title: Stanford_ChipSeq_HepG2_c-Jun_IgG-rab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: hepatocellular carcinoma

value: cancer

tag: cell lineage

value: endoderm

value: M

tag: treatment

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

tag: antibody targetdescription

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

value: Santa Cruz Biotech


title: Stanford_ChipSeq_HeLa-S3_ZKSCAN1_(HPA006672)_IgG-rab

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: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: human

value: cervical carcinoma

tag: cell karyotype

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit polyclonal, Immunogen:Zinc finger with KRAB and SCAN domain-containing protein 1 recombinant protein epitope signature tag (PrEST). Antibody Target:ZKSCAN1

value: The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation.

tag: antibody vendorname

value: Sigma-Aldrich

tag: antibody vendorid

tag: control

value: IgG-rab

tag: control description

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

tag: controlid

tag: replicate


title: Yale_ChipSeq_HeLa-S3_IFNg30_STAT1_std

value: Yale

value: Snyder - Yale University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: cancer

tag: cell lineage

tag: treatment

value: Interferon gamma treatment - 30 minutes (Snyder)

tag: antibody antibodydescription

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

tag: antibody targetdescription

value: transcription factor, activated by interferon signalling

value: std

value: Standard input signal for most experiments.

tag: labversion

value: remapped from hg18


title: Yale_ChipSeq_NB4_Input_std

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: human

value: acute promyelocytic leukemia cell line. (PMID:1995093)

value: mesoderm

value: U

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.


title: Yale_ChipSeq_K562_Pol2_std

value: Yale

value: Snyder - Yale University

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 sex

value: F

tag: treatment description

tag: antibody

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

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: control


title: Stanford_ChipSeq_GM12878_SMC3_(ab9263)_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

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

value: normal

tag: cell lineage

tag: treatment

tag: antibody antibodydescription

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.

value: Abcam

value: IgG-mus

tag: control description

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

tag: controlid

tag: replicate


title: Yale_ChipSeq_NB4_Pol2_std

tag: lab

value: Yale

tag: lab description

value: Snyder - Yale University

tag: datatype

tag: datatype description

tag: cell

value: human

value: acute promyelocytic leukemia cell line. (PMID:1995093)

value: cancer

value: mesoderm

value: U

value: No special treatment or protocol applies

tag: antibody targetdescription

value: std

value: Standard input signal for most experiments.


title: USC_ChipSeq_H1-hESC_Input_UCDavis

value: USC

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: embryonic stem cells

tag: cell karyotype

value: inner cell mass

tag: cell sex

value: M

tag: treatment description

tag: antibody

value: Input

tag: antibody description

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

value: UCDavis

value: Input library was prepared at UC Davis.


title: USC_ChipSeq_HeLa-S3_ELK4_UCDavis

value: human

tag: cell description

value: cervical carcinoma

value: cancer

tag: cell lineage

value: ectoderm

value: F

tag: treatment

value: Rabbit polyclonal IgG. Antibody Target:ELK4

value: This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control


title: USC_ChipSeq_H1-hESC_SUZ12_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

value: ChipSeq

value: normal

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:SUZ12

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

value: Antibody made by Farnham lab

tag: control description

tag: controlid

tag: replicate


title: USC_ChipSeq_HepG2_ZNF274_UCDavis

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: hepatocellular carcinoma

tag: cell karyotype

value: endoderm

value: M

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

tag: antibody targetdescription

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.


title: Yale_ChipSeq_HeLa-S3_IFNg30_Input_std

value: Yale

value: Snyder - Yale University

value: human

tag: cell description

value: cervical carcinoma

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: Interferon gamma treatment - 30 minutes (Snyder)

tag: antibody

value: Input

tag: antibody description

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

value: std

value: Standard input signal for most experiments.

tag: labversion

value: remapped from hg18


title: USC_ChipSeq_H1-hESC_Max_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

tag: treatment

value: No special treatment or protocol applies

value: Max

tag: antibody antibodydescription

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).

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control


title: USC_ChipSeq_HUVEC_GATA-2_UCDavis

source_name: HUVEC

tag: datatype

tag: datatype description

tag: cell

value: HUVEC

tag: cell organism

value: human

value: umbilical vein endothelial cells

value: mesoderm

value: U

value: Rabbit polyclonal. Antibody Target:GATA2

value: GATA binding protein 2

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

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: USC_ChipSeq_GM12878_ZNF274_std

value: USC

value: Farnham - University of Southern California

value: ChipSeq

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

tag: cell sex

value: F

tag: treatment description

tag: antibody

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

tag: antibody targetdescription

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: std

value: Standard input signal for most experiments.


title: USC_ChipSeq_HUVEC_Input_UCDavis

tag: lab

tag: lab description

value: HUVEC

value: human

value: umbilical vein endothelial cells

value: mesoderm

value: U

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.


title: Yale_ChipSeq_K562_Input_std

value: Yale

value: Snyder - Yale University

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

value: cancer

tag: control

tag: labversion

value: remapped from hg18, V2


title: Stanford_ChipSeq_K562_Max_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: cell

tag: cell organism

value: F

value: Max

tag: antibody antibodydescription

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).

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: IgG-rab

tag: control description

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

tag: controlid


title: Stanford_ChipSeq_GM12878_ELK1_(1277-1)_IgG-mus

value: human

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

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit polyclonal, a synthetic peptide corresponding to residues in C-terminus of human ELK-1 was used as immunogen. The antibody does not cross-react with other ETS family members. Antibody Target:ELK1

value: Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli.

value: Epitomics

value: IgG-mus

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

tag: replicate


title: Harvard_ChipSeq_HeLa-S3_TFIIIC-110_std

tag: lab

value: Harvard

tag: lab description

value: Struhl - Harvard University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: cervical carcinoma

value: cancer

value: ectoderm

value: F

tag: treatment

value: rabbit polyclonal. Antibody Target:TFIIIC-110

tag: antibody targetdescription

value: TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. Antiserum 4286 was raised by immunizing rabbits with synthetic peptide RPGFSPTSHRLLPTP (human TFIIIC110 residues 897 to 911) coupled to keyhole limpet hemocyanin.

value: Dr. Robert J. White, Beatson Institute for Cancer Research, UK

value: std

value: Standard input signal for most experiments.

value: remapped from hg18


title: Stanford_ChipSeq_HeLa-S3_Input_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: cell

tag: cell organism

value: human

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: control

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: Stanford_ChipSeq_HeLa-S3_c-Jun_IgG-rab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: cervical carcinoma

tag: cell karyotype

value: cancer

value: ectoderm

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.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control description

tag: controlid


title: Harvard_ChipSeq_K562_TFIIIC-110_std

tag: lab

value: Harvard

tag: lab description

value: Struhl - Harvard University

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: F

tag: treatment description

tag: antibody

value: rabbit polyclonal. Antibody Target:TFIIIC-110

value: TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. Antiserum 4286 was raised by immunizing rabbits with synthetic peptide RPGFSPTSHRLLPTP (human TFIIIC110 residues 897 to 911) coupled to keyhole limpet hemocyanin.

value: Dr. Robert J. White, Beatson Institute for Cancer Research, UK

value: std

value: Standard input signal for most experiments.

tag: replicate


title: Harvard_ChipSeq_K562_ATF1_(06-325)_std

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: treatment

value: No special treatment or protocol applies

value: Sheep polyclonal, immunogen:CPVTLTSQTTKTDDPQL. Antibody Target:ATF1

tag: antibody targetdescription

value: ATF1 is a bZip transcription factor from the CREB family.  ATF1 binds to both cAMP response elements (TGACGTCA).

value: Millipore


title: Stanford_ChipSeq_K562_MAZ_(ab85725)_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: cell description

tag: cell karyotype

value: cancer

tag: antibody antibodydescription

value: Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target:MAZ

value: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

tag: antibody vendorname

value: Abcam

tag: control

value: IgG-rab

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


title: Yale_ChipSeq_K562_c-Fos_std

tag: lab

value: Yale

tag: lab description

value: Snyder - Yale University

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

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: antibody vendorid

value: std

tag: control description

tag: controlid


title: Stanford_ChipSeq_K562_UBF_(sc-13125)_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell lineage

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: UBF (F-9) is a mouse monoclonal antibody raised against amino acids 1-220 of UBF of human origin. Antibody Target:UBF

value: Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes

value: IgG-mus

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

tag: replicate


title: Stanford_ChipSeq_K562_ARID3A_(sc-8821)_IgG-rab

tag: datatype

tag: datatype description

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: mesoderm

tag: treatment

value: affinity purified goat polyclonal antibody raised against a peptide mapping at the N-terminus of ARID3A of human origin. Antibody Target:ARID3A

value: This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq)

value: IgG-rab

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


title: Stanford_ChipSeq_GM12878_Rad21_IgG-rab

value: Stanford

tag: cell description

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

tag: cell karyotype

value: normal

value: F

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:RAD21

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: labversion

value: remapped from hg18


title: Anti-H3K4me3 Spo11-/-

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: Sample 17

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
SPO11_H3K4me3_peaks.bedGraph: mm9
Spo11_H3K4Me3_Sample1_Testis.bed: mm9

organism: Mus musculus

source_name: Anti-H3K4me3 Spo11-/-_testis_ChIP-Seq

growth_protocol: Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol: Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation.

tag: strain

tag: genotype/variation

tag: tissue

value: testis

tag: chip antibody

value: Anti-H3K4me3 Millipore (#07-473)

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: sequencing technique

value: ChIP-Seq


title: USC_ChipSeq_PBDEFetal_GATA-1_UCDavis

source_name: PBDEFetal

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: PBDEFetal

value: human

value: peripheral blood-derived erythroblasts from 16-19 week human fetal liver

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: treatment description

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

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

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: Stanford_ChipSeq_K562_USF2_IgG-rab

value: Stanford

value: Snyder - Stanford University

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

tag: cell karyotype

value: cancer

value: F

tag: treatment

tag: antibody antibodydescription

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

tag: antibody targetdescription

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').

tag: antibody vendorname

value: abcam

value: IgG-rab

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


title: Stanford_ChipSeq_HepG2_MAZ_(ab85725)_IgG-rab

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

value: hepatocellular carcinoma

tag: cell lineage

value: endoderm

value: M

value: Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target:MAZ

value: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

value: Abcam


title: USC_ChipSeq_PBDEFetal_Input_UCDavis

value: USC

value: Farnham - University of Southern California

value: PBDEFetal

value: peripheral blood-derived erythroblasts from 16-19 week human fetal liver

value: normal

value: mesoderm

tag: cell sex

value: U

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Input

tag: antibody description

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

tag: control

value: UCDavis

value: Input library was prepared at UC Davis.


title: Stanford_ChipSeq_GM12878_SIN3A_(NB600-1263)_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

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

value: F

value: Rabbit polyclonal, Immunogen:Synthetic peptide:MKRRLDDQESDVYAAQQRR, corresponding to amino acids 1-19 of Mouse mSin3A. Antibody Target:SIN3A (NB600-1263)

value: Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid & thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR).

value: Novus Biologicals

tag: antibody vendorid

value: IgG-mus

tag: control description

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

tag: controlid

tag: replicate


title: Stanford_ChipSeq_GM12878_E2F4_IgG-mus

tag: cell description

tag: cell karyotype

value: normal

value: mesoderm

tag: treatment

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:E2F4

tag: antibody targetdescription

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

tag: antibody vendorname

value: Santa Cruz Biotech


title: Anti-H3K4me3 9R

description: Sample 14

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
9R_H3K4me3_peaks.bedGraph: mm9
9R_H3K4Me3_Sample1_Testis.bed: mm9

source_name: Anti-H3K4me3 9R_testis_ChIP-Seq

tag: strain

tag: genotype/variation

tag: tissue

value: testis

tag: chip antibody

value: Anti-H3K4me3 Millipore (#07-473)

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: sequencing technique

value: ChIP-Seq


title: Anti-H3K4me3 13R

description: Sample 13

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
13R_H3K4me3_peaks.bedGraph: mm9
13R_H3K4Me3_Sample1_Testis.bed: mm9

source_name: Anti-H3K4me3 13R_testis_ChIP-Seq


title: Stanford_ChipSeq_HeLa-S3_JunD_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

value: cervical carcinoma

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

tag: treatment description

tag: antibody

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)

tag: antibody vendorid

tag: control

value: IgG-rab

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

tag: labversion

value: remapped from hg18


title: USC_ChipSeq_HEK293-T-REx_Input_UCDavis

value: USC

value: Farnham - University of Southern California

tag: cell description

value: embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX

tag: cell karyotype

value: mesoderm

value: F

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.

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid


title: USC_ChipSeq_GM08714_ZNF274_UCDavis

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: human

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

tag: antibody antibodydescription

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

tag: antibody targetdescription

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: replicate


title: Stanford_ChipSeq_K562_TAL1_(SC-12984)_IgG-mus

value: Stanford

value: Snyder - Stanford University

tag: datatype description

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

tag: cell lineage

tag: cell sex

tag: treatment description

tag: antibody

value: goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target:TAL1

value: TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis.

value: Santa Cruz Biotech

value: IgG-mus

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


title: Stanford_ChipSeq_HeLa-S3_ELK1_(1277-1)_IgG-rab

tag: cell description

value: cervical carcinoma

tag: cell karyotype

value: ectoderm

value: F

tag: treatment

value: No special treatment or protocol applies

value: Rabbit polyclonal, a synthetic peptide corresponding to residues in C-terminus of human ELK-1 was used as immunogen. The antibody does not cross-react with other ETS family members. Antibody Target:ELK1

value: Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli.

value: Epitomics

tag: antibody vendorid

tag: control

value: IgG-rab

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


title: Anti-H3K4me3 B6 Sample 1

description:
Sample 11
processed data file: B6_H3K4me3_peaks.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
C57_H3K4Me3_Sample1_Testis.bed: mm9

source_name: Anti-H3K4me3 B6_testis_ChIP-Seq

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: chip antibody

value: Anti-H3K4me3 Millipore (#07-473)

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: sequencing technique

value: ChIP-Seq


title: Anti-H3K4me3 B6 Sample 2

description:
Sample 12
processed data file: B6_H3K4me3_peaks.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
C57_H3K4Me3_Sample2_Testis.bed: mm9


title: Stanford_ChipSeq_GM19193_Input_IgG-mus

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

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

value: normal

value: mesoderm

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

tag: labversion

value: Illumina 2.0, low confidence sequences excluded

tag: replicate


title: Stanford_ChipSeq_GM19099_Pol2_IgG-mus

tag: cell description

tag: cell karyotype

tag: cell lineage

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

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

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: control

value: IgG-mus

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

value: remapped from hg18, llumina 2.0, low confidence sequences excluded.  Data paired with GM19099_IgG_Control.


title: Stanford_ChipSeq_GM19193_Pol2_IgG-mus

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded.  Data paired with GM19193_IgG_Control.


title: USC_ChipSeq_SH-SY5Y_Input_UCDavis

value: USC

value: Farnham - University of Southern California

value: Chromatin IP Sequencing

value: human

tag: cell description

value: neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q

tag: cell karyotype

value: cancer

value: ectoderm

tag: antibody description

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid


title: Input DNA with Kinetic Enrichment

description: Sample 9

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
F1C_SSDS_Sample1_Testis_ssDNA_type1.bed: mm9

source_name: Input DNA with Kinetic Enrichment_testis_SSDS

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: Yale_ChipSeq_K562_Rad21_std

value: Yale

value: Snyder - Yale University

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: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:RAD21

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.

tag: labversion

value: Contains incomplete fastq files

tag: replicate


title: Stanford_ChipSeq_GM19099_Input_IgG-mus

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: normal

value: Input

tag: antibody description

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

tag: control

value: IgG-mus

tag: control description

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

value: Illumina 2.0, low confidence sequences excluded


title: Yale_ChipSeq_HeLa-S3_c-Myc_std

value: Yale

value: Snyder - Yale University

value: cervical carcinoma

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

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: controlid


title: Anti-DMC1 F1 Sample 1

description:
Sample 7
processed data file: F1_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
F1_SSDS_Sample1_Testis_ssDNA_type1.bed: mm9

source_name: Anti-DMC1 F1_testis_SSDS

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: chip antibody

value: Anti-DMC1 (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: Yale_ChipSeq_GM12878_Pol3_std

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: normal

value: mesoderm

value: mouse monoclonal IgG1. Antibody Target:POL3

tag: antibody targetdescription

value: RNA Polymerase III

tag: antibody vendorname

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.

tag: labversion

value: Incomplete fastq due to Illumina pipeline version

tag: replicate


title: Yale_ChipSeq_HepG2_pravastatin_SREBP1_std

treatment_protocol: pravastatin

value: Yale

value: Snyder - Yale University

value: hepatocellular carcinoma

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment

value: pravastatin

tag: treatment description

value: For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder)

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:SREBP1

value: Sterol regulatory element binding transcription factor 1

value: Santa Cruz Biotech

tag: control

tag: control description

tag: controlid

value: remapped from hg18


title: Yale_ChipSeq_HeLa-S3_Max_std

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

value: cervical carcinoma

value: ectoderm

value: F

value: No special treatment or protocol applies

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: Contains incomplete fastq files


title: Yale_ChipSeq_HeLa-S3_c-Fos_std

value: Yale

value: Snyder - Yale University

tag: cell description

tag: cell karyotype

value: cancer

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

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.

tag: labversion


title: Yale_ChipSeq_HepG2_pravastatin_SREBP2_std

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: hepatocellular carcinoma

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment

value: pravastatin

tag: treatment description

value: For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder)

tag: antibody

value: Rabbit polyclonal. Antibody Target:SREBP2

value: Sterol regulatory element binding transcription factor 2

value: Cayman Chemical

value: remapped from hg18

tag: replicate


title: Anti-DMC1 13R Sample 1

description:
Sample 3
processed data file: 13R_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
13R_SSDS_Sample1_Testis_ssDNA_type1.bed: mm9

source_name: Anti-DMC1 13R_testis_SSDS

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: chip antibody

value: Anti-DMC1 (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: Anti-DMC1 B6 Sample 2

description:
Sample 2
processed data file: B6_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
C57_SSDS_Sample2_Testis_ssDNA_type1.bed: mm9

source_name: Anti-DMC1 B6_testis_SSDS


title: Anti-DMC1 9R Sample 2

description:
Sample 6
processed data file: 9R_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
9R_SSDS_Sample2_Testis_ssDNA_type1.bed: mm9

source_name: Anti-DMC1 9R_testis_SSDS


title: Stanford_ChipSeq_K562_MafK_(ab50322)_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

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

tag: cell karyotype

value: cancer

value: mesoderm

value: F

value: No special treatment or protocol applies

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

tag: control

value: IgG-rab

tag: control description

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

tag: controlid


title: Stanford_ChipSeq_H1-hESC_Nrf1_IgG-rab

value: Chromatin IP Sequencing

value: human

value: embryonic stem cells

value: normal

tag: cell lineage

value: inner cell mass

tag: cell sex

value: M

tag: treatment

tag: treatment description

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

tag: antibody vendorid

tag: replicate


title: Stanford_ChipSeq_GM12878_Nrf1_IgG-mus

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

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

value: IgG-mus

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


title: Anti-DMC1 B6 Sample 1

description:
Sample 1
processed data file: B6_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
C57_SSDS_Sample1_Testis_ssDNA_type1.bed: mm9

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: chip antibody

value: Anti-DMC1 (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: P4936_T24_CDK9

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against Cdk9  in P493-6 Time = 24 hr
barcode (already removed): TAGCTT

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
etc..

source_name: B-cell lymphoma

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 24 hours.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody details (vendor, catalog number)

value: Santa Cruz SC-8338

tag: cell type

tag: time

value: 24 hr


title: Stanford_ChipSeq_HepG2_MafF_(M8194)_IgG-rab

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

value: hepatocellular carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal. Raised against synthetic peptide corresponding to amino acids 147-163 of human MAFF. The immunizing peptide does not cross-react with other members of the family. Antibody Target:MafF

tag: antibody targetdescription

value: The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response.

tag: antibody vendorname

value: Sigma-Aldrich

tag: antibody vendorid

tag: control

value: IgG-rab

tag: control description

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

tag: controlid


title: Stanford_ChipSeq_HepG2_MafK_(ab50322)_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

value: M

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

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

tag: replicate


title: Stanford_ChipSeq_HepG2_CHD2_(AB68301)_IgG-rab

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

tag: cell karyotype

tag: cell lineage

tag: cell sex

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.


title: Stanford_ChipSeq_H1-hESC_TBP_IgG-rab

value: embryonic stem cells

value: normal

value: inner cell mass

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: TBP

tag: antibody antibodydescription

value: Mouse monoclonal. Immunogen is synthetic peptide conjugated to KLH derived from within residues 1 - 100 of HumanTATA binding protein TBP. Antibody Target:TBP

tag: antibody targetdescription

value: General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription.

value: abcam


title: Anti-DMC1 9R Sample 1

description:
Sample 5
processed data file: 9R_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
9R_SSDS_Sample1_Testis_ssDNA_type1.bed: mm9

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: chip antibody

value: Anti-DMC1 (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: Stanford_ChipSeq_K562_SMC3_(ab9263)_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

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

value: cancer

value: mesoderm

value: F

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: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control

value: IgG-rab

tag: control description

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

tag: controlid

tag: replicate


title: Stanford_ChipSeq_A549_Rad21_IgG-rab

value: human

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:RAD21

tag: antibody targetdescription

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


title: Stanford_ChipSeq_GM12878_CHD1_(A301-218A)_IgG-mus

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

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

value: normal

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:CHD1

value: CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains:a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337.

value: Bethyl Laboratories

value: IgG-mus

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


title: Stanford_ChipSeq_HeLa-S3_GCN5_std

tag: cell organism

value: human

value: cervical carcinoma

value: cancer

value: ectoderm

value: F

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

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

value: std

tag: control description

value: Standard input signal for most experiments.


title: P4936_T1_CDK9

description:
Chromatin IP against Cdk9  in P493-6 Time = 1 hr
barcode (already removed): CGATGT

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 1 hours.

tag: chip antibody

tag: chip antibody details (vendor, catalog number)

value: Santa Cruz SC-8338

tag: cell type

tag: time

value: 1 hr


title: Stanford_ChipSeq_A549_Pol2(phosphoS2)_IgG-rab

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

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

value: IgG-rab

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

tag: controlid

tag: replicate


title: P4936_T0_CDK9

description:
Chromatin IP against Cdk9  in P493-6 Time = 0 hr
barcode (already removed): GCCAAT

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 0 hours.

value: 0 hr


title: Yale_ChipSeq_HepG2_pravastatin_Input_std

tag: lab

value: Yale

tag: lab description

value: Snyder - Yale University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: human

value: hepatocellular carcinoma

value: cancer

value: pravastatin

value: For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder)

value: Input

tag: antibody description

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

value: std

value: Standard input signal for most experiments.

tag: labversion

value: remapped from hg18


title: Yale_ChipSeq_HepG2_pravastatin_Pol2_std

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: endoderm

value: M

tag: antibody antibodydescription

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

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: control

tag: control description


title: Stanford_ChipSeq_GM12878_Input_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: human

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

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: IgG-mus

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

tag: controlid

value: Illumina 2.0, low confidence sequences excluded


title: Stanford_ChipSeq_H1-hESC_CHD2_(AB68301)_IgG-rab

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: embryonic stem cells

value: inner cell mass

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

value: IgG-rab

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

tag: replicate


title: Stanford_ChipSeq_A549_Max_IgG-rab

value: Stanford

value: Snyder - Stanford University

value: human

tag: cell description

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

value: endoderm

value: M

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

tag: antibody vendorid


title: Stanford_ChipSeq_H1-hESC_Mxi1_(AF4185)_IgG-rab

value: ChipSeq

value: Chromatin IP Sequencing

value: embryonic stem cells

tag: cell karyotype

value: normal

tag: cell lineage

value: inner cell mass

tag: cell sex

value: No special treatment or protocol applies

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

tag: control description


title: Stanford_ChipSeq_GM12878_p300_IgG-mus

tag: lab

value: Stanford

value: Snyder - Stanford University

value: human

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

value: mesoderm

value: F

tag: treatment

tag: treatment description

tag: antibody

value: Rabbit Polyclonal. Antibody Target:P300

value: IgG-mus

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

tag: controlid


title: Stanford_ChipSeq_GM15510_Pol2_IgG-mus

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

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

value: U

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

value: RNA Polymerase II

value: Covance

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded. Data paired with GM15510_IgG_Control.


title: Stanford_ChipSeq_H1-hESC_CEBPB_IgG-rab

value: Stanford

tag: cell description

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

value: No special treatment or protocol applies

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

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: IgG-rab

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

tag: replicate


title: Stanford_ChipSeq_H1-hESC_MafK_(ab50322)_IgG-rab

tag: lab

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell karyotype

tag: cell lineage

tag: cell sex

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

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

tag: control

tag: control description


title: Stanford_ChipSeq_HeLa-S3_MafK_(ab50322)_IgG-rab

value: Stanford

tag: lab description

tag: datatype

value: cervical carcinoma

value: cancer

value: ectoderm

value: F

tag: treatment

tag: treatment description

tag: antibody

tag: controlid


title: Stanford_ChipSeq_H1-hESC_SIN3A_(NB600-1263)_IgG-rab

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal, Immunogen:Synthetic peptide:MKRRLDDQESDVYAAQQRR, corresponding to amino acids 1-19 of Mouse mSin3A. Antibody Target:SIN3A (NB600-1263)

value: Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid & thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR).

value: Novus Biologicals


title: USC_ChipSeq_U2OS_Input_UCDavis

tag: lab

value: USC

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

value: human

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: mesoderm

value: Input

tag: antibody description

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

value: UCDavis

value: Input library was prepared at UC Davis.


title: Stanford_ChipSeq_GM12892_Input_IgG-mus

value: Stanford

value: Snyder - Stanford University

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

tag: cell karyotype

value: normal

tag: cell lineage

value: F

value: IgG-mus

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

tag: labversion

value: Illumina 2.0, low confidence sequences excluded

tag: replicate


title: Stanford_ChipSeq_GM12892_TNFa_NFKB_IgG-rab

treatment_protocol: TNFa

tag: lab description

value: ChipSeq

tag: cell sex

value: TNFa

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

value: NFKB

value: Rabbit polyclonal. Antibody Target:NFKB

tag: antibody targetdescription

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

tag: control

value: IgG-rab

tag: control description

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

value: remapped from hg18, Data paired with IgG_Control


title: Stanford_ChipSeq_GM12891_Pol2_IgG-mus

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: human

value: mesoderm

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

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

value: RNA Polymerase II

value: Covance

tag: controlid

value: remapped from hg18, Data paired with GM12891_IgG_Control.


title: Stanford_ChipSeq_HepG2_RFX5_(200-401-194)_IgG-rab

tag: lab

value: ChipSeq

tag: cell organism

tag: cell description

value: hepatocellular carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

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

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

value: Rockland Immunochemicals


title: Stanford_ChipSeq_GM15510_Input_IgG-mus

value: Stanford

tag: lab description

value: Snyder - Stanford University

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

value: normal

tag: cell sex

value: U

value: Input

tag: antibody description

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

value: IgG-mus

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

tag: labversion

value: Illumina 2.0, low confidence sequences excluded

tag: replicate


title: Stanford_ChipSeq_GM18505_TNFa_NFKB_IgG-rab

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

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

value: mesoderm

value: F

value: TNFa

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

value: NFKB

value: Rabbit polyclonal. Antibody Target:NFKB

tag: antibody targetdescription

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

tag: control

value: IgG-rab

tag: control description

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

value: remapped from hg18, Data paired with GM18505_IgG_Control


title: Stanford_ChipSeq_GM12878_MAZ_(ab85725)_IgG-mus

tag: lab

value: Stanford

value: Snyder - Stanford University

tag: cell

tag: cell organism

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

value: normal

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target:MAZ

value: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

value: Abcam

value: IgG-mus

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

tag: controlid


title: Stanford_ChipSeq_GM18526_TNFa_NFKB_IgG-rab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: TNFa

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

value: NFKB

tag: antibody antibodydescription

value: remapped from hg18, Data paired with GM18526_IgG_Control


title: Stanford_ChipSeq_HepG2_TBP_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype

tag: datatype description

value: hepatocellular carcinoma

value: cancer

value: endoderm

value: M

value: TBP

value: Mouse monoclonal. Immunogen is synthetic peptide conjugated to KLH derived from within residues 1 - 100 of HumanTATA binding protein TBP. Antibody Target:TBP

tag: antibody targetdescription

value: General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription.

tag: antibody vendorname

value: abcam

value: IgG-rab

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

tag: replicate


title: LB_medium_midlog

city: Storrs

first: Joerg

last: Graf

state: CT

address: 91 North Eagleville Road

institute: University of Connectiuct

library_source: transcriptomic

data_processing:
Illumina cDNA reads were mapped to reference genomes using CLC Genomics Workbench version 4.0.2, reads that mapped to more than one region of the genome or with greater than 2 mismatches were excluded from analysis.
Expression values were calculated for each gene using the following equation: EV = (total numbers of reads mapped to the target)/([length of the target in kb)X(total number of reads mapped in millions)]
genome build: Reference genomes not yet published.
Processed data files format and content: The processed data files are in a tab delimited text format and contain three columns. Column 1 = "Feature ID" which is the gene or gene product predicted from our reference genomes;Column 2 = "Expression Value" which is the expression value of the corresponding target gene in Column 1; Column 3 = "Gene Length" which is the length of the target gene in Column 1

molecule: total RNA

organism: Aeromonas veronii

source_name: midlog phase cells grown in LB medium

growth_protocol: sample specific

extract_protocol: 100 ng of mRNA-enriched RNA was used to construct a double stranded cDNA library using Illumina's mRNA-seq kit (RS-100-0801) following the manufacturer's instructions except that the polyT bead enrichment step was omitted.

treatment_protocol: sample specific

tag: protocol

value: In vitro


title: Stanford_ChipSeq_GM19099_TNFa_NFKB_IgG-rab

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

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

value: normal

value: mesoderm

value: F

value: TNFa

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

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: control description

tag: labversion

value: remapped from hg18, Data paired with GM19099_IgG_Control


title: Stanford_ChipSeq_GM19193_TNFa_NFKB_IgG-rab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: cell description

tag: cell karyotype

tag: treatment

tag: treatment description

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

tag: antibody

value: NFKB

tag: controlid

value: remapped from hg18, Data paired with GM19193_IgG_Control


title: Stanford_ChipSeq_H1-hESC_CHD1_(A301-218A)_IgG-rab

tag: datatype

value: ChipSeq

tag: datatype description

value: embryonic stem cells

tag: cell lineage

value: inner cell mass

tag: cell sex

value: M

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:CHD1

tag: antibody targetdescription

value: CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains:a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337.

tag: antibody vendorname

value: Bethyl Laboratories

value: IgG-rab

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


title: Stanford_ChipSeq_GM12878_TBP_IgG-mus

tag: lab

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

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

value: normal

value: mesoderm

value: F

value: TBP

value: Mouse monoclonal. Immunogen is synthetic peptide conjugated to KLH derived from within residues 1 - 100 of HumanTATA binding protein TBP. Antibody Target:TBP

value: General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription.

value: abcam

tag: antibody vendorid

tag: control

value: IgG-mus

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

tag: replicate


title: Stanford_ChipSeq_HepG2_ARID3A_(NB100-279)_IgG-rab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

tag: cell description

value: hepatocellular carcinoma

tag: cell karyotype

value: cancer

value: endoderm

value: M

tag: treatment

value: No special treatment or protocol applies

value: Rabbit polyclonal, Immunogen:A synthetic peptide, which represented a portion of human Dead Ringer-Like 1 encoded within exon 8. Antibody Target:ARID3A

value: This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq)

value: Novus Biologicals

tag: control description


title: Stanford_ChipSeq_HeLa-S3_STAT3_IgG-rab

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: human

value: cervical carcinoma

value: ectoderm

value: F

tag: treatment description

tag: antibody

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.

value: Santa Cruz Biotech

value: IgG-rab

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

tag: controlid


title: Stanford_ChipSeq_HepG2_CEBPZ_IgG-rab

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: hepatocellular carcinoma

value: cancer

tag: cell lineage

tag: cell sex

value: CEBPZ

tag: antibody antibodydescription

value: Rabbit polyclonal, immunogen sequence= KDNASLKQLRWEAERDDWLHNRDAKSIIKKKKHFKKKRIKTTQKTKKQRK. Antibody Target:CEBPZ

tag: antibody targetdescription

value: Stimulates transcription from the HSP70 promoter.

tag: antibody vendorname

value: Sigma-Aldrich


title: Stanford_ChipSeq_HeLa-S3_MAZ_(ab85725)_IgG-rab

tag: lab

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

value: cervical carcinoma

value: No special treatment or protocol applies

value: Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target:MAZ

value: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

value: Abcam

tag: antibody vendorid

tag: control


title: Crop_42hrs_enzyme_run2

source_name: Leech crop intraluminal fluid

tag: protocol

value: In vivo, crop microbiome


title: Crop_42hrs_enzyme_run1