title: Broad_ChipSeq_HUVEC_EZH2_(39875)

source_name: HUVEC

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

value: U

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: HUVEC/None/Input/std

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: Broad_ChipSeq_NHEK_H2A.Z

status: Public on Sep 13 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: NHEK

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: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

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: antibody vendorid

tag: controlid

tag: replicate

tag: softwareversion

tag: cell sex

value: M

tag: antibody

value: Upstate (Millipore)

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: NHEK/Input/std


title: LU2

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 stage of late umbo larvae at 15.73 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.

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: later umbo larva2

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: later umbo larva

tag: tissue

tag: exptl group

value: developmental stage


title: U5

description: Sequenced reads were generated from the stage of umbo larvae at 12.76 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 larva5

value: umbo larva


title: Broad_ChipSeq_HeLa-S3_H2A.Z

value: F

tag: treatment

tag: treatment description


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K4me2

tag: datatype

tag: datatype description

value: rabbit polyclonal. Antibody Target:H3K4me2

value: Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters.

value: abcam

value: Abcam

value: No special treatment or protocol applies

tag: labversion

tag: labversion description


title: Broad_ChipSeq_GM12878_EZH2_(39875)

value: ChipSeq

value: Chromatin IP Sequencing

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

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

value: Active Motif

tag: antibody vendorid


title: U3

description: Sequenced reads were generated from the stage of umbo larvae at 9.75 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 larva3


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_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.

tag: controlid

tag: replicate

tag: softwareversion

tag: cell sex

value: std


title: Broad_ChipSeq_HUVEC_H3K9me3

value: primary cell

value: endothelial cell of umbilical vein

value: U

tag: antibody

tag: control

tag: control description

value: Standard input signal for most experiments.

value: HUVEC/None/Input/std

value: Illumina HiSeq 2000


title: U2

description: Sequenced reads were generated from the stage of umbo larvae at 8.75 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 larva2

tag: developmental stage

value: umbo larva

tag: tissue

tag: exptl group

value: developmental stage


title: U1

description: Sequenced reads were generated from the stage of umbo larvae at 7.75 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 larva1


title: Broad_ChipSeq_Osteobl_P300_KAT3B

source_name: Osteobl

tag: datatype

tag: datatype description

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid

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.

value: Bethyl Laboratories

value: Bethyl

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: Osteobl/None/Input/std


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K9ac

value: ChipSeq

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.

value: abcam

value: F

value: Abcam

tag: labversion

tag: labversion description


title: Broad_ChipSeq_Dnd41_H4K20me1

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.

tag: antibody vendorname

tag: antibody vendorid

tag: controlid

tag: replicate

value: M

value: std

value: Standard input signal for most experiments.


title: Broad_ChipSeq_A549_H3K79me2_EtOH_0.02pct

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

tag: antibody

value: 1 h with 0.02% Ethanol (Myers)

tag: control

value: Illumina HiSeq 2000


title: Broad_ChipSeq_HeLa-S3_H3K9me3

value: immortalized cell line

tag: line

value: ChipSeq

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: No special treatment or protocol applies

tag: control description


title: Broad_ChipSeq_H1-hESC_JMJD2A_(A300-861A-1)

growth_protocol: missing

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: rabbit polyclonal antigen affinity purified, unconjugated, liquid

value: JMJD2A is a member of the jumonji (jmj) domain containing gene family of histone demethylases that plays a role in chromatin regulation and influences transcriptional activation and suppression. JMJD2A is a trimethylation-specific demethylase and functions as a transcriptional repressor.

value: Bethyl Laboratories

value: Bethyl

value: Illumina Genome Analyzer IIx


title: EU1

description: Sequenced reads were generated from the stage of early umbo larvae at 4.77 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: early umbo larva1

tag: developmental stage

value: early umbo larva

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_K562_CHD4_Mi2

tag: antibody antibodydescription

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid Antibody Target:CHD4

tag: antibody targetdescription

value: CHD4/Mi2beta is a helicase component of the nucleosome remodeling and deacetylase (NuRD) complex that functions to remodel chromatin and repress transcription. Outside of the NuRD complex, CHD4/Mi2beta can function as an activator of transcription in association with p300 histone acetyltransferase.

value: F

tag: treatment

tag: treatment description

value: std

value: Standard input signal for most experiments.

