title: Stanford_ChipSeq_A549_c-Myc_IgG-rab

value: Stanford

value: human

tag: cell lineage

tag: cell sex

tag: antibody

value: c-Myc

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

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

value: IgG-rab

tag: control description

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


title: Metal_C-DG

status: Public on Sep 13 2012

type: SRA

city: Qingdao

first: Fei

last: Xu

address: 7 Nanhai Road

country: China

institute: Institute of Oceanology, Chinese Academy of Sciences

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were with no metals challenges.

library_source: transcriptomic

data_processing: use oyster_v9 genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 5 -g 20 -I 10000 --solexa1.3-quals

molecule: total RNA

organism: Magallana gigas

source_name: Pool of three oyster digestive glands, with no metals challenge

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 Î¼g total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3â dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200Â±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: developmental stage

value: adult

tag: tissue

value: digestive gland

tag: exptl group

value: tissue


title: Stanford_ChipSeq_GM12878_CDP_(sc-6327)_IgG-mus

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

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

tag: lab

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

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

tag: cell karyotype

value: normal

value: mesoderm

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: CDP (C-20) is an affinity purified goat polyclonal antibody raised against a peptide mapping at the C-terminus of CDP of mouse origin.

tag: antibody targetdescription

value: CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase.

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: control

value: IgG-mus

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

tag: controlid

tag: labversion


title: Stanford_ChipSeq_GM12878_SREBP2_IgG-rab

tag: lab

value: Stanford

value: human

tag: cell lineage

tag: cell sex

tag: antibody

value: Rabbit polyclonal. Antibody Target:SREBP2

value: Sterol regulatory element binding transcription factor 2

value: Cayman Chemical

value: IgG-rab

tag: control description

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


title: Stanford_ChipSeq_GM12878_ZNF384_(HPA004051)_IgG-mus

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

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

value: Rabbit polyclonal generated using the immunogen:Zinc finger protein 384 recombinant protein epitope signature tag (PrEST)

value: This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7.

value: SIGMA


title: Cd9d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Cadmium(100 ug/L) for 9 days.

source_name: Pool of three oyster digestive glands, sampled at time 9d, Cd

tag: developmental stage

value: adult

tag: tissue

value: digestive gland

tag: exptl group

value: tissue


title: Metal_C-gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were with no metals challenges.

source_name: Pool of three oyster gills, with no metals challenge

value: gill


title: NCC_RNAseq

first: Alvaro

last: Rada

address: 269 Campus Drive, CCSR Building

department: Chemical and Systems Biology

institute: Stanford University

description: RNA-seq experiments in human neural crest cells (hNCC)

data_processing: RNA-seq libraries were sequenced with Illumina Genome Analyzer and both mapping and analysis of resulting reads were perfomed with DNAnexus software tools (https://dnanexus.com)

molecule: polyA RNA

growth_protocol: hNCC were differentiated in vitro from hESC. hESCs (H9 line, Wi-Cell) were expanded in feeder free, serum free medium, mTESR-1 from StemCell technologies. Cells were passaged 1:7 every 5-6 days by incubation with accutase (Invitrogen) long and resultant small cell clusters were subsequently re-plated on tissue culture dishes coated overnight with growth factor reduced matrigel (BD biosciences). hESCs quality was regularly tested by evaluating the expression of a panel of hESC markers (e.g. Alkaline phosphatase, OCT4) and the capacity to differentiate into cell types derived from the three germ layers.

extract_protocol: RNAs from hNCC were extracted with Trizol (invitrogen), following manufacturerâs recommendations. 10 Âµg of total RNA were subjected to two rounds of oligo-dT purification using Dynal oligo (dT) beads (Invitrogen). 100 ng of the purified RNA were fragmented with 10x Fragmentation Buffer (Ambion). Fragmented RNA was used for first strand cDNA synthesis, using random hexamer primers (Invitrogen) and SuperScript II enzyme (Invitrogen). Second strand cDNA was obtained by adding RNAseH (Invitrogen) and DNA Pol I (New England Biolabs) to the first strand cDNA mix. The resulting double-stranded cDNA was used for Illumina library preparation  according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation, DNA was size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: hESCs were differentiated into hNCCs by first incubating hESC with 2mg/ml collagenase. Once detached, cells were plated in NCC differentiation media: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5x B-27 supplement with Vitamin A (50x stock, Invitrogen),  0.5x N-2 supplement (100x stock, Invitrogen),  20 ng/ml bFGF (Peprotech),  20 ng/ml EGF (Sigma-Aldrich), 5 Âµg/ml bovine insulin (Sigma-Aldrich) and 1x Glutamax-I supplement (100x stock, Invitrogen). Cells  differentiated into floating hNEC neurospheres and after approximately seven days, they started to attach to the cell culture plates and give rise to hNCC. After three days since the appearance of the first hNCC, neuroectodermal spheres were eliminated and hNCC harvested for subsequent experiments. Media was changed every other day during the approximately ten days of differentiation

tag: cell type

value: Neural crest cells (hNCC) derived from H9 ESC


title: NCC_NR2F1/2_input

description: Total genomic DNA (input from NR2F1/2 ChIPs)

data_processing: Enrichment analysis was performed using QuEST software

extract_protocol: All antibodies used in this study have been previously reported as specific and suitable for ChIP and/or ChIP-seq: p300 (sc-585, Santa Cruz Biotechnology) , H3K4me1 (ab8895, Abcam), H3K27ac (ab4729, Abcam), H3K4me3 (39159, Active Motif), H3K27me3 (39536, Active Motif) , NR2F1 (PP-H8132-00, Perseus Proteomics), NR2F2 (PP-H7147-00, Perseus Proteomics). Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation, DNA was size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: hESCs were differentiated into hNCCs by first incubating hESC with 2mg/ml collagenase. Once detached, cells were plated in NCC differentiation media: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5x B-27 supplement with Vitamin A (50x stock, Invitrogen),  0.5x N-2 supplement (100x stock, Invitrogen),  20 ng/ml bFGF (Peprotech),  20 ng/ml EGF (Sigma-Aldrich), 5 Âµg/ml bovine insulin (Sigma-Aldrich) and 1x Glutamax-I supplement (100x stock, Invitrogen). Cells  differentiated into floating hNEC neurospheres and after approximately seven days, they started to attach to the cell culture plates and give rise to hNCC. After three days since the appearance of the first hNCC, neuroectodermal spheres were eliminated and hNCC harvested for subsequent experiments. Media was changed every other day during the approximately ten days of differentiation.

tag: chip antibody


title: Stanford_ChipSeq_GM12878_MafK_(ab50322)_IgG-mus

value: Stanford

value: human

tag: cell description

tag: cell karyotype

value: normal

value: mesoderm

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control

value: IgG-mus

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

tag: controlid


title: Stanford_ChipSeq_IMR90_RFX5_(200-401-194)_IgG-rab

tag: lab

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

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

tag: cell lineage

value: endoderm

tag: cell sex

tag: antibody

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

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

value: Rockland Immunochemicals

value: IgG-rab

tag: control description

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


title: Zn12h_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 12 hours.

source_name: Pool of three oyster digestive glands, sampled at time 12h, Zn

tag: developmental stage

value: adult

tag: tissue

value: digestive gland

tag: exptl group

value: tissue


title: NCC_NR2F1

description: ChIP against NR2F1

tag: cell type

value: Neural crest cells (hNCC) derived from H9 ESC

tag: chip antibody

value: NR2F1 (PP-H8132-00, Perseus Proteomics)


title: Hg9d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Hydrargyrum (100 ug/L) for 9 days.

source_name: Pool of three oyster digestive glands, sampled at time 9d, Hg


title: NCC_NR2F2

description: ChIP against NR2F2

value: NR2F2 (PP-H7147-00, Perseus Proteomics)


title: Cu9d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Copper (100 ug/L) for 9 days.

source_name: Pool of three oyster digestive glands, sampled at time 9d, Cu


title: Broad_ChipSeq_NH-A_H4K20me1

source_name: NH-A

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=wgEncodeBroadHistone

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H4K20me1

tag: antibody targetdescription

value: Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

tag: replicate

tag: softwareversion

value: U

value: Abcam

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

value: NH-A/Input/std


title: Pb9d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Plumbum (500 ug/L) for 9 days.

source_name: Pool of three oyster digestive glands, sampled at time 9d, Pb


title: NCC_FAIRE

description: FAIRE (formaldehyde assisted isolation of regulatory elements) in crosslinked H9 ESC


title: Stanford_ChipSeq_GM12878_ERRA_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: F

value: ERRA

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

value: epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin

value: Santa Cruz Biotech

tag: control

value: IgG-rab

tag: controlid


title: Cd9d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Cadmium(100 ug/L) for 9 days.

source_name: Pool of three oyster gills, sampled at time 9d, Cd

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Broad_ChipSeq_Osteobl_H3K4me3

source_name: Osteobl

value: primary cell

value: osteoblast

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: 1)abcam; 2)Millipore

tag: antibody vendorid

tag: replicate

tag: softwareversion

tag: cell sex

value: U

tag: antibody

value: Millipore

value: No special treatment or protocol applies

value: std

tag: control description

value: Standard input signal for most experiments.

value: Osteobl/None/Input/std

tag: labversion

tag: labversion description

value: Illumina Genome Analyzer IIe


title: Zn_Cd9d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (500 Î¼g/L) and Cadmium (50 Î¼g/L) for 9 days.

source_name: Pool of three oyster digestive glands, sampled at time 9d, Zn & Cd

value: digestive gland


title: Broad_ChipSeq_NHDF-Ad_H4K20me1

source_name: NHDF-Ad

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: rabbit polyclonal. Antibody Target:H4K20me1

value: Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair.

value: abcam

value: F

value: Abcam

tag: treatment

tag: treatment description

value: NHDF-Ad/Input/std


title: Broad_ChipSeq_HSMMtube_H3K27me3

source_name: HSMMtube

value: in vitro differentiated cells

value: myotube

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

tag: controlid

tag: control

value: HSMMtube/None/Input/std


title: NCC_H3K4me3

description: ChIP against H3K4me3

tag: cell type

value: Neural crest cells (hNCC) derived from H9 ESC

tag: chip antibody

value: H3K4me3 (39159, Active Motif)


title: Hg9d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Hydrargyrum (100 ug/L) for 9 days.

source_name: Pool of three oyster gills, sampled at time 9d, Hg

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Zn_Cd9d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (500 Î¼g/L) and Cadmium (50 Î¼g/L) for 9 days.

source_name: Pool of three oyster gills, sampled at time 9d, Zn & Cd


title: Broad_ChipSeq_Osteobl_H3K27me3

value: primary cell

value: osteoblast

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: replicate

tag: softwareversion

value: U

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

value: Osteobl/Input/std


title: Broad_ChipSeq_Osteobl_H4K20me1

tag: datatype

value: rabbit polyclonal. Antibody Target:H4K20me1

value: Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair.

value: abcam

tag: cell sex

tag: antibody

value: Abcam

tag: control description


title: NCC_H3K4me1

description: ChIP against H3K4me1

value: Neural crest cells (hNCC) derived from H9 ESC

value: H3K4me1 (ab8895, Abcam)


title: PSU_DnaseSeq_G1E-ER4_diffProtD_24hr

organism: Mus musculus

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodePsuDnase

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

tag: treatment

tag: treatment description

value: 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

tag: strain

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: Pb9d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Plumbum (500 ug/L) for 9 days.

source_name: Pool of three oyster gills, sampled at time 9d, Pb

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: NCC_H3K27ac

description: ChIP against H3K27ac

tag: cell type

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: NCC_H3K27me3

description: ChIP against H3K27me3

value: H3K27me3 (39536, Active Motif)


title: NCC_input

description: Total genomic DNA (input from ChIPs)

value: Neural crest cells (hNCC) derived from H9 ESC


title: NCC_p300

description: ChIP against p300

value: p300 (sc-585, Santa Cruz Biotechnology)


title: Cd12h_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Cadmium(100 ug/L) for 12 hours.

source_name: Pool of three oyster digestive glands, sampled at time 12h, Cd

value: digestive gland


title: Hg12h_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Hydrargyrum (100 ug/L) for 12 hours.

source_name: Pool of three oyster digestive glands, sampled at time 12h, Hg


title: Pb12h_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Plumbum (500 ug/L) for 12 hours.

source_name: Pool of three oyster digestive glands, sampled at time 12h, Pb


title: Zn_Cd12h_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (500 Î¼g/L) and Cadmium (50 Î¼g/L) for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, Zn & Cd


title: Cd12h_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Cadmium(100 ug/L) for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, Cd


title: Hg12h_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Hydrargyrum (100 ug/L) for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, Hg


title: Pb12h_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Plumbum (500 ug/L) for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, Pb


title: Zn12h_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, Zn


title: Th0 42hr IRF4

city: South San Francisco

first: Smita

last: Agrawal

address: 1 DNA Way

department: Immunology

institute: Genentech Inc.

description: Sample 4

data_processing:
Illumina Casava1.7 software used for basecalling and generating eland extended files mapped onto mm9
Sequenced reads for the BMDCs were mapped to mm9 whole genome using gsnap with parameter s-d mm9 -Q -n 2 -A sam
QuEST was used for peak calling on the aligned eland extended or SAM files with the recommended 30 -fold enrichment used as threshold.
Genome_build: mm9
Supplementary_files_format_and_content: wig files indicating the reads aligned to the mm9 genome

source_name: Th0 polarized cells

extract_protocol: 20000000 cells were harvested, crosslinked with formaldehyde, sonicated, IPed with appropriate antibodies and reverse-crosslinked to obtain 300-500 bp DNA fragments. These DNA fragments were ligated to Illumina TruSeq adapters  for sequencing on the Illumina GAIIx.

tag: cell type/growth condition

value: Naïve T-cells from spleen activated by anti-CD3 and anti-CD28

tag: timepoint

value: 42 hrs

value: IRF-4 Antibody (M-17)

tag: chip antibody vendor

value: Santa Cruz Biotechnologies

tag: chip antibody cat. #

tag: chip antibody lot #


title: Th0 42hr Input

description: Sample 7


title: PSU_DnaseSeq_G1E

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Gata1- erythroid progenitor

tag: cell sex

value: No special treatment or protocol applies

tag: replicate


title: Cu12h_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Copper (100 ug/L) for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, Cu

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Th17 42hr Input

description: Sample 6

source_name: Th17 polarized cells

tag: strain

tag: cell type/growth condition

value: Naïve T-cells from spleen under Th17 polarizing conditions


title: Th2 42hr IRF4

description: Sample 3

source_name: Th2 polarized cells

value: Naïve T-cells from spleen under Th2 polarizing conditions

tag: timepoint

tag: chip antibody

tag: chip antibody vendor


title: dried_muscle_11d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 11 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster adductor muscles, sampled at time 11d, exposure to air

value: adductor muscle


title: Cu9d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Copper (100 ug/L) for 9 days.

source_name: Pool of three oyster gills, sampled at time 9d, Cu


title: Cu12h_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Copper (100 ug/L) for 12 hours.

source_name: Pool of three oyster digestive glands, sampled at time 12h, Cu

value: digestive gland


title: Chicken_st20_NCC_H3K27ac

description: ChIP against H3K27ac

data_processing:
Enrichment analysis was performed using QuEST software with suggested settings for transcription factor binding.
Genome_build: galGal3
Supplementary_files_format_and_content: aligned.bed and calls.bed files including aligned reads and annotated peaks/regions are provided respectively

organism: Gallus gallus

growth_protocol: Chicken stage 11-14 NCC: Chick embryos were harvested at st.8 and the dorsal neural tube was excised and plated on matrigel coated plates.  After between 48-72 hours cranial neural crest cells began to migrate out of the dorsal neural tube explants and considered to resemble st11-14 NCC from embryos. Cells were then trypsinized an pooled for ChIP assays. Chicken stage 20 NCC: Frontonasal prominences (FNP)  NCCs were isolated  in cold PBS at St20 according to Hamburger-Hamilton criteria. FNPs were placed in 1.26 U dispase in 1x PBS for 15 minutes at room temperature, then into DMEM with 10% FBS. Surface ectoderm and forebrain neuroectoderm were removed using sharpened tungsten needles leaving only FNP NCCs. Cells were then trypsinized an pooled for ChIP assays.

extract_protocol: Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Chicken stage 11-14 NCC: Chick embryos were harvested at st.8 and the dorsal neural tube was excised and plated on matrigel coated plates in NCC differentiation media: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5x B-27 supplement with Vitamin A (50x stock, Invitrogen),  0.5x N-2 supplement (100x stock, Invitrogen),  20 ng/ml bFGF (Peprotech),  20 ng/ml EGF (Sigma-Aldrich), 5 µg/ml bovine insulin (Sigma-Aldrich) and 1x Glutamax-I supplement (100x stock, Invitrogen).

tag: tissue source

value: stage 20 chicken embryos

tag: cell type

value: Neural crest cells (NCC)

value: Anti-Histone H3 (acetyl K27) antibody

tag: chip antibody cat. #

value: Abcam


title: Th17 42hr BATF

description: Sample 2

value: 42 hrs

value: BATF

tag: chip antibody ref.

value: generated in-house by immunizing rabbits with a mixture of two peptides (1-22 aa and 108-125 aa) followed by affinity purification.


title: dried_muscle_9d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 9 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster adductor muscles, sampled at time 9d, exposure to air


title: Broad_ChipSeq_A549_CTCF_DEX_100nM

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: controlid

tag: softwareversion

value: M

tag: antibody

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

tag: treatment

tag: treatment description

value: 1 h with 100 nM Dexamethasone (Myers)

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: Zn5d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 5 days.

source_name: Pool of three oyster digestive gills, sampled at time 5d, Zn

tag: developmental stage

value: adult

tag: tissue

value: digestive gland

tag: exptl group

value: tissue


title: Broad_ChipSeq_K562_PLU1

tag: datatype

tag: datatype description

value: Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:PLU1

value: JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B.

value: YangShi lab

tag: replicate

tag: cell sex

value: F

value: No special treatment or protocol applies


title: Broad_ChipSeq_H1-hESC_H3K9me3

growth_protocol: missing

value: stem cell

tag: line

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

value: Abcam


title: Broad_ChipSeq_A549_CTCF_EtOH_0.02pct

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: controlid

tag: softwareversion

value: M

tag: antibody

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

tag: treatment

tag: treatment description

value: 1 h with 0.02% Ethanol (Myers)

value: std

value: Standard input signal for most experiments.


title: Chicken_st20_NCC_input

description: Input DNA

tag: tissue source

value: stage 20 chicken embryos

tag: cell type

value: Neural crest cells (NCC)


title: Th17 42hr IRF4

description: Sample 1

tag: strain

tag: cell type/growth condition

value: Naïve T-cells from spleen under Th17 polarizing conditions

tag: timepoint

value: 42 hrs

tag: chip antibody

value: IRF-4 Antibody (M-17)

tag: chip antibody vendor

value: Santa Cruz Biotechnologies

tag: chip antibody cat. #

tag: chip antibody lot #


title: Zn_Cd12h_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (500 Î¼g/L) and Cadmium (50 Î¼g/L) for 12 hours.

source_name: Pool of three oyster digestive glands, sampled at time 12h, Zn & Cd

tag: developmental stage

value: adult

tag: tissue

value: digestive gland

tag: exptl group

value: tissue


title: Chicken_st11-14_NCC_H3K27ac

description: ChIP against H3K27ac

value: stage 11-14 chicken embryos

value: Anti-Histone H3 (acetyl K27) antibody

value: Abcam


title: dried_muscle_10d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 10 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster adductor muscles, sampled at time 10d, exposure to air

value: adductor muscle


title: Chicken_st11-14_NCC_input

description: Input DNA


title: dried_muscle_7d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 7 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster adductor muscles, sampled at time 7d, exposure to air


title: Broad_ChipSeq_A549_H3K27ac_EtOH_0.02pct

value: immortalized cell line

tag: line

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

value: Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

tag: controlid

tag: replicate

tag: cell sex

value: M

tag: control

tag: control description

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: dried_muscle_3d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 3 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster adductor muscles, sampled at time 3d, exposure to air

tag: developmental stage


title: Broad_ChipSeq_A549_H2A.Z_DEX_100nM

value: Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ. Antibody Target:H2AZ

value: H2A.Z is a sequence variant of Histone H2A.

value: Millipore

tag: softwareversion

tag: antibody

value: Upstate (Millipore)

tag: treatment

tag: treatment description

value: 1 h with 100 nM Dexamethasone (Myers)

value: std

value: Standard input signal for most experiments.


title: Broad_ChipSeq_H1-hESC_H2A.Z

tag: datatype

tag: datatype description

value: No special treatment or protocol applies


title: Broad_ChipSeq_K562_LSD1

tag: antibody antibodydescription

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid

tag: antibody targetdescription

value: BHC110/LSD1 is a histone demethylase and a component of several histone deacetylase complexes. BHC110/LSD1 is able to specifically catalyze the demethylation of Lys4 of histone H3. As part of histone deacetylase complexes BHC110/LSD1 functions as a corepressor of transcription.

value: Bethyl Laboratories

value: F

value: Bethyl


title: dried_muscle_5d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 5 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster adductor muscles, sampled at time 5d, exposure to air

value: adult

tag: tissue

value: adductor muscle

tag: exptl group

value: tissue


title: Broad_ChipSeq_K562_CHD1_(A301-218A)

value: ChipSeq

value: Chromatin IP Sequencing

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

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

tag: antibody vendorname

tag: antibody vendorid

tag: controlid

tag: replicate


title: Broad_ChipSeq_K562_p300

value: Rabbit Polyclonal. Antibody Target:P300

value: Santa Cruz Biotechnology

tag: cell sex

value: Santa Cruz Biotech

tag: control

tag: control description


title: Broad_ChipSeq_A549_H3K27me3_DEX_100nM

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

tag: softwareversion

value: M

value: 1 h with 100 nM Dexamethasone (Myers)

value: std

value: Standard input signal for most experiments.

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: dried_muscle_1d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 1 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster adductor muscles, sampled at time 1d, exposure to air

tag: developmental stage

value: adult

value: adductor muscle


title: dried_muscle_0d

description: Sequenced reads were generated from the pool of three adult oyster adductor muscles, samples was collected immidiately after the treatment.

source_name: Pool of three oyster adductor muscles, sampled at time 0d, exposure to air

value: tissue


title: Broad_ChipSeq_K562_PCAF

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid

value: PCAF (P300/CBP-associated factor) is a histone acetyltransferase (HAT) identified as a factor that associates with P300/CBP, a transcriptional coactivator of nuclear hormone receptors and other transcription factors.

value: Bethyl Laboratories

value: F

tag: antibody

value: PCAF

value: Bethyl

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: Broad_ChipSeq_H1-hESC_RBBP5_(A300-109A)

tag: datatype description

tag: antibody antibodydescription

value: Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:RBBP5

tag: antibody targetdescription

value: Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1.

value: M


title: Broad_ChipSeq_K562_EZH2_(39875)

value: This EZH2 antibody was raised against a recombinant protein corresponding to amino acids 353-451 of human EZH2. Antibody Target:EZH2

value: EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers.

tag: antibody vendorname

value: Active Motif

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.


title: dried_gills_10d

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 10 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster gills, sampled at time 10d, exposure to air

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: dried_gills_7d

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 7 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster gills, sampled at time 7d, exposure to air


title: dried_gills_11d

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 11 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster gills, sampled at time 11d, exposure to air


title: Broad_ChipSeq_H1-hESC_SUZ12_(05-1317)

value: ChipSeq

value: Chromatin IP Sequencing

value: Recombinant protein corresponding to human SUZ12. Antibody Target:SUZ12

value: SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3.

value: Millipore

tag: controlid

tag: replicate

tag: cell sex

tag: control

value: Illumina Genome Analyzer IIx


title: dried_gills_5d

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 5 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster gills, sampled at time 5d, exposure to air


title: Broad_ChipSeq_K562_CBP_(sc-369)

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

value: CBP is a histone acetyl transferase that promotes transcription. CBP is recruited by a variety of transcription factors to promoters and enhancers.

value: Santa Cruz Biotechnology

tag: softwareversion

value: F

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

value: Santa Cruz Biotech

value: No special treatment or protocol applies

tag: control description

tag: labversion

tag: labversion description


title: Broad_ChipSeq_K562_CBX8

tag: datatype

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:CBX8

value: CBX8 is part of the polycomb group of proteins that are important in embryogenesis and human tumorigenesis and regulates a number of genes involved in cell growth and survival. There are at least 5 CBX proteins in mammals. CBX proteins associate with the core polycomb repressive complex 1 (PRC1) that functions to maintain the transcriptionally repressive state of genes during development.

value: Bethyl Laboratories

tag: antibody

value: Bethyl

tag: treatment

value: std

value: Standard input signal for most experiments.

value: Illumina HiSeq 2000


title: Broad_ChipSeq_H1-hESC_HDAC6_(A301-341A)

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:HDAC6

value: Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules.

value: M

tag: treatment description


title: Broad_ChipSeq_K562_CBX3_(SC-101004)

value: Mouse monoclonal IgG, raised against recombinant CBX3 of human origin. Antibody Target:CBX3

tag: antibody targetdescription

value: At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

value: Illumina Genome Analyzer IIx


title: dried_gills_9d

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 9 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster gills, sampled at time 9d, exposure to air

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Broad_ChipSeq_K562_NCoR

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid Antibody Target:NCOR1

value: The nuclear receptor corepressor protein (NCoR) mediates gene repression by interacting with nuclear receptors. NCoR mediates repression by associating with SIN3A/B and the histone deacetylases, HDAC1 and HDAC2, and promoting the formation of repressive chromatin structures.

value: Bethyl Laboratories

tag: controlid

tag: replicate

tag: cell sex

value: F

value: NCoR

value: No special treatment or protocol applies

tag: control


title: Broad_ChipSeq_K562_RNF2

value: ChipSeq

value: Chromatin IP Sequencing

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid

value: Ring finger protein 2 (RNF2) is a polycomb group (PcG) protein. RNF2 has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2).

tag: softwareversion

value: Bethyl

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: Broad_ChipSeq_K562_SIRT6

tag: datatype

tag: datatype description

value: Rabbit polyclonal. Antibody Target:SIRT6

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

value: abcam

tag: antibody

value: Abcam

tag: treatment

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K36me3

value: primary cell

value: CD14-positive monocyte

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: antibody vendorname

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: treatment description


title: dried_gills_3d

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 3 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster gills, sampled at time 3d, exposure to air

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: wild type meristem replicate 2

city: Cold Spring Harbor

first: Ke

last: Jiang

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Illumina GA Iix base-calling with default parameters.
Bowtie 0.12.5 64 bit for read mapping againt predicted tomato CDS (iTAG version 2.3) with parameters: 3 mismatches allowed in first 25bp, unlimited mismatches in the remaining length with mismatch quality score <=70, insert size between 50bp and 500bp. Only one best alignment were retained.
Raw counts were normalized against library sizes and gene lengths.
Genes showing more than 10 normalized counts were retained for furthere analyses.
Normalization and tests of differential expression were conducted with statistical software R package edgeR.
Genome_build: Solanum lycopersicum var. Heinz predicted CDS, iTAG version 2.3
Supplementary_files_format_and_content: tmf_counts_norm.xlsx: Excel spreadsheet, normalized counts for all samples.

organism: Solanum lycopersicum

source_name: meristem

growth_protocol: Tomato seeds were germinated at 27 degree Celcius and transplanted to 72-cell insert flats, then kept in greenhouse until tissue harvest. Meristems were collected at 8 Days after germination and fixed in acetone.

extract_protocol:
Total RNAs were extracted with PicoPure RNA extraction kit from acetone fixed tissues.
mRNA purification was conducted by oligo-dT beads. cDNA synthesis from the mRNAs was followed by gel size selection, end repair, A addition and adaptor ligation, as well as PCR enrichment.

tag: genotype

value: wild type

value: late vegetative meristem


title: wild type meristem replicate 1


title: Broad_ChipSeq_Dnd41_Input

value: ChipSeq

value: Chromatin IP Sequencing

tag: controlid

tag: replicate

tag: cell

tag: cell organism

value: human

tag: cell description

value: T cell leukemia with Notch mutation

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: M

value: Input

tag: antibody description

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

value: No special treatment or protocol applies

tag: control

value: std

value: Standard input signal for most experiments.


title: Broad_ChipSeq_K562_CBX2

tag: datatype

tag: datatype description

tag: antibody antibodydescription

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated. Antibody Target:CBX2

tag: antibody targetdescription

value: Chromobox protein homolog 2 is a component of the polycomb group (PcG) multiprotein PRC1 complex, a complex required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. [taken from the Universal Protein Resource (UniProt) www.uniprot.org/uniprot/P19474]

value: Bethyl Laboratories

tag: antibody vendorid

tag: softwareversion

value: F

tag: antibody

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid

value: Bethyl

tag: treatment

tag: control description

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: Broad_ChipSeq_A549_H3K4me3_EtOH_0.02pct

value: ChipSeq

value: Chromatin IP Sequencing

value: rabbit polyclonal. Antibody Target:H3K4me3

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: 1)abcam; 2)Millipore

tag: controlid

tag: replicate

value: Millipore

tag: treatment description

value: 1 h with 0.02% Ethanol (Myers)


title: Broad_ChipSeq_H1-hESC_SAP30_(39731)

value: This SAP30 antibody (pAb) was raised against recombinant full length human SAP30 protein. Antibody Target:SAP30

value: SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes.

value: Active Motif

tag: cell sex

value: M

value: No special treatment or protocol applies

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_NHDF-Ad_H3K9me3

source_name: NHDF-Ad

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: abcam

value: F

value: Abcam

tag: control

value: std

value: Standard input signal for most experiments.

value: NHDF-Ad/Input/std


title: salt_40

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 40 ppt for 7 days.

source_name: Pool of three oyster gills, sampled at time 12h, salinity 40 ppt

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: salt_30

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 30 ppt for 7 days.

source_name: Pool of three oyster gills, sampled at time 12h, salinity 30 ppt


title: mutant meristem replicate 2

tag: genotype

value: mutant TERMINARING FLOWER

value: late vegetative meristem


title: mutant meristem replicate 1


title: salt_20

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 20 ppt for 7 days.

source_name: Pool of three oyster gills, sampled at time 12h, salinity 20 ppt


title: Broad_ChipSeq_Dnd41_H3K9ac

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

tag: antibody targetdescription

value: Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: antibody vendorid


title: salt_25

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 25 ppt for 7 days.

source_name: Pool of three oyster gills, sampled at time 12h, salinity 25 ppt


title: Broad_ChipSeq_Dnd41_H3K9me3

value: immortalized cell line

tag: line

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: softwareversion

value: M

tag: antibody

tag: treatment

value: No special treatment or protocol applies

tag: control description


title: Stanford_ChipSeq_MEL_Input_DMSO_2.0pct_std (superseded by GSE94232)

description:
****************************
GSM1003758 record metadata submitted on Sep 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE94232
****************************

source_name: MEL

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhHist

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: Input

tag: antibody description

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

tag: treatment description

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: replicate

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Broad_ChipSeq_HMEC_H3K79me2

source_name: HMEC

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target:H3K79me2

tag: antibody targetdescription

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3).

tag: antibody vendorname

value: Active Motif

tag: antibody vendorid

tag: softwareversion

tag: cell sex

value: U

tag: control

value: std

value: Standard input signal for most experiments.

value: HMEC/Input/std


title: Stanford_ChipSeq_MEL_H3K4me1_DMSO_2.0pct_std

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: M

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam

tag: treatment

tag: control description

tag: labversion


title: Broad_ChipSeq_HUVEC_H2A.Z

source_name: HUVEC

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ. Antibody Target:H2AZ

value: H2A.Z is a sequence variant of Histone H2A.

value: Millipore

tag: controlid

tag: replicate

value: Upstate (Millipore)

tag: treatment description

value: No special treatment or protocol applies

value: HUVEC/Input/std


title: Broad_ChipSeq_NHLF_H3K79me2

source_name: NHLF

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target:H3K79me2

tag: antibody targetdescription

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3).

tag: antibody vendorname

value: Active Motif

tag: antibody vendorid

tag: softwareversion

value: U

value: std

value: Standard input signal for most experiments.

value: NHLF/Input/std


title: Broad_ChipSeq_HUVEC_H3K79me2

tag: cell sex

tag: control


title: salt_15

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 15 ppt for 7 days.

source_name: Pool of three oyster gills, sampled at time 12h, salinity 15 ppt

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: dried_gills_1d

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 1 days. During the whole expriment, the oyster were under starvation.

source_name: Pool of three oyster gills, sampled at time 1d, exposure to air


title: salt_10

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 10 ppt for 7 days.

source_name: Pool of three oyster gills, sampled at time 12h, salinity 10 ppt


title: Broad_ChipSeq_H1-hESC_H3K79me2

value: ChipSeq

value: Chromatin IP Sequencing

value: M

tag: antibody

tag: treatment

tag: control description


title: Broad_ChipSeq_K562_SUZ12_(05-1317)

tag: datatype

tag: datatype description

value: Recombinant protein corresponding to human SUZ12. Antibody Target:SUZ12

value: SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3.

value: Millipore

value: F

tag: labversion

tag: labversion description

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_NHDF-Ad_EZH2_(39875)

tag: antibody antibodydescription

value: This EZH2 antibody was raised against a recombinant protein corresponding to amino acids 353-451 of human EZH2. Antibody Target:EZH2

value: EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers.

tag: controlid

tag: replicate

tag: treatment description

value: No special treatment or protocol applies

value: NHDF-Ad/Input/std


title: Stanford_ChipSeq_MEL_H3K9me3_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: IgG-rab

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

tag: age

value: immortalized

tag: age description

value: Immortal cells

value: MEL/None/Input/IgG-rab

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Broad_ChipSeq_NHDF-Ad_H3K79me2

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target:H3K79me2

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3).

value: Active Motif

tag: softwareversion

tag: cell sex

value: F

tag: antibody

tag: treatment

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: salt_5

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 5 ppt for 7 days.

source_name: Pool of three oyster gills, sampled at time 12h, salinity 5 ppt

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K27ac

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

value: Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: antibody vendorname

value: abcam

tag: controlid

tag: replicate

value: Abcam

tag: treatment description


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H2A.Z

tag: datatype

value: Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ. Antibody Target:H2AZ

value: H2A.Z is a sequence variant of Histone H2A.

value: Millipore

tag: antibody vendorid

value: Upstate (Millipore)


title: Stanford_ChipSeq_MEL_H3K4me3_DMSO_2.0pct_std (superseded by GSE94233)

description:
****************************
GSM1003754 record metadata submitted on Sep 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE94233
****************************

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: M

value: rabbit polyclonal. Antibody Target:H3K4me3

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

value: 1)Abcam; 2)Millipore

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: labversion

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: temperature_35

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 35  ÂºC for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, 35 ÂºC

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Broad_ChipSeq_NHEK_H3K9me3

source_name: NHEK

value: ChipSeq

tag: antibody antibodydescription

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

value: abcam

tag: controlid

tag: replicate

tag: softwareversion

tag: cell sex

tag: antibody

value: Abcam

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: NHEK/Input/std


title: Stanford_ChipSeq_MEL_H3K4me3_IgG-rab (superseded by GSE94231)

description:
****************************
GSM1003753 record metadata submitted on Sep 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE94231
****************************

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: M

value: rabbit polyclonal. Antibody Target:H3K4me3

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

value: 1)Abcam; 2)Millipore

tag: antibody vendorid

value: IgG-rab

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

tag: age

tag: age description

value: MEL/None/Input/IgG-rab

tag: labversion

tag: strain


title: Broad_ChipSeq_A549_H2A.Z_EtOH_0.02pct

value: ChipSeq

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ. Antibody Target:H2AZ

tag: antibody targetdescription

value: H2A.Z is a sequence variant of Histone H2A.

tag: antibody vendorname

value: Millipore

tag: controlid

tag: replicate

tag: softwareversion

tag: cell sex

tag: antibody

value: Upstate (Millipore)

value: 1 h with 0.02% Ethanol (Myers)

tag: labversion description

value: Illumina HiSeq 2000


title: Broad_ChipSeq_NHEK_H3K79me2

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target:H3K79me2

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3).

value: Active Motif

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: NHEK/Input/std


title: temperature_30

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 30  ÂºC for 12 hours.

source_name: Pool of three oyster gills, sampled at time 12h, 30 ÂºC

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Broad_ChipSeq_A549_H3K9ac_EtOH_0.02pct

value: ChipSeq

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

tag: antibody targetdescription

value: Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

value: abcam

tag: antibody vendorid

value: M

value: Abcam

tag: labversion


title: Stanford_ChipSeq_ES-E14_H3K4me3_std

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: mouse embryonic stem cell line E14

value: rabbit polyclonal. Antibody Target:H3K4me3

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: 1)Abcam; 2)Millipore

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

tag: controlid

tag: strain

tag: strain description

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.


title: Broad_ChipSeq_Dnd41_EZH2_(39875)

tag: datatype

tag: datatype description

value: This EZH2 antibody was raised against a recombinant protein corresponding to amino acids 353-451 of human EZH2. Antibody Target:EZH2

value: EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers.

value: Active Motif

tag: replicate

tag: softwareversion

tag: cell sex

tag: antibody

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labversion description

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_A549_H3K79me2_DEX_100nM

value: ChipSeq

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target:H3K79me2

tag: antibody targetdescription

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3).

tag: antibody vendorname

tag: antibody vendorid

value: M

value: 1 h with 100 nM Dexamethasone (Myers)

tag: labversion

value: Illumina HiSeq 2000


title: temperature_20

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 20  ÂºC for 7 days.

source_name: Pool of three oyster gills, sampled at time 7d, 20 ÂºC

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: temperature_25

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 25  ÂºC for 7 days.

source_name: Pool of three oyster gills, sampled at time 7d, 25 ÂºC


title: Broad_ChipSeq_NHDF-Ad_H3K4me1

source_name: NHDF-Ad

value: primary cell

value: fibroblast of dermis

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: abcam

tag: controlid

tag: replicate

value: F

value: Abcam

value: NHDF-Ad/Input/std


title: Broad_ChipSeq_Dnd41_H3K27me3

value: ChipSeq

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

tag: softwareversion

tag: cell sex

tag: antibody

tag: treatment

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_A549_H3K4me3_DEX_100nM

value: immortalized cell line

tag: line

value: rabbit polyclonal. Antibody Target:H3K4me3

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

value: 1)abcam; 2)Millipore

value: M

tag: treatment description

value: 1 h with 100 nM Dexamethasone (Myers)

tag: control

tag: control description

tag: labversion description

value: Illumina HiSeq 2000


title: Stanford_ChipSeq_ES-E14_H3K9me3_std

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: mouse embryonic stem cell line E14

tag: antibody antibodydescription

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

tag: labversion

tag: strain

tag: strain description

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.


title: Stanford_ChipSeq_ES-E14_H3K4me1_std

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell sex

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

value: Standard input signal for most experiments.

tag: controlid


title: temperature_15

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 15  ÂºC for 7 days.

source_name: Pool of three oyster gills, sampled at time 7d, 15 ÂºC

tag: developmental stage

value: adult

tag: tissue

value: gill

tag: exptl group

value: tissue


title: Stanford_ChipSeq_MEL_H3K36me3B_DMSO_2.0pct_std

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

tag: cell description

value: Leukemia (K562 analog)

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions

tag: antibody vendorname

value: Cell Signaling

tag: antibody vendorid

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: control description

value: immortalized

value: Immortal cells

value: Unknown

value: Unknown strain origin


title: temperature_10

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 10  ÂºC for 7 days.

source_name: Pool of three oyster gills, sampled at time 7d, 10 ÂºC

value: adult


title: temperature_5

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 5  ÂºC for 7 days.

source_name: Pool of three oyster gills, sampled at time 7d, 5 ÂºC

value: gill


title: Broad_ChipSeq_A549_Control_EtOH_0.02pct

value: immortalized cell line

tag: datatype

value: ChipSeq

tag: datatype description

tag: replicate

tag: line

value: human

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

tag: antibody

value: Control

tag: treatment

value: 1 h with 0.02% Ethanol (Myers)

value: std

value: Standard input signal for most experiments.

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: Broad_ChipSeq_H1-hESC_PHF8_(A301-772A)

value: Chromatin IP Sequencing

value: Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:PHF8

value: PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111.

value: Bethyl Laboratories

tag: controlid

tag: softwareversion

value: M

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_A549_Control_DEX_100nM

value: ChipSeq

tag: cell

tag: cell organism

tag: cell description

value: 1 h with 100 nM Dexamethasone (Myers)


title: Broad_ChipSeq_H1-hESC_P300_KAT3B

tag: datatype

tag: datatype description

tag: antibody antibodydescription

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid

tag: antibody targetdescription

value: Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation.

tag: antibody vendorname

tag: antibody vendorid

value: Bethyl

tag: control description


title: Broad_ChipSeq_NHDF-Ad_H2A.Z

value: Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ. Antibody Target:H2AZ

value: H2A.Z is a sequence variant of Histone H2A.

value: Millipore

tag: replicate

tag: cell sex

value: F

tag: antibody

value: Upstate (Millipore)

tag: treatment

value: NHDF-Ad/None/Input/std


title: Stanford_ChipSeq_MEL_H3K9me3_DMSO_2.0pct_std

source_name: MEL

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

value: Chromatin IP Sequencing

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: Abcam

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

value: std

value: Standard input signal for most experiments.

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H4K20me1

tag: datatype

value: ChipSeq

tag: datatype description

value: rabbit polyclonal. Antibody Target:H4K20me1

value: Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair.

value: abcam

tag: softwareversion

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: control


title: Broad_ChipSeq_K562_HDAC6_(A301-341A)

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:HDAC6

tag: antibody targetdescription

value: Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules.

tag: antibody vendorname

value: Bethyl Laboratories

tag: antibody vendorid

value: Bethyl

tag: control description


title: Stanford_ChipSeq_MEL_Input_IgG-rab (superseded by GSE94229)

description:
****************************
GSM1003747 record metadata submitted on Sep 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE94229
****************************

tag: lab

value: Stanford-m

value: Snyder - Stanford University

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

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

tag: treatment

value: IgG-rab

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

value: MEL/None/Input/IgG-rab

tag: replicate


title: J

description: Sequenced reads were generated from the stage of juvenile at 215 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of  before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day to the first one month. Then the culutre was performed in natural sea area.

source_name: juvenile

tag: developmental stage

value: juvenile

tag: tissue

tag: exptl group

value: developmental stage


title: S

description: Sequenced reads were generated from the stage of spat at 22.15 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.

source_name: spat

value: spat


title: Stanford_ChipSeq_IMR90_COREST_(sc-30189)_IgG-rab

value: Stanford

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

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

tag: cell karyotype

value: normal

tag: cell lineage

value: endoderm

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody antibodydescription

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

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

value: Santa Cruz Biotech

tag: control

tag: controlid


title: Stanford_ChipSeq_MEL_H3K27me3B_DMSO_2.0pct_std

tag: lab

value: Stanford-m

value: Snyder - Stanford University

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

value: rabbit monoclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27) marks repressed chromatin regions

tag: antibody vendorname

value: Cell Signaling

tag: antibody vendorid

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

value: std

tag: control description

value: Standard input signal for most experiments.

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Broad_ChipSeq_NH-A_H2A.Z

source_name: NH-A

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ. Antibody Target:H2AZ

value: H2A.Z is a sequence variant of Histone H2A.

value: Millipore

tag: replicate

tag: softwareversion

value: U

tag: antibody

value: Upstate (Millipore)

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: NH-A/Input/std


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K79me2

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target:H3K79me2

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3).

value: Active Motif

tag: controlid

value: F

tag: control


title: P2

description: Sequenced reads were generated from the stage of eyed larvae at 18.19 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.

source_name: competent pediveliger for metamorphosis

tag: developmental stage

value: competent pediveliger for metamorphosis

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_H1-hESC_EZH2_(39875)

value: This EZH2 antibody was raised against a recombinant protein corresponding to amino acids 353-451 of human EZH2. Antibody Target:EZH2

tag: antibody targetdescription

value: EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers.

tag: antibody vendorname

tag: antibody vendorid

tag: cell sex

value: M

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: P1

description: Sequenced reads were generated from the stage of eyed larvae at 18.03 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.


title: Stanford_ChipSeq_MEL_H3K4me1_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam

value: IgG-rab

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

tag: age

value: immortalized

tag: age description

value: Immortal cells

value: MEL/None/Input/IgG-rab

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Stanford_ChipSeq_K562_ZC3H11A_(NB100-74650)_IgG-rab

value: Stanford

value: human

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal antibody. The immunogen recognized by this antibody maps to a region between residue 250 and 300 of human zinc finger CCCH-type containing 11A.

tag: antibody targetdescription

value: ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized.

tag: antibody vendorname

value: NovusBio

tag: control

tag: controlid


title: Broad_ChipSeq_K562_NSD2_(ab75359)

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mouse monoclonal, raised against a fusion protein, corresponding to amino acids 1-647 of Human GST-WHSC1/NSD2.

value: This is a probable histone methyltransferase, which may act as a transcription regulator that binds DNA and suppresses IL5 transcription.

value: abcam

tag: antibody vendorid

tag: replicate

tag: softwareversion

tag: cell sex

value: Abcam

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labversion

tag: labversion description

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_NH-A_H3K9me3

value: primary cell

value: astrocyte

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: U

tag: treatment

value: NH-A/Input/std


title: Broad_ChipSeq_HSMMtube_EZH2_(39875)

source_name: HSMMtube

value: This EZH2 antibody was raised against a recombinant protein corresponding to amino acids 353-451 of human EZH2. Antibody Target:EZH2

value: EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers.

value: Active Motif

tag: treatment description

value: No special treatment or protocol applies

value: HSMMtube/None/Input/std

value: Illumina HiSeq 2000


title: Broad_ChipSeq_HeLa-S3_EZH2_(39875)

value: ChipSeq

value: Chromatin IP Sequencing

value: F

tag: antibody


title: LU1

description: Sequenced reads were generated from the stage of late umbo larvae at 14.73 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.

source_name: later umbo larva1

tag: developmental stage

value: later umbo larva

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_NH-A_H3K79me2

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target:H3K79me2

tag: antibody targetdescription

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3).

tag: antibody vendorname

tag: control

value: std

value: Standard input signal for most experiments.


title: U6

description: Sequenced reads were generated from the stage of umbo larvae at 13.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.

source_name: umbo larva6

value: umbo larva


title: Broad_ChipSeq_NHEK_EZH2_(39875)

tag: datatype

tag: datatype description

tag: antibody vendorid

tag: controlid

value: M

value: NHEK/Input/std


title: Broad_ChipSeq_HepG2_H3K9me3

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: abcam

tag: replicate

tag: softwareversion

tag: cell sex

value: Abcam

tag: control description