and precipitated with protein A sepharose beads

tag: replicate


title: USC_ChipSeq_HeLa-S3_AP-2alpha_std

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: cervical carcinoma

value: cancer

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: Rabbit polyclonal - AP-2alpha (H-79) is a rabbit polyclonal antibody raised against amino acids 130-209 mapping within an internal region of AP-2alpha of human origin. Antibody Target:AP-2alpha

value: Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes.  AP-2 factors bind to the consensus sequence 5' -GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development.  They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC.  AP-2alpha is the only AP-2 protein required for early morphogenesis of the lens vesicle (by similarity).

tag: antibody vendorname

tag: controlid

value: Fragmented using Bioruptor, precipitated with StaphA

value: PeakSeq1.0 (fdr 0.001)


title: USC_ChipSeq_HeLa-S3_TR4_std

tag: datatype description

tag: cell

tag: cell organism

value: human

tag: cell karyotype

value: No special treatment or protocol applies

tag: antibody

value: Rabbit polyclonal. Antibody Target:TR4

value: (Also:NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus.

value: Donated by Dr. J.D.Engel, University of Michigan

tag: labversion

value: Fragmented using Bioruptor, precipitated with protein A agarose beads,

tag: softwareversion


title: USC_ChipSeq_HeLa-S3_E2F4_std

value: USC

value: Farnham - University of Southern California

tag: cell description

tag: cell lineage

tag: treatment

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:E2F4

tag: antibody targetdescription

value: mapping at the C-terminus of E2F4 of human origin

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

value: std

value: Standard input signal for most experiments.


title: USC_ChipSeq_HeLa-S3_HA-E2F1_std

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: cervical carcinoma

value: cancer

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: Mouse Monoclonal antibody HA.11 clone 16B12 was raised against the twelve amino acid peptide CYPYDVPDYASL. This second-generation HA antibody is an excellent substitute for the 12CA5 monoclonal antibody. The HA.11 antibody recognizes the influenza hemagglutinin epitope (YPYDVPDYA) which has been used extensively as a general epitope tag in expression vectors. The extreme specificity of the antibody allows unambiguous identification and quantitative analysis of the tagged protein. The HA.11 antibody recognizes HA epitopes located in the middle of protein sequences as well as at the N- or C-terminus. Antibody Target:HA-E2F1

value: The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus.

value: Covance

tag: control description

value: HeLa cells stably expressed a tagged HA-E2F1 were fragmented using a Bioruptor, precipitated with StaphA and an antibody to the  HA tag,

tag: replicate


title: Stanford_ChipSeq_K562_Nrf1_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype description

tag: cell

tag: cell organism

value: human

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

tag: cell karyotype

value: mesoderm

value: No special treatment or protocol applies

tag: antibody

value: Mouse monoclonal, Immunogen corresponding to amino acids 201-286 of Human NRF1. Antibody Target:NRF1

value: NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding.

tag: antibody vendorname

value: Abcam

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid