title: Reference Epigenome: ChIP-Seq Analysis of H2A.Z in hESC H9 Cells; renlab.H2A.Z.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2A.Z in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK532
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9576
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM807391_UCSD.H9.H2A.Z.SK532.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.hESC.H9.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2A.Z ChIP-Seq on H9 Cell Line, Library SK532, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12393
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,808,653
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0318
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.114
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.8787
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2153
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM807391_UCSD.H9.H2A.Z.SK532.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.hESC.H9.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2A.Z ChIP-Seq read mappings from the H9 Cell Line, Library SK532, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12466
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: H9 H2A.Z 32
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2A.Z Library SK532 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,808,653
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0318
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.114
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.8787
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2153
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2A.Z.hESC.H9.01.01

tag: sample alias

value: H9 Cell Line

value: James Thompson Laboratory

value: mTeSER

value: Female

value: Histone H2A.Z

value: Biorupter

value: 500 micrograms

value: Active Motif


title: Input Replicate2

status: Public on Sep 30 2011

type: SRA

city: MADISON

first: Emery

middle: H

last: Bresnick

state: Wisconsin

address: 1111 Highland Avenue

department: Department of Cell and Regenerative Biology

country: USA

institute: University of Wisconsin School of Medicine and Public Health

library_source: genomic

data_processing: Sequence reads were aligned to the UCSC human genome assembly HG19 using the Eland pipeline (Illumina). Uniquely aligned sequences were used to identify GATA-1 occupancy peaks with Sole-search version 2 (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi). Peaks were called with an alpha value of 0.001 and an FDR of 0.0001 after merging two biological replicates together.

molecule: genomic DNA

organism: Homo sapiens

source_name: erythroblasts

growth_protocol: To differentiate erythroblasts from human peripheral blood mononuclear cells, fresh blood was collected in a heparin-containing tube, diluted with 2 to 4 volumes of PBS, and overlayed on Ficoll-Paque PLUS (GE Healthcare). Samples were centrifuged at 400 x g for 30 min at room temperature. The upper layer was removed, and mononuclear cells were washed twice with PBS. Mononuclear cells were cultured in StemSpan (STEMCELL Technologies) containing SCF (100 ng/ml), Flt3-L (33.3 ng/ml), IL-3 (13.3 ng/ml), BMP4 (13.3 ng/ml), EPO (2.67 U/ml) and 1 mM hydrocortisone (Sigma) for 7 days. Cells were then cultured in StemSpan with SCF (40 ng/ml), IGF-1 (40 ng/ml), IL-3 (13.3 ng/ml) BMP4 (13.3 ng/ml), EPO (3.3 U/ml) and hydrocortisone (1 mM) for another 7 days. Fresh medium was added every other day, and the cell density was maintained at ~3 x 105/ml. After 14 days, cells were collected by centrifugation at 2500 x g for 10 min, washed twice with PBS, and crosslinked with 1% formaldehyde in PBS for 10 min. The reaction was stopped by adding glycine at a final concentration of 125 mM. After 5 min, cells were washed twice with ice-cold PBS (Ca2+/Mg2+-free), collected by centrifugation at 2000 x g at 4°C and flash frozen in liquid nitrogen.

extract_protocol: ChIP assays were conducted with crosslinked human peripheral blood mononuclear cell-derived erythroblasts as described previously (O'Geen H et.al, 2010). Chromatin from 108 cells was incubated with 60 μl rabbit polyclonal anti-GATA-1 antibody. Following overnight incubation at 4°C, protein/DNA complexes were captured with 100 µl Staph-Seq (Sigma). After washing, crosslinks were reversed, DNA purified, and qPCR was used to confirm enrichment of target sequences in ChIP versus input samples. Libraries were created as described with minor modifications. Gel size selection of the 150-450 bp fraction was conducted after the adapter ligation step, followed by 18 amplification cycles. ChIP-seq libraries were analyzed with an Illumina GAIIx.

tag: cell type

value: primary human PBMC derived erythroblasts

tag: chip antibody


title: m12_r1

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description:
m12_r1
secondary-transplanted HSCs
Mspi cut fragment at size 40~200bp.

data_processing: Reads are mapped to genome (mm9) using RRBSMAP, then using a customized pipeline for downstream analysis.

organism: Mus musculus

extract_protocol: 50-100ng of genomic DNA digested with 10 Unit MspI (NEB, Ipswich, MA, USA) which cuts at CCGG sites methylation insensitively. Digested fragments were end-repaired, A-tailed and ligated to illumine adapters. End-repair and 3’ adenylation was performed in 50 μl reaction containing 4 mM 5′ methylated dCTP, 4 mM dGTP, 40 mM dATP, and 10U of 3′ to 5′ exo- Klenow DNA polymerase (NEB) and incubated at 30°C for 20 min followed by 20 min at 37°C. Adaptor ligation was performed in 50 μl reactions containing 300mM pre-methylated adapters and 1000 Unit T4 DNA polymerase and incubated at 16 °C overnight. Adaptor-ligated DNA was subjected to a size selection on a 3% NuSieve 3:1 agarose gel. DNA marker lanes were excised from the gel and stained with SYBR Gold (Invitrogen). 160-350 bp slices were excised from the unstained gel and purified using MinElute spin column (Qiagen, Valencia, CA, USA). Size-selected fragments were bisulphite-treated using the EpiTect Bisulphite Kit (Qiagen) with minor modifications by adding 5 more cycles (5 min 95 °C followed by 90 min at 60 °C). After bisulphite conversion, DNA was eluted in 40μl EB buffer and 0.8 μl DNA was used for analytical PCR reactions to determine the minimum number of PCR cycles required to obtain enough material for sequencing. Final PCR products were purified on MinElute columns (Qiagen) and assessed on 4–20% polyacrylamide Criterion TBE Gel (Bio-Rad, Hercules, CA, USA) and quantified using a Qubit fluorometer (Invitrogen).

tag: strain

tag: tissue type

value: Hematopoietic stem cell (HSC)

tag: genotype/variation

value: wild type (Mx1-cre-;Dnmt3afl/fl)

tag: gender

value: mixed donor HSC genders


title: m12_r2

description:
m12_r2
secondary-transplanted HSCs
Mspi cut fragment at size 40~200bp.


title: KO3a_r1

description:
KO3a_r1
secondary-transplanted HSCs
Mspi cut fragment at size 40~200bp.

value: Dnmt3a knockout (Mx1-cre+;Dnmt3a∆/∆)


title: KO3a_r2

description:
KO3a_r2
secondary-transplanted HSCs
Mspi cut fragment at size 40~200bp.


title: min_total_RNA

status: Public on Oct 01 2011

city: Cambridge

first: Tsute

last: Chen

state: MA

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

library_source: transcriptomic

data_processing: Pileup forward: The Illumina sequence reads were mapped to the reference genome Porphyromonas gingivalis W83 (Accession No. NC_002950.2) using the software PerM allowing a maximum of two mismatches. Reads that did not align to the genome were trimmed from the 3' end, one base at a time, and the mapping-trimming process was repeated until the read was aligned or the trimmed length reached 24nt in length. Reads that were not aligned after being trimmed to 24-nt were discarded. The aligned results were separated into forward and reverse-complement groups and converted to the 'pileup' format by SAMtools. This process generated the reads that were mapped to the forward strand of the reference genome

molecule: total RNA

organism: Porphyromonas gingivalis W83

source_name: P. gingivalis cells

growth_protocol: P. gingivalis strain W83 was routinely maintained on the blood agar plates BAPHK containing defibrinated sheep blood (5% v/v), hemin (1µg/ml), and vitK/menadione (0.5µg/ml), at 37°C in an anaerobic chamber containing 95% nitrogen and 5% carbon dioxide. Cells were cultured under the same conditions in three different media: i) BAPHK; ii) TSB: trypticase soy broth supplemented with hemin (1µg/ml) and vitK/menadione (0.5µg/ml); and iii) MIN: a chemically defined minimal liquid medium providing alpha-ketogluterate and bovine serum albumin (BSA) as the only protein sources. For BAPHK cultures, colonies grown on the plates for 48 hours were used. For liquid cultures, pre-warmed and pre-reduced medium was inoculated with an aliquot of overnight TSB culture so that the dilution rates were 1:100 and 2:100 for TSB and MIN, respectively. Liquid cultures were allowed to reach mid-log phase (OD550 0.4-0.5) prior to harvest.

extract_protocol: Lysis of pelleted cells was performed using the MasterPure RNA Purification Kit (Epicentre, Madison, WI, USA). The lysate was treated with Proteinase K at 65°C for 15 min and then filter purified applying the mirVana miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the recommended protocol. To remove genomic DNA, the RNA extract was treated twice with Turbo DNase (Applied Biosystems/Ambion) at 37°C for 30 min, and purified again with the mirVana miRNA Isolation Kit. All samples were subjected to similar procedures except from the purifications steps where the mirVana filter based method was exchanged for MasterPure based RNA purification when preparing the MIN samples. The resulting total RNA samples were subject to partial removal of 16S and 23S RNAs applying the MICROBExpress Bacterial mRNA Enrichment Kit (Applied Biosystems/Ambion) and then fragmented with RNA Fragmentation Reagents (Applied Biosystems/Ambion) followed by ethanol precipitation. Antarctic Phosphatase (New England Biolabs, Cambridge, MA) was used, 5 U in a 20 ul reaction incubated at 37°C for 30 min, to remove 5' phosphate group from the RNA. Fragmented RNA was then subjected to size selection in a 15% Novex TBE-urea polyacrylamide gel (Invitrogen, Carlsbad, CA, USA), eluted, and ethanol precipitated prior to ligation of the 3' oligonucleotide adapter (5'-UCGUAUGCCGUCUUCUGCUUGUidT-3'). The adapter ligation was performed using T4 RNA ligase in 10% DMSO, incubated at 20°C for 6 hrs. The 3' adapter ligated RNA was purified on a 15% Novex TBE-urea polyacrylamide gel (Invitrogen), eluted, ethanol precipitated, and then phosphorylated in a 50 ul reaction containing 40 U T4 Polynucleotide Kinase (New England Biolabs) and 1 mM ATP (Epicentre) for 1h at 37°C. After phenol: chloroform purification and ethanol precipitation, the 5' oligonucleotide adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3') was ligated to the phosphorylated RNA under conditions similar to the 3' adapter ligation. The adapter ligated RNA was gel-purified and reverse transcribed using a primer specific to the 3' adapter (5'-CAAGCAGAAGACGGCATACGA-3') followed by PCR (15 cycles) using the reverse (5'-AATGATACGGCGACCACCGACAGGTTCAGAG TTCTACAGTCCGA-3') and forward (5'-CAAGCAGAAGACGGCATACGA-3') primers. The entire amplified product was size separated, ethanol precipitated, and dissolved in 10 ul resuspension buffer (Illumina) before the samples were subjected to sequencing.

tag: medium

value: MIN

tag: harvest time

value: mid-log phase


title: Input Replicate1


title: HudsonAlpha_ChipSeq_H1-hESC_p300_v041610.2

status: Public on Sep 29 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

growth_protocol: missing

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=wgEncodeHaibTfbs

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Rabbit Polyclonal. Antibody Target:P300

tag: antibody targetdescription

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: controlid

tag: labexpid

tag: replicate

tag: softwareversion

value: MACS

tag: antibody

value: Rabbit Polyclonal

value: Santa Cruz Biotech

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: protocol

tag: protocol description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate description

value: tier 1


title: HudsonAlpha_ChipSeq_T-47D_ERalpha_a_Estradiol_10nM_v041610.2

tag: cell description

value: epithelial cell line derived from a mammary ductal carcinoma.

value: Rabbit affinity purified polyclonal antibody. Epitope is the C-terminus of human estrogen receptor alpha (ESR1). Recommended for detection of estrogen receptor of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:ESR1

value: This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq)

value: 1 h with 10 nM Estradiol (Myers)

value: 1 h with 10 nM Estradiol  (Myers)


title: HudsonAlpha_ChipSeq_ECC-1_ERalpha_a_Genistein_100nM_v041610.2

tag: datatype

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

tag: cell lineage

value: endoderm

value: 1 h with 100 nM Genistein (Myers)

value: 1 h with 100 nM Genistein   (Myers)


title: YQH_total RNA minus rRNA

city: Madison

first: Nicholas

last: Eakley

state: WI

address: 1675 Observatory Drive

department: Animal Sciences

institute: UW-Madison

description: RNA from yqhC mutant

data_processing:
Cluster generation was performed using standard Cluster Kits (v2) and the Illumina Cluster Station, with each sample placed in a single lane.  A paired end, 75bp run was performed, using standard 36 bp SBS kits (v3) and SCS 2.4 software, on an Illumina Genome Analyzer IIx.  Images were analyzed using the standard Illumina Pipeline, version 1.4.
CLC Genomics Workbench Version 3.7 (CLC Bio, Cambridge, MA.).
CLC data processing details linked as supplementary file on Series record.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: yqhC mutant

growth_protocol: Lauria Bertani (LB) broth medium to mid-exponential phase at 37oC

extract_protocol: Total RNA was submitted to the University of Wisconsin-Madison Biotechnology Center for quality control testing (NanoDrop Spectrophotometer and Agilent 2100 BioAnalyzer for purity and integrity verification, respectively) and RNA Seq library preparation.   Each library was generated using Illumina’s “Preparing Samples for Sequencing of mRNA” (Rev. D) guide and the Illumina mRNA-Seq 8 Sample Preparation Kit (Illumina Inc., San Diego, California, USA) with minimal modification.  To create the libraries, mRNA was purified from 10ug total RNA using poly-T oligo-attached magnetic beads.  Subsequently, each mRNA sample was fragmented into small pieces using divalent cations under elevated temperature, and ethanol precipitated.  Each mRNA pellet was suspended in 11.1ul RNase-free water.   Double-stranded cDNAs were synthesized using SuperScript II (Invitrogen, Carlsbad, California, USA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA Polymerase I and RNAse H for removal of mRNA.  Double-stranded cDNA was purified using QIAquick PCR Purification columns (Qiagen, Valencia, California, USA).   cDNAs were end-repaired by T4 DNA polymerase and Klenow DNA Polymerase, and phosphorylated by T4 polynucleotide kinase.  The blunt ended cDNA was purified using QIAquick PCR Purification columns.  The cDNA products were incubated with Klenow DNA Polymerase to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments and then purified using MinElute PCR Purification columns (Qiagen).  DNA fragments were ligated to Illumina adapters, which have a single ‘T’ base (Thymine) overhang at their 3’end.  The adapter-ligated products were purified using MinElute PCR Purification columns.  Products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen, Carlsbad, California, USA) targeting 200bp fragments.  cDNA products were PCR-amplified with PhusionTM DNA Polymerase using Illumina's genomic DNA primer set and purified using QIAquick PCR Purification columns.  Quality and quantity of the finished libraries were assessed using an Agilent DNA 1000 series chip assay and QuantIT PicoGreen dsDNA Kit (Invitrogen, Carlsbad, California, USA), respectively, and libraries were standardized to 10μM.

tag: genotype/variation

value: yqhC mutant

tag: strain


title: HudsonAlpha_ChipSeq_GM12878_BATF_PCR1x

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

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

tag: antibody antibodydescription

value: Mouse monoclonal. Raised against recombinant B-ATF of human origin. Recommended for detection of B-ATF of m, r and h origin by WB, IP and ELISA. Antibody Target:BATF

tag: antibody targetdescription

value: The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events.

tag: antibody vendorname

value: Santa Cruz Biotechnology

value: one 15-cycle round of PCR (Myers)

tag: labversion

value: 1-cycle of PCR (Myers)


title: WT_total RNA minus rRNA

description: RNA from WT Salmonella

source_name: WT

value: WT


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in BMP4 Mesendoderm Cells; renlab.H2BK5ac.BMP4M.01.01

status: Public on Oct 04 2011

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK127
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9584
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM807394_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK5ac.AK127.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4M.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK127, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12421
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,557,315
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.017
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0436
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8221
IROC_PERCENTILE: 29
POISSON_SCORE: 0.1248
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM807394_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK5ac.AK127.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4M.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK127, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12494
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HBDM H2BK5ac 27
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK127 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,557,315
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.017
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0436
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8221
IROC_PERCENTILE: 29
POISSON_SCORE: 0.1248
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H2BK5ac.BMP4M.01.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: passage

value: Between 20 and 30

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H2BK5ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: HudsonAlpha_ChipSeq_GM12878_TAF1_PCR1x

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

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

value: Mouse monoclonal (p250). Antibody Target:TAF1

value: TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: protocol description

value: one 15-cycle round of PCR (Myers)

tag: controlid

tag: labexpid

tag: replicate

value: Santa Cruz Biotech

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: protocol

tag: replicate description

value: tier 1


title: HudsonAlpha_ChipSeq_GM12878_Pbx3_PCR1x

tag: datatype description

tag: antibody antibodydescription

value: Rabbit Polyclonal IgG. Antibody Target:PBX3

tag: antibody targetdescription

tag: antibody vendorname

tag: labversion

tag: softwareversion

value: MACS

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_HeLa-S3_Pol2_PCR1x

tag: datatype

tag: cell lineage

value: ectoderm

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

value: RNA Polymerase II

value: Covance


title: HudsonAlpha_ChipSeq_GM12891_YY1_(SC-281)_v041610.1

value: ChipSeq

tag: cell description

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

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of YY1 of human origin. Antibody Target:YY1

value: YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1

tag: antibody vendorid

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: GATA1 Replicate2

description: Chromatin IP against GATA1

tag: cell type

value: primary human PBMC derived erythroblasts

tag: chip antibody

value: GATA1 made in-house


title: HudsonAlpha_ChipSeq_HepG2_Sin3Ak-20_PCR1x

value: Chromatin IP Sequencing

value: hepatocellular carcinoma

value: Rabbit polyclonal, Sin3A (k-20). Antibody Target:SIN3AK20

value: Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2

value: Santa Cruz Biotechnology

tag: protocol description

value: one 15-cycle round of PCR (Myers)

tag: controlid

tag: labexpid

tag: replicate

value: Santa Cruz Biotech


title: HudsonAlpha_ChipSeq_GM12878_PU.1_PCR1x

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

value: Rabbit Polyclonal IgG. Antibody Target:PU1

value: MACS

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: protocol

value: 1-cycle of PCR (Myers)

tag: replicate description

value: tier 1


title: HudsonAlpha_ChipSeq_ECC-1_Pol2_DMSO_0.02pct_v041610.2

value: ChipSeq

tag: datatype description

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

value: endoderm

tag: antibody antibodydescription

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

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

value: 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)

value: 1 h with 0.02% DMSO (Myers)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_SK-N-SH_RevXlinkChromatin_PCR2x

source_name: SK-N-SH

tag: datatype

value: Chromatin IP Sequencing

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

value: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: antibody

value: RevXlinkChromatin

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_USF-1_PCR1x

value: ChipSeq

tag: cell description

value: hepatocellular carcinoma

value: Rabbit polyclonal, USF-1 (C-20). Antibody Target:USF1

value: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: protocol description

value: one 15-cycle round of PCR (Myers)

tag: labversion

tag: softwareversion

value: MACS

value: Santa Cruz Biotech

value: No special treatment or protocol applies

value: 1-cycle of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_SK-N-SH_RA_RevXlinkChromatin_v041610.2

value: Chromatin IP Sequencing

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: controlid

tag: labexpid

tag: cell organism

value: human

value: neuroblastoma cell line, treatment:differentiated with retinoic acid. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: treatment

tag: treatment description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate


title: HudsonAlpha_ChipSeq_K562_GATA2_(SC-267)_PCR1x

tag: datatype description

tag: antibody antibodydescription

value: Mouse monoclonal IgG. Antibody Target:GATA2

tag: antibody targetdescription

value: This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq).

tag: antibody vendorname

value: Mouse monoclonal IgG.

tag: protocol

tag: replicate description


title: HudsonAlpha_ChipSeq_K562_SRF_v041610.1

tag: datatype

value: ChipSeq

value: Rabbit polyclonal. Antibody Target:SRF

value: Serum response transcription factor

tag: antibody

value: SRF

value: Rabbit polyclonal

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_Sin3Ak-20_v041610.1

value: Rabbit polyclonal, Sin3A (k-20). Antibody Target:SIN3AK20

value: Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2

value: Santa Cruz Biotechnology

tag: antibody vendorid

value: MACS

value: Rabbit polyclonal, Sin3A (k-20).

value: Santa Cruz Biotech

value: No special treatment or protocol applies

tag: protocol description


title: HudsonAlpha_ChipSeq_K562_Max_v041610.2

value: Chromatin IP Sequencing

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: cell sex

value: F

value: Max

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_H1-hESC_JunD_v041610.2

value: ChipSeq

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: controlid

tag: softwareversion

value: JunD

value: rabbit polyclonal IgG


title: HudsonAlpha_ChipSeq_K562_GABP_v041610.1

value: Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target:GABP

value: The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.

value: Santa Cruz Biotechnology

tag: labexpid

value: GABP

value: Mouse monoclonal, GABPa(G-1), IgG1

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_RevXlinkChromatin_PCR1x

value: Chromatin IP Sequencing

tag: cell description

value: hepatocellular carcinoma

value: one 15-cycle round of PCR (Myers)

tag: labversion

tag: cell lineage

value: endoderm

value: M

value: RevXlinkChromatin

tag: treatment

value: No special treatment or protocol applies

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12878_POU2F2_PCR1x

value: ChipSeq

tag: datatype description

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

tag: antibody antibodydescription

value: Oct-2(C-20) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of Oct-2 of human origin. Recommended for detection of Oct-2 of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:POU2F2

value: Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter.

tag: replicate

value: MACS

value: Santa Cruz Biotech

tag: treatment description

value: tier 1


title: HudsonAlpha_ChipSeq_T-47D_p300_DMSO_0.02pct_v041610.2

value: epithelial cell line derived from a mammary ductal carcinoma.

value: Rabbit Polyclonal. Antibody Target:P300

tag: antibody targetdescription

tag: antibody vendorname

value: Santa Cruz Biotechnology

value: 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)

value: 1 h with 0.02% DMSO (Myers)

tag: protocol

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_HepG2_Rad21_v041610.1

tag: datatype

value: Chromatin IP Sequencing

value: hepatocellular carcinoma

value: Rabbit polyclonal. Antibody Target:RAD21

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

value: abcam

tag: antibody vendorid

value: Rabbit polyclonal

value: Abcam

tag: protocol description

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12892_YY1_v041610.1

value: ChipSeq

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

value: Rabbit polyclonal. Antibody Target:YY1

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

tag: controlid

tag: softwareversion

value: MACS

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_T-47D_GATA3_(SC-268)_DMSO_0.02pct_v041610.2

tag: cell description

value: epithelial cell line derived from a mammary ductal carcinoma.

value: Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target:GATA3

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

value: Santa Cruz Biotechnology

value: 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)

tag: labexpid

value: Santa Cruz Biotech

value: tier 1


title: HudsonAlpha_ChipSeq_K562_BCLAF1_(SC-101388)_PCR1x

value: Chromatin IP Sequencing

value: Mouse monoclonal IgG, raised against a synthetic peptide corresponding to a.a. 900-909 of BCLAF1 of human origin. Antibody Target:BCLAF1

value: This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq).

value: one 15-cycle round of PCR (Myers)

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_H1-hESC_ATF3_v041610.2

value: ChipSeq

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

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

tag: antibody

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12878_BCLAF1_(SC-101388)_v041610.1

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

value: MACS

value: Mouse monoclonal IgG, raised against a synthetic peptide corresponding to a.a. 900-909 of BCLAF1 of human origin.

tag: treatment

value: No special treatment or protocol applies

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_H1-hESC_YY1_(SC-281)_v041610.2

tag: datatype description

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of YY1 of human origin. Antibody Target:YY1

value: YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1

value: Santa Cruz Biotechnology


title: HudsonAlpha_ChipSeq_GM12878_ETS1_PCR1x

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Rabbit polyclonal IgG. Antibody Target:ETS1

value: ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis

value: Rabbit polyclonal IgG

value: Santa Cruz Biotech

value: tier 1


title: HudsonAlpha_ChipSeq_GM12878_MEF2A_PCR1x

value: ChipSeq

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of MEF-2 of human origin. Antibody Target:MEF2A

value: The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes.

value: one 15-cycle round of PCR (Myers)

tag: replicate

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12878_ATF3_PCR1x

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

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

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

value: MACS

tag: treatment description


title: HudsonAlpha_ChipSeq_HepG2_SP1_PCR1x

value: hepatocellular carcinoma

value: Sp1(E-3) is a mouse monoclonal antibody raised against amino acids 121-345 mapping near the N-terminus of Sp1 ofhuman origin. Recommended for detection of Sp1 of m, r and h origin by WB, IP, IF and ELISA. Antibody Target:SP1

tag: antibody targetdescription

value: SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter.

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_HepG2_SRF_v041610.1

value: Chromatin IP Sequencing

value: Rabbit polyclonal. Antibody Target:SRF

value: Serum response transcription factor

tag: antibody vendorname

value: Santa Cruz Biotechnology

value: Rabbit polyclonal

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_ATF3_v041610.1

value: ChipSeq

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

value: Santa Cruz Biotech

tag: protocol

value: tier 1


title: HudsonAlpha_ChipSeq_K562_ZBTB33_PCR1x

value: Kaiso (6F8) Mouse monoclonal IgG1. Raised against amino acids 1-504 representing full length Kaiso of human origin. Recommended for detection of Kaiso of m, r, h, canine and chicken origin by WB, IP, IF and ELISA. Antibody Target:ZBTB33

value: KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA

value: one 15-cycle round of PCR (Myers)

value: 1-cycle of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_K562_SP1_PCR1x

tag: datatype

value: Sp1(E-3) is a mouse monoclonal antibody raised against amino acids 121-345 mapping near the N-terminus of Sp1 ofhuman origin. Recommended for detection of Sp1 of m, r and h origin by WB, IP, IF and ELISA. Antibody Target:SP1

tag: labversion

value: MACS


title: HudsonAlpha_ChipSeq_H1-hESC_TAF7_(SC-101167)_v041610.2

value: Mouse monoclonal IgG, raised against recombinant TAF II p55 (TAF7) of human origin. Antibody Target:TAF7

value: The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq).

tag: antibody vendorid

value: No special treatment or protocol applies

tag: protocol description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_H1-hESC_RXRA_v041610.2

value: Chromatin IP Sequencing

value: RXRa(D-20) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the N-terminus of RXRalpha of human origin. Recommended for detection of RXRalpha of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:RXRA

value: Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators.

value: Santa Cruz Biotechnology

tag: controlid

tag: cell sex

value: M

value: RXRA


title: HudsonAlpha_ChipSeq_K562_BCL3_PCR1x

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

value: ChipSeq

value: ChIP-Seq

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

value: F

value: Bcl-3(C-14) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of Bcl-3 of human origin. Recommended for detection of Bcl-3 of m, r and h origin by WB, IP, IF and ELISA.

value: This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq).

value: Santa Cruz Biotech

tag: labexpid

value: tier 1


title: HudsonAlpha_ChipSeq_T-47D_ERalpha_a_DMSO_0.02pct_v041610.2

tag: datatype description

value: Chromatin IP Sequencing

value: epithelial cell line derived from a mammary ductal carcinoma.

tag: antibody antibodydescription

value: Rabbit affinity purified polyclonal antibody. Epitope is the C-terminus of human estrogen receptor alpha (ESR1). Recommended for detection of estrogen receptor of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:ESR1

tag: antibody targetdescription

value: This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq)

tag: antibody vendorname

tag: treatment description

value: 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)

tag: replicate

tag: treatment

value: 1 h with 0.02% DMSO (Myers)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_SK-N-SH_RA_YY1_(SC-281)_v041610.2

tag: datatype

value: ChipSeq

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of YY1 of human origin. Antibody Target:YY1

value: YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: controlid

tag: softwareversion

value: MACS

value: No special treatment or protocol applies

tag: protocol

tag: protocol description

tag: replicate description


title: HudsonAlpha_ChipSeq_HepG2_JunD_PCR1x

tag: cell description

value: hepatocellular carcinoma

value: rabbit polyclonal IgG. Antibody Target:JunD

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

value: one 15-cycle round of PCR (Myers)

tag: labversion

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_SK-N-SH_RA_p300_v041610.2

value: Chromatin IP Sequencing

value: Rabbit Polyclonal. Antibody Target:P300

tag: labexpid

value: Rabbit Polyclonal

value: Santa Cruz Biotech

value: tier 1


title: HudsonAlpha_ChipSeq_SK-N-SH_RA_Rad21_v041610.2

value: ChipSeq

tag: datatype description

value: Rabbit polyclonal. Antibody Target:RAD21

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

value: abcam

value: Rabbit polyclonal

value: Abcam

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_ELF1_(SC-631)_v041610.2

tag: antibody antibodydescription

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin. Antibody Target:ELF1

value: This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq)

value: Santa Cruz Biotechnology

value: MACS

tag: antibody

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_GM12878_ELF1_(SC-631)_v041610.1

value: Chromatin IP Sequencing

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

tag: antibody targetdescription

tag: antibody vendorname

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin.

value: This gene encodes an E26 transformation-specific related transcription factor.  The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes.  Alternative splicing results in multiple transcript variants. (provided by RefSeq)

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_HDAC2_(SC-6296)_v041610.1

value: ChipSeq

value: hepatocellular carcinoma

value: Goat polyclonal IgG, epitope mapping at the C-terminus of HDAC2 of human origin. Antibody Target:HDAC2

value: This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq)

tag: replicate

value: Santa Cruz Biotech

tag: treatment description

value: tier 1


title: HudsonAlpha_ChipSeq_SK-N-MC_RevXlinkChromatin_PCR2x

source_name: SK-N-MC

tag: datatype

value: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)

tag: cell organism

value: human

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

value: RevXlinkChromatin

tag: treatment

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12892_RevXlinkChromatin_v041610.2

value: Chromatin IP Sequencing

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

tag: controlid

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: No special treatment or protocol applies

tag: protocol

tag: protocol description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_U87_RevXlinkChromatin_v041610.1

value: ChipSeq

tag: datatype description

tag: labexpid

tag: cell

tag: cell description

value: M

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_H1-hESC_Pol2-4H8_v041610.2

tag: antibody antibodydescription

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL2

tag: antibody targetdescription

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

tag: antibody vendorname

value: abcam

tag: antibody vendorid

tag: antibody

value: Abcam

value: tier 1


title: HudsonAlpha_ChipSeq_GM12892_Pol2-4H8_v041610.2

tag: datatype

tag: replicate

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade

tag: treatment description


title: HudsonAlpha_ChipSeq_HepG2_p300_v041610.1

value: hepatocellular carcinoma

value: Rabbit Polyclonal. Antibody Target:P300

value: Santa Cruz Biotechnology

tag: softwareversion

value: MACS

value: Rabbit Polyclonal

value: Santa Cruz Biotech

tag: treatment


title: HudsonAlpha_ChipSeq_GM12878_Pol2-4H8_PCR1x

value: Chromatin IP Sequencing

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

value: one 15-cycle round of PCR (Myers)

tag: controlid

tag: labversion

value: No special treatment or protocol applies

tag: protocol

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12892_TAF1_v041610.2

value: ChipSeq

tag: datatype description

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

value: Mouse monoclonal (p250). Antibody Target:TAF1

value: TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.

value: Mouse monoclonal (p250)

tag: protocol description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_GM12892_Pol2_v041610.2

tag: cell description

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

value: RNA Polymerase II

value: Covance

tag: labexpid

value: mouse monoclonal, clone 8WG16

value: tier 1


title: HudsonAlpha_ChipSeq_HepG2_CTCF_(SC-5916)_v041610.1

value: hepatocellular carcinoma

tag: antibody antibodydescription

value: Goat polyclonal IgG, epitope mapping at the N-terminus of CTCF of human origin. Antibody Target:CTCF

tag: antibody targetdescription

value: This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)

value: Santa Cruz Biotechnology

value: Santa Cruz Biotech

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12892_RevXlinkChromatin_v041610.1

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, Treatment:Epstein-Barr Virus transformed

tag: cell karyotype

value: unknown

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: RevXlinkChromatin

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_PFSK-1_FOXP2_PCR2x

tag: datatype

value: neuroectodermal cell line derived from a cerebral brain tumor, (PMID:1316433)

value: Rabbit polyclonal, raised against C-terminal 127 amino acids of FOXP2 of human origin. Antibody Target:FOXP2

value: This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech

tag: antibody vendorname

value: abcam

tag: antibody vendorid

value: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)

tag: replicate

value: rabbit polyclonal

value: transcriptional repressor, involved in development of speech

value: Abcam

tag: treatment description

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_GM12891_RevXlinkChromatin_PCR1x

value: ChipSeq

value: Chromatin IP Sequencing

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

value: one 15-cycle round of PCR (Myers)

tag: controlid

tag: labversion

value: M

tag: antibody

tag: treatment

tag: protocol

value: 1-cycle of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_HepG2_BHLHE40_v041610.1

tag: datatype description

tag: cell description

value: hepatocellular carcinoma

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

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

value: Santa Cruz Biotechnology

tag: labexpid

tag: softwareversion

value: MACS

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

value: Santa Cruz Biotech

value: No special treatment or protocol applies

tag: protocol description

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_K562_E2F6_v041610.2

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HCT-116_Pol2-4H8_v041610.1

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL2

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

tag: antibody vendorname

value: abcam

value: Abcam


title: HudsonAlpha_ChipSeq_HeLa-S3_RevXlinkChromatin_PCR1x

tag: cell lineage

value: ectoderm

value: one 15-cycle round of PCR (Myers)

value: cervical carcinoma

tag: cell karyotype

value: cancer

tag: cell sex

value: F

value: RevXlinkChromatin

value: 1-cycle of PCR (Myers)

tag: replicate

value: tier 1


title: HudsonAlpha_ChipSeq_GM12891_RevXlinkChromatin_v041610.1

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

tag: controlid

tag: cell organism

value: human

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: M

tag: antibody

tag: treatment description

value: No special treatment or protocol applies

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HCT-116_RevXlinkChromatin_v041610.1

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell description

value: colorectal carcinoma (PMID:7214343)

value: endoderm

tag: treatment

tag: protocol


title: HudsonAlpha_ChipSeq_A549_RevXlinkChromatin_DEX_100nM_PCR2x

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: 1 h with 100 nM Dexamethasone (Myers)

tag: protocol description

value: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)

tag: labexpid

value: cancer

value: 1 h with 100 nM DEX (Myers)

value: 2-cycles of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_K562_YY1_v041610.2

tag: datatype

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:YY1

tag: antibody targetdescription

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

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: softwareversion

value: MACS

value: Rabbit polyclonal

value: Santa Cruz Biotech

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_K562_ZBTB7A_(SC-34508)_v041610.1

value: ChipSeq

value: Chromatin IP Sequencing

value: Goat polyclonal IgG, epitope mapping at the C-terminus of LRF of human origin. Antibody Target:ZBTB7A

value: Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity).

tag: controlid

tag: replicate

value: No special treatment or protocol applies

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_SK-N-SH_RA_USF1_(SC-8983)_v041610.2

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: Rabbit polyclonal IgG, epitope corresponding to a.a. 75-160 mapping within internal region of USF1 of human origin. Antibody Target:USF1

value: This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq).

tag: treatment description


title: HudsonAlpha_ChipSeq_H1-hESC_BCL11A_v041610.2

tag: datatype description

value: Mouse monoclonal [18B12DE6] to Ctip1. Raised against a cocktail of BCL11A fusion proteins. Reacts with human and mouse. Tested for ICC/IF, IHC-P, IP, WB. Antibody Target:BCL11A

value: This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity)

value: abcam

tag: cell lineage

value: inner cell mass

tag: cell sex

value: M

tag: antibody

value: Abcam

value: tier 2


title: HudsonAlpha_ChipSeq_GM12878_SRF_v041610.1

tag: cell description

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

value: Rabbit polyclonal. Antibody Target:SRF

value: Serum response transcription factor

value: Santa Cruz Biotechnology

value: MACS

value: Rabbit polyclonal

value: Santa Cruz Biotech

tag: treatment

tag: protocol

value: tier 1


title: HudsonAlpha_ChipSeq_K562_HDAC2_(SC-6296)_v041610.2

value: ChipSeq

value: Chromatin IP Sequencing

value: Goat polyclonal IgG, epitope mapping at the C-terminus of HDAC2 of human origin. Antibody Target:HDAC2

value: This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq)

tag: labexpid

value: No special treatment or protocol applies

tag: protocol description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_H1-hESC_Rad21_v041610.2

tag: datatype

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

value: abcam


title: HudsonAlpha_ChipSeq_HeLa-S3_NRSF_PCR1x

value: ectoderm

value: Mouse monoclonal. Antibody Target:NRSF

value: Neuron-restrictive silencer transcription factor

tag: antibody vendorname

value: Dr. David Anderson at Caltech

tag: antibody vendorid

value: (Made by Protein Expression Center:pec@caltech.edu)

value: one 15-cycle round of PCR (Myers)

tag: softwareversion

value: David Anderson, Caltech

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_RevXlinkChromatin_v041610.1

value: ChipSeq

value: hepatocellular carcinoma

tag: controlid

tag: replicate

value: liver carcinoma

tag: cell karyotype

value: cancer

value: endoderm

value: M

value: RevXlinkChromatin

tag: treatment description

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_HepG2_FOXA1_(SC-6553)_v041610.1

tag: datatype description

value: Chromatin IP Sequencing

value: Goat polyclonal IgG, epitope mapping at the C-terminus of FOXA1 of human origin. Antibody Target:FOXA1

value: This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq).

value: Santa Cruz Biotechnology

value: MACS

value: Santa Cruz Biotech

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_ECC-1_GR_EtOH_0.02pct_v041610.2

tag: cell description

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

tag: cell lineage

value: Rabbit Polyclonal. Antibody Target:GR

value: Glucocorticoid Receptor

value: 1 h with 0.02% Ethanol (Myers)

value: 1 h with 0.02% EtOH (Myers)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_RevXlinkChromatin_PCR2x

value: ChipSeq

value: hepatocellular carcinoma

value: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)

value: cancer

value: endoderm

tag: cell sex

value: M

tag: antibody

tag: treatment

tag: protocol

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_HNF4A_(SC-8987)_v041610.1

tag: datatype

value: Chromatin IP Sequencing

value: Rabbit polyclonal IgG, epitope corresponding to a.a. 295-465 mapping at the C-terminus of HNF4A of human origin. Antibody Target:HNF4A

value: The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq).

value: Santa Cruz Biotechnology

tag: labexpid

tag: protocol description

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)

tag: replicate description

value: tier 1


title: HudsonAlpha_ChipSeq_U87_Pol2-4H8_v041610.1

tag: antibody antibodydescription

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL2

tag: antibody targetdescription

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

tag: antibody vendorname

value: abcam

tag: antibody vendorid

value: MACS

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_K562_RevXlinkChromatin_v041610.1

value: ChipSeq

tag: controlid

tag: replicate

tag: cell organism

value: human

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

tag: cell karyotype

value: mesoderm

value: F

value: RevXlinkChromatin


title: HudsonAlpha_ChipSeq_HCT-116_ZBTB33_v041610.1

tag: datatype description

value: Chromatin IP Sequencing

value: Kaiso (6F8) Mouse monoclonal IgG1. Raised against amino acids 1-504 representing full length Kaiso of human origin. Recommended for detection of Kaiso of m, r, h, canine and chicken origin by WB, IP, IF and ELISA. Antibody Target:ZBTB33

value: KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA

tag: softwareversion

value: Santa Cruz Biotech

tag: treatment description


title: HudsonAlpha_ChipSeq_A549_USF-1_DEX_100nM_PCR1x

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: Rabbit polyclonal, USF-1 (C-20). Antibody Target:USF1

value: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.

value: Santa Cruz Biotechnology

value: 1 h with 100 nM Dexamethasone (Myers)

value: one 15-cycle round of PCR (Myers)

tag: treatment

value: 1 h with 100 nM DEX (Myers)

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_HeLa-S3_GABP_PCR1x

tag: datatype

value: ChipSeq

tag: cell lineage

value: ectoderm

value: Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target:GABP

value: The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.

tag: labversion

value: MACS

value: No special treatment or protocol applies

tag: protocol

value: tier 1


title: HudsonAlpha_ChipSeq_HeLa-S3_TAF1_PCR1x

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Mouse monoclonal (p250). Antibody Target:TAF1

value: TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.

tag: protocol description

tag: labexpid

tag: replicate description


title: HudsonAlpha_ChipSeq_A549_CTCF_(SC-5916)_EtOH_0.02pct_PCR1x

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: Goat polyclonal IgG, epitope mapping at the N-terminus of CTCF of human origin. Antibody Target:CTCF

tag: antibody targetdescription

value: This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)

tag: antibody vendorname

tag: antibody vendorid

value: 1 h with 0.02% Ethanol (Myers)

tag: controlid

value: Santa Cruz Biotech

value: 1 h with 0.02% EtOH (Myers)


title: HudsonAlpha_ChipSeq_A549_CTCF_(SC-5916)_DEX_100nM_PCR1x

tag: datatype description

value: Santa Cruz Biotechnology

value: 1 h with 100 nM Dexamethasone (Myers)

value: one 15-cycle round of PCR (Myers)

tag: replicate

value: 1 h with 100 nM DEX (Myers)

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_FOSL2_v041610.1

value: ChipSeq

value: hepatocellular carcinoma

value: Rabbit polyclonal. Fra-2(Q-20) is an affinity purified raised against the N-terminus of Fra-2 of human origin. Recommended for detection of Fra-2 of m, r, h and chicken origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:FOSL2

value: The Fos gene family consists of 4 members:FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation.

tag: softwareversion

value: MACS

tag: treatment description

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_HEY1_v041610.1

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

value: ChIP-Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: liver carcinoma

tag: cell karyotype

value: cancer

value: endoderm

tag: cell sex

value: M

tag: antibody

value: HRT1 (C-20) Goat polyclonal IgG, 200 ?g/ml. Epitope mapping near the C-terminus of HRT1 of human origin

value: This gene encodes a nuclear protein belonging to the hairy and enhancer of split-related (HESR) family of basic helix-loop-helix (bHLH)-type transcriptional repressors. Expression of this gene is induced by the Notch and c-Jun signal transduction pathways. Two similar and redundant genes in mouse are required for embryonic cardiovascular development, and are also implicated in neurogenesis and somitogenesis. Alternative splicing results in multiple transcript variants.

tag: treatment

value: No special treatment or protocol applies

value: tier 1


title: HudsonAlpha_ChipSeq_H1-hESC_TAF1_v041610.2

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Mouse monoclonal (p250). Antibody Target:TAF1

tag: antibody targetdescription

value: TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.

value: Santa Cruz Biotechnology

tag: labexpid

value: Mouse monoclonal (p250)

value: Santa Cruz Biotech

tag: protocol

tag: protocol description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate description


title: HudsonAlpha_ChipSeq_HepG2_ZBTB33_PCR1x

tag: datatype description

value: hepatocellular carcinoma

value: Kaiso (6F8) Mouse monoclonal IgG1. Raised against amino acids 1-504 representing full length Kaiso of human origin. Recommended for detection of Kaiso of m, r, h, canine and chicken origin by WB, IP, IF and ELISA. Antibody Target:ZBTB33

value: KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA

tag: antibody vendorname

tag: antibody vendorid

value: one 15-cycle round of PCR (Myers)

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion

value: MACS

tag: treatment description

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_YY1_(SC-281)_v041610.1

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of YY1 of human origin. Antibody Target:YY1

value: YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1

tag: cell sex

value: F

tag: antibody

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_HepG2_RXRA_PCR1x

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: RXRa(D-20) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the N-terminus of RXRalpha of human origin. Recommended for detection of RXRalpha of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:RXRA

value: Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators.

tag: treatment

value: No special treatment or protocol applies

value: tier 1


title: HudsonAlpha_ChipSeq_ECC-1_RevXlinkChromatin_DMSO_0.02pct_v041610.2

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

tag: cell lineage

value: endoderm

value: 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)

tag: labexpid

tag: cell karyotype

value: cancer

value: epithelia

value: RevXlinkChromatin

value: 1 h with 0.02% DMSO (Myers)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_ETS1_v041610.1

tag: antibody antibodydescription

value: Rabbit polyclonal IgG. Antibody Target:ETS1

tag: antibody targetdescription

value: ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis

value: Santa Cruz Biotechnology

value: MACS

value: Rabbit polyclonal IgG

value: Santa Cruz Biotech

tag: protocol

tag: protocol description

tag: replicate description


title: HudsonAlpha_ChipSeq_K562_Pol2-4H8_v041610.1

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL2

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

tag: antibody vendorname

value: abcam

tag: antibody vendorid

tag: controlid

value: Abcam

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_FOSL1_(SC-183)_v041610.1

value: Rabbit polyclonal IgG, epitope mapping at the N-terminus of FOSL1 of human origin. Antibody Target:FOSL1

value: The Fos gene family consists of 4 members:FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq)

tag: replicate

tag: softwareversion

tag: treatment description

value: No special treatment or protocol applies

value: tier 1


title: HudsonAlpha_ChipSeq_H1-hESC_NANOG_(SC-33759)_v041610.2

tag: datatype

value: Rabbit polyclonal IgG, epitope corresponding to amino acids 151-305 mapping at the C-terminus of Nanog of human origin. Antibody Target:NANOG

value: Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq).

tag: antibody

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_H1-hESC_POU5F1_(SC-9081)_v041610.2

value: Rabbit polyclonal IgG, epitope corresponding to amino acids 1-134 of Oct3/4 of human origin. Antibody Target:POU5F1

value: This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq).

value: Santa Cruz Biotechnology

value: MACS

tag: treatment


title: HudsonAlpha_ChipSeq_GM12878_RevXlinkChromatin_v041610.1

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

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

tag: labexpid

tag: cell organism

value: human

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: RevXlinkChromatin


title: HudsonAlpha_ChipSeq_A549_RevXlinkChromatin_EtOH_0.02pct_PCR2x

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: 1 h with 0.02% Ethanol (Myers)

tag: protocol description

value: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)

tag: cell karyotype

value: cancer

value: endoderm

value: M

value: 1 h with 0.02% EtOH (Myers)

tag: protocol

value: 2-cycles of PCR (Myers)


title: HudsonAlpha_ChipSeq_ECC-1_FOXA1_(SC-6553)_DMSO_0.02pct_v041610.2

tag: datatype description

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

tag: antibody antibodydescription

value: Goat polyclonal IgG, epitope mapping at the C-terminus of FOXA1 of human origin. Antibody Target:FOXA1

tag: antibody targetdescription

value: This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq).

tag: antibody vendorname

value: Santa Cruz Biotechnology

value: 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)

value: MACS

value: Santa Cruz Biotech

value: 1 h with 0.02% DMSO (Myers)

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

tag: replicate description

value: tier 1


title: HudsonAlpha_ChipSeq_T-47D_RevXlinkChromatin_DMSO_0.02pct_v041610.2

value: ChipSeq

value: Chromatin IP Sequencing

value: epithelial cell line derived from a mammary ductal carcinoma.

tag: treatment description

tag: controlid

value: T-47D is a human epithelial cell line derived from an mammary ductal carcinoma.

value: F

value: RevXlinkChromatin

tag: replicate


title: HudsonAlpha_ChipSeq_K562_Rad21_v041610.2

tag: datatype

value: Rabbit polyclonal. Antibody Target:RAD21

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

value: abcam

tag: antibody vendorid

tag: softwareversion

tag: antibody

value: Rabbit polyclonal

value: Abcam

tag: treatment

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_K562_USF-1_v041610.1

value: Rabbit polyclonal, USF-1 (C-20). Antibody Target:USF1

value: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.

value: Santa Cruz Biotechnology

tag: labexpid

value: MACS

value: Rabbit polyclonal, USF-1 (C-20).

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_NRSF_v041610.2

value: ChipSeq

value: Chromatin IP Sequencing

value: Mouse monoclonal. Antibody Target:NRSF

value: Neuron-restrictive silencer transcription factor

value: Dr. David Anderson at Caltech

value: (Made by Protein Expression Center:pec@caltech.edu)

value: NRSF

value: Mouse monoclonal

value: David Anderson, Caltech

tag: protocol description

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_HepG2_FOXA1_(SC-101058)_v041610.1

tag: cell description

value: hepatocellular carcinoma

value: Mouse monoclonal IgG, raised against recombinant HNF-3a of human origin. Antibody Target:FOXA1

value: This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq)

value: Santa Cruz Biotech

value: No special treatment or protocol applies


title: HudsonAlpha_ChipSeq_GM12878_Egr-1_v041610.1

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

value: Rabbit polyclonal, EGR-1 (588). Antibody Target:EGR1

value: Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner.

value: Santa Cruz Biotechnology

value: MACS

value: Rabbit polyclonal, EGR-1 (588).

tag: protocol

value: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)


title: HudsonAlpha_ChipSeq_K562_TAF1_v041610.1

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Mouse monoclonal (p250). Antibody Target:TAF1

value: TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.

value: Mouse monoclonal (p250)


title: HudsonAlpha_ChipSeq_H1-hESC_Egr-1_v041610.2

tag: antibody antibodydescription

value: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)

value: tier 1


title: HudsonAlpha_ChipSeq_A549_USF-1_EtOH_0.02pct_PCR1x

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: Rabbit polyclonal, USF-1 (C-20). Antibody Target:USF1

tag: antibody targetdescription

value: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.

value: 1 h with 0.02% Ethanol (Myers)

value: one 15-cycle round of PCR (Myers)

tag: labversion

value: 1 h with 0.02% EtOH (Myers)

value: 1-cycle of PCR (Myers)


title: HudsonAlpha_ChipSeq_H1-hESC_Sin3Ak-20_PCR1x

value: Rabbit polyclonal, Sin3A (k-20). Antibody Target:SIN3AK20

value: Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2

tag: antibody vendorname

value: Santa Cruz Biotechnology

value: MACS

value: Rabbit polyclonal, Sin3A (k-20).

value: Santa Cruz Biotech

value: No special treatment or protocol applies

tag: replicate description


title: HudsonAlpha_ChipSeq_H1-hESC_TCF12_PCR1x

value: ChipSeq

value: Chromatin IP Sequencing

value: HEB (A-20) Rabbit polyclonal IgG, 200 ?g/ml. Epitope mapping within the C-terminus of HEB of human origin. Antibody Target:TCF12

value: The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.

tag: controlid

tag: treatment description


title: HudsonAlpha_ChipSeq_H1-hESC_GABP_PCR1x

tag: datatype

value: Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target:GABP

value: The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.

tag: replicate

value: Mouse monoclonal, GABPa(G-1), IgG1

value: tier 1