tag: labversion


title: D7

description: Sequenced reads were generated from the stage of D-shaped larvae at 3.77 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Dshaped larva7

value: Dshaped larva


title: U4

description: Sequenced reads were generated from the stage of umbo larvae at 10.77 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 larva4

value: umbo larva


title: Broad_ChipSeq_K562_REST

value: ChipSeq

value: Rabbit Polyclonal Antigen Affinity Purified, Unconjugated, Liquid

value: A transcriptional repressor which represses neuronal genes in non-neuronal tissues. A member of the Kruppel-type zinc finger transcription factor family. Represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE) by associating with two corepressors, mSin3 and CoREST, which recruit HDACs to the promoters of REST-regulated genes. Target is GST fusion amino acids 801-1097 of human REST.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: controlid

tag: replicate

value: REST

tag: labversion description

value: Illumina HiSeq 2000


title: D5

description: Sequenced reads were generated from the stage of D-shaped larvae at 1.09 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Dshaped larva5


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_CTCF

value: Chromatin IP Sequencing

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.

tag: softwareversion

tag: cell sex

tag: antibody

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: No special treatment or protocol applies

tag: control


title: Broad_ChipSeq_K562_CHD7_(A301-223A-1)

tag: datatype

tag: datatype description

value: Rabbit polyclonal antigen affinity purified, unconjugated, liquid. Antibody Target:CHD7

value: CHD7 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.

value: Bethyl Laboratories

value: F

value: rabbit polyclonal antigen affinity purified, unconjugated, liquid

value: Bethyl

tag: control description

value: Illumina Genome Analyzer IIx


title: D6

description: Sequenced reads were generated from the stage of D-shaped larvae at 1.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Dshaped larva6

tag: developmental stage

value: Dshaped larva

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_H1-hESC_CHD7_(A301-223A-1)

value: ChipSeq

tag: antibody antibodydescription

tag: antibody targetdescription

value: M

tag: treatment

tag: treatment description

value: std

value: Standard input signal for most experiments.


title: Broad_ChipSeq_H1-hESC_HDAC2_(A300-705A)

value: Chromatin IP Sequencing

value: Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:HDAC2

value: Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1.

tag: antibody vendorname

tag: antibody vendorid

tag: controlid

tag: labversion


title: Broad_ChipSeq_HSMMtube_H3K9me3

source_name: HSMMtube

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: U

value: Abcam

value: No special treatment or protocol applies

value: HSMMtube/Input/std


title: D4

description: Sequenced reads were generated from the stage of D-shaped larvae at 20 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Dshaped larva4


title: Broad_ChipSeq_Dnd41_H3K4me3

value: immortalized cell line

tag: line

tag: datatype

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

value: Millipore

tag: control


title: Broad_ChipSeq_HMEC_EZH2_(39875)

source_name: HMEC

value: ChipSeq

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

value: std

tag: control description

value: HMEC/Input/std


title: Broad_ChipSeq_HMEC_H2A.Z

value: Chromatin IP Sequencing

tag: antibody antibodydescription

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: Upstate (Millipore)

value: Standard input signal for most experiments.


title: Broad_ChipSeq_Dnd41_H2A.Z

tag: antibody targetdescription

value: M

value: No special treatment or protocol applies


title: D2

description: Sequenced reads were generated from the stage of D-shaped larvae at 18 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Dshaped larva2

tag: developmental stage

value: Dshaped larva

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_Osteobl_H3K79me2

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).

tag: antibody vendorname

tag: antibody vendorid

value: U

tag: treatment

tag: treatment description

value: Osteobl/Input/std


title: EU2

description: Sequenced reads were generated from the stage of early umbo larvae at 6.75 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: early umbo larva2

value: early umbo larva


title: D3

description: Sequenced reads were generated from the stage of D-shaped larvae at 19 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Dshaped larva3


title: Broad_ChipSeq_Dnd41_CTCF

value: ChipSeq

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: replicate

tag: softwareversion

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF


title: Broad_ChipSeq_CD20+_RO01794_H4K20me1

tag: datatype

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

tag: cell sex

value: F

value: Abcam

value: std

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: Broad_ChipSeq_A549_H3K4me2_EtOH_0.02pct

tag: datatype description

value: rabbit polyclonal. Antibody Target:H3K4me2

value: Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters.

value: M

tag: antibody

value: 1 h with 0.02% Ethanol (Myers)

tag: control

tag: control description

value: Standard input signal for most experiments.


title: D1

description: Sequenced reads were generated from the stage of D-shaped larvae at 17 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Dshaped larva1

tag: developmental stage

value: Dshaped larva

tag: tissue

value: developmental stage


title: ED2

description: Sequenced reads were generated from the stage of early D-shaped larvae at 16 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: early Dshaped larva2

value: early Dshaped larva

tag: exptl group


title: Broad_ChipSeq_Dnd41_H3K36me3

value: immortalized cell line

tag: line

value: ChipSeq

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

tag: antibody vendorid

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

value: No special treatment or protocol applies


title: ED1

description: Sequenced reads were generated from the stage of early D-shaped larvae at 15 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: early Dshaped larva1


title: Broad_ChipSeq_A549_H3K27ac_DEX_100nM

value: Chromatin IP Sequencing

value: rabbit polyclonal. Antibody Target:H3K27ac

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.

value: abcam

tag: controlid

tag: replicate

tag: softwareversion

value: Abcam

tag: treatment

tag: treatment description

value: 1 h with 100 nM Dexamethasone (Myers)


title: Broad_ChipSeq_Dnd41_H3K79me2

tag: datatype

tag: datatype description

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: cell sex

value: M

value: std


title: T5

description: Sequenced reads were generated from the stage of trochophore at 14 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

value: trochophore

value: developmental stage


title: Broad_ChipSeq_Dnd41_H3K4me1

value: ChipSeq

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: antibody

tag: control

tag: control description

value: Standard input signal for most experiments.


title: Broad_ChipSeq_HepG2_EZH2_(39875)

value: Chromatin IP Sequencing

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: No special treatment or protocol applies


title: Broad_ChipSeq_H1-hESC_PLU1

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: labversion

tag: labversion description

value: Illumina Genome Analyzer IIx


title: T4

description: Sequenced reads were generated from the stage of trochophore at 13 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

tag: developmental stage

tag: tissue

tag: exptl group


title: T3

description: Sequenced reads were generated from the stage of trochophore at 12 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.


title: Broad_ChipSeq_HMEC_H3K9me3

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: U

value: Abcam

value: HMEC/Input/std


title: T2

description: Sequenced reads were generated from the stage of trochophore at 11 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

value: trochophore

value: developmental stage


title: T1

description: Sequenced reads were generated from the stage of trochophore at 9 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.


title: Broad_ChipSeq_A549_H3K36me3_DEX_100nM

value: immortalized cell line

tag: line

value: ChipSeq

value: rabbit polyclonal. Antibody Target:H3K36me3

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: controlid

tag: replicate

tag: softwareversion

value: M

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

tag: treatment

value: 1 h with 100 nM Dexamethasone (Myers)

value: std

value: Standard input signal for most experiments.

value: Illumina HiSeq 2000


title: Broad_ChipSeq_H1-hESC_SIRT6

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal. Antibody Target:SIRT6

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

tag: cell sex

tag: antibody

tag: treatment description

value: No special treatment or protocol applies

value: Illumina Genome Analyzer IIx


title: Broad_ChipSeq_K562_SETDB1

value: Rabbit polyclonal. Antibody Target:SETDB1

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

value: Proteintech

value: F

value: Proteintech Group

tag: control

tag: control description

tag: labversion

tag: labversion description


title: Broad_ChipSeq_K562_PHF8_(A301-772A)

value: ChipSeq

tag: antibody antibodydescription

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

tag: antibody targetdescription

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


title: Broad_ChipSeq_A549_H3K4me2_DEX_100nM

value: rabbit polyclonal. Antibody Target:H3K4me2

value: Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

value: M

value: Abcam

value: 1 h with 100 nM Dexamethasone (Myers)

value: std


title: G

description: Sequenced reads were generated from the stage of gastrula at 8 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: gastrula stage

tag: developmental stage

value: gastrula stage

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_A549_H3K4me1_DEX_100nM

value: immortalized cell line

tag: line

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.

tag: controlid

tag: replicate

tag: softwareversion

tag: treatment

value: Standard input signal for most experiments.

value: Illumina HiSeq 2000


title: Broad_ChipSeq_Dnd41_H3K27ac

tag: datatype

value: ChipSeq

tag: datatype description

value: rabbit polyclonal. Antibody Target:H3K27ac

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: cell sex

tag: antibody

tag: treatment description

value: No special treatment or protocol applies


title: Broad_ChipSeq_K562_RBBP5_(A300-109A)

tag: antibody antibodydescription

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

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: Bethyl Laboratories

value: F

tag: control

tag: control description


title: Broad_ChipSeq_K562_HDAC1_(SC-6298)

value: goat polyclonal IgG, 200 micrograms/ml, epitope mapping at the C-terminus of HDAC1 of human origin. Antibody Target:HDAC1

tag: antibody targetdescription

value: Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203.

tag: antibody vendorname

value: Santa Cruz Biotechnology

tag: antibody vendorid

value: Santa Cruz Biotech

value: std


title: Broad_ChipSeq_CD20+_Control

value: primary cell

value: B cell

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: B cells from donors RO01778 and RO01794, newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: Control

tag: labversion

tag: labversion description


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_Control

tag: datatype

value: ChipSeq

tag: datatype description

tag: controlid

tag: replicate

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2:not in 2011 analysis

tag: treatment

value: No special treatment or protocol applies

value: Standard input signal for most experiments.

value: Illumina HiSeq 2000


title: Broad_ChipSeq_CD20+_H2A.Z

tag: antibody antibodydescription

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: cell sex

value: F

tag: antibody

value: Upstate (Millipore)

tag: treatment description

tag: control


title: EG

description: Sequenced reads were generated from the stage of early gastrula at 7 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: early gastrula stage

tag: developmental stage

value: early gastrula stage

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_Dnd41_H3K4me2

value: Chromatin IP Sequencing

value: rabbit polyclonal. Antibody Target:H3K4me2

tag: antibody targetdescription

value: Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

value: M

value: Abcam

value: std

tag: control description


title: Broad_ChipSeq_CD20+_CTCF

tag: datatype

value: ChipSeq

tag: datatype description

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: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: No special treatment or protocol applies

tag: labversion

tag: labversion description


title: Broad_ChipSeq_CD20+_RO01794_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.

value: Active Motif

tag: controlid

tag: replicate

value: F

tag: treatment

value: Standard input signal for most experiments.

value: Illumina HiSeq 2000


title: Broad_ChipSeq_H1-hESC_JARID1A_(ab26049)

value: Chromatin IP Sequencing

value: Rabbit polyclonal to KDM5A / Jarid1A / RBBP2. Antibody Target:JARID1A

value: Histone demethylase that specifically demethylates

tag: softwareversion

tag: cell sex

tag: antibody

tag: treatment description


title: Broad_ChipSeq_CD20+_H3K4me2

value: rabbit polyclonal. Antibody Target:H3K4me2

value: Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters.

value: abcam

value: Abcam

tag: control


title: Broad_ChipSeq_K562_SAP30_(39731)

value: ChipSeq

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

tag: antibody targetdescription

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: std


title: RM

description: Sequenced reads were generated from the stage when the embryo start rotate at 5 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: rotary movement

tag: developmental stage

value: rotary movement

tag: tissue

tag: exptl group

value: developmental stage


title: Broad_ChipSeq_K562_HDAC2_(A300-705A)

tag: datatype

value: Polyclonal Antigen Affinity Purified, Unconjugated, Liquid. Antibody Target:HDAC2

value: Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1.

tag: antibody vendorname

value: Bethyl Laboratories

tag: antibody vendorid

value: No special treatment or protocol applies

tag: control description


title: Broad_ChipSeq_HSMM_EZH2_(39875)

source_name: HSMM

tag: datatype description

value: Chromatin IP Sequencing

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.

value: Active Motif

value: U

value: Standard input signal for most experiments.

value: HSMM/Input/std


title: EM

description: Sequenced reads were generated from the stage of early morula at 2 h 25 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: early morula stage

value: early morula stage


title: Broad_ChipSeq_H1-hESC_CHD1_(A301-218A)

value: ChipSeq

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: controlid

tag: replicate

value: M


title: FC

description: Sequenced reads were generated from the stage of four cell at 1 h 32 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: four cells

value: four cells

value: developmental stage


title: Broad_ChipSeq_A549_H4K20me1_EtOH_0.02pct

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: Abcam

tag: treatment

value: 1 h with 0.02% Ethanol (Myers)

value: std

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: Broad_ChipSeq_A549_H3K27me3_EtOH_0.02pct

value: Chromatin IP Sequencing

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: cell sex

tag: antibody

tag: treatment description

tag: control


title: LA-N-2 neuroblastoma cell line

city: Ghent

first: Maté

last: Ongenaert

address: De Pintelaan 185 - MRB

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

description: MBD2 captured genomic DNA after shearing (MethylCollector, ActiveMotif)

data_processing:
Paired-end reads were mapped on the human reference genome (GRCh37) using Bowtie 0.12.7 and wig-files were generated using MACS1,4beta
Paired-end reads were mapped on the human reference genome (GRCh37) using Bowtie 0.12.7 and peaks were called using MACS 1.4beta

source_name: LA-N-2 neuroblastoma cell line

extract_protocol: Library preparation for multiplex Illumina sequencing was done by combining the DNA Sample Prep Master Mix Set 1 (New England Biolabs) and the Multiplexing Sample Preparation Oligo Kit (Illumina). Size selection of the library was done on a 2% agarose gel. Fragments of around 300 bp (Â± 50 bp) are excised and purified. Illumina library amplification (21 cycles) was performed and concentration was determined.

treatment_protocol: DNA samples (1Âµg DNA) of the 8 NB cell lines were sheared (Covaris S2) with an average length of 200 bp. Fragment distribution is determined by the Agilent 2100 Bioanalyzer and the concentration is determined by using the Quant-iT PicoGreen dsDNA HS Assay Kit (Invitrogen). Starting from 200 ng sheared DNA, the MethylCollector Kit (ActiveMotif) was used to enrich for methylated fragments (bound by the methyl-CpG-binding domain (MBD) of the protein MBD2).

tag: mycn

value: amplified


title: Broad_ChipSeq_A549_H3K9me3_EtOH_0.02pct

value: immortalized cell line

tag: line

tag: datatype

value: ChipSeq

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.

value: Standard input signal for most experiments.


title: CHP-902R neuroblastoma cell line

source_name: CHP-902R neuroblastoma cell line


title: SJNB-1 neuroblastoma cell line

source_name: SJNB-1 neuroblastoma cell line

value: not amplified


title: Broad_ChipSeq_CD20+_RO01794_H3K27ac

value: rabbit polyclonal. Antibody Target:H3K27ac

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

tag: antibody vendorid

value: F

value: No special treatment or protocol applies

tag: control description


title: NCC_TFAP2A

first: Alvaro

last: Rada

address: 269 Campus Drive, CCSR Building

department: Chemical and Systems Biology

institute: Stanford University

description: ChIP against TFAP2A

data_processing:
Enrichment analysis was performed using QuEST software with suggested settings for transcription factor binding.
Genome_build: hg18
Supplementary_files_format_and_content: aligned.bed and calls.bed files including aligned reads and annotated peaks/regions are provided respectively

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: 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: 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 µg/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

tag: chip antibody

value: TFAP2A (Santa Cruz, catalog#:sc-184, lot#:H0911)


title: E

description: Sequenced reads were generated from the egg stage at 0 h in Crassostrea gigas.

source_name: egg

tag: developmental stage

value: egg

tag: tissue

tag: exptl group

value: developmental stage


title: FS

description: Sequenced reads were generated from the stage when the embryo can freely swimming at 6 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: free swimming

value: free swimming


title: SK-N-AS neuroblastoma cell line

source_name: SK-N-AS neuroblastoma cell line


title: Broad_ChipSeq_A549_H3K4me1_EtOH_0.02pct

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

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

tag: softwareversion

value: M

value: Abcam

tag: treatment

value: 1 h with 0.02% Ethanol (Myers)

value: std

tag: labversion

tag: labversion description

value: Illumina HiSeq 2000


title: N206 neuroblastoma cell line

source_name: N206 neuroblastoma cell line

tag: mycn

value: amplified


title: G3

description: Sequenced reads were generated from the female gonad of an individual of "G3" family in Crassostrea gigas.

value: adult

value: tissue


title: B

description: Sequenced reads were generated from the stage of blatula at 4 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: blastula stage

value: blastula stage


title: M

description: Sequenced reads were generated from the stage of morula at 3 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: morula stage

value: morula stage


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: MeDIP-Seq analysis of foreskin fibroblast from skin03 (A14100) using Illumina HiSeq 2000
library name: A14100
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.74 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 91103
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM958182_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MeDIP-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14100-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13779
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,116,989
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.6151
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5764
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9924
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6201
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958182_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MeDIP-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14100-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13782
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFF MeDIP 03 00
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin03 Library A14100 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,116,989
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.6151
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5764
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9924
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6201
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

extract_protocol: library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Fibroblast

tag: is tumor

value: No

value: primary cell culture

value: foreskin fibroblast


title: Mgo

description: Sequenced reads were generated from male gonad in Crassostrea gigas. The male gonad is sampled from a individual in the F1 generation of the "G3" family.

source_name: male gonad

tag: developmental stage

value: male gonad


title: SH-SY5Y neuroblastoma cell line

source_name: SH-SY5Y neuroblastoma cell line

value: not amplified


title: Lpa

description: Sequenced reads were generated from labial palp in Crassostrea gigas, an organ just out of the mouth.

source_name: labial palp

tag: tissue

value: labial palp


title: IMR-32 neuroblastoma cell line

source_name: IMR-32 neuroblastoma cell line


title: TC

description: Sequenced reads were generated from the stage of two cell at 1 h 20 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: two cells

value: two cells

tag: exptl group

value: developmental stage


title: Hem

description: Sequenced reads were generated from hemolymph in Crassostrea gigas. The RNA were extracted from the blood.

source_name: hemolymph

value: hemolymph


title: Broad_ChipSeq_A549_H3K36me3_EtOH_0.02pct

value: immortalized cell line

tag: line

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

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: abcam

tag: antibody vendorid

tag: cell sex

value: M

tag: antibody

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

value: Abcam

tag: treatment description

value: 1 h with 0.02% Ethanol (Myers)

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: Illumina HiSeq 2000


description:
design description: MeDIP-Seq analysis of foreskin melanocyte from skin03 (A14102) using Illumina HiSeq 2000
library name: A14102
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.66 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 91103
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM958181_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14102-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13780
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,719,547
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.6036
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.5769
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9931
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6141
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958181_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14102-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13783
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFM MeDIP 03 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin03 Library A14102 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,719,547
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.6036
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.5769
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9931
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6141
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

value: Melanocyte

value: No

value: primary cell culture

tag: cell type

value: foreskin melanocyte


description:
design description: MeDIP-Seq analysis of foreskin keratinocyte from skin03 (A14101) using Illumina HiSeq 2000
library name: A14101
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.48 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 91103
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM958180_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MeDIP-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14101-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13778
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,871,476
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.6375
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5906
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9919
IROC_PERCENTILE: 33
POISSON_SCORE: 0.617
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958180_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MeDIP-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14101-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13781
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFK MeDIP 03 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin03 Library A14101 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,871,476
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.6375
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5906
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9919
IROC_PERCENTILE: 33
POISSON_SCORE: 0.617
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

tag: histological type

value: Keratinocyte

tag: is tumor

value: foreskin keratinocyte


title: Man2

description: Sequenced reads were generated from the inner part of mantle in Crassostrea gigas. The inner part of mantle and the inner surface of shell are in close proximity.

source_name: inner part of mantle

tag: developmental stage

value: adult

tag: tissue

value: inner part of mantle

tag: exptl group

value: tissue


title: BMDC 6hr LPS Input

city: South San Francisco

first: Smita

last: Agrawal

address: 1 DNA Way

department: Immunology

institute: Genentech Inc.

description: Sample 8

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

organism: Mus musculus

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: strain

tag: cell type/growth condition

value: Bone marrow derived dendritic cells stimulated with LPS for 6hrs

tag: timepoint

value: 6 hrs


title: BMDC 6hr LPS IRF4

description: Sample 5

source_name: Bone marrow derived dendritic cells stimulated with LPS

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: Amu

description: Sequenced reads were generated from adductor muscle in Crassostrea gigas.

source_name: adductor muscle

value: adductor muscle


title: Dgl

description: Sequenced reads were generated from digestive gland in Crassostrea gigas, the sample includes all the tissues in visceral mass.

source_name: digestive gland

value: digestive gland


title: Bisulfite-Seq analysis of WGBS_Lib 6 derived from human HUES64 derived CD184+ cells; WGBS_Lib 6

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 6
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11650
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11680
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916051_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_6.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 6.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor WGBS_Lib 6 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13768
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: hDCE BS 6
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,019,659,432
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.18
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; WGBS_Lib 6

extract_protocol: Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

value: CD184+ endoderm cultured cells

tag: sample alias

value: BioSam 311

tag: sample common name

tag: lineage

value: endoderm

tag: medium

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

tag: molecule

value: genomic DNA

tag: disease

value: presumed normal

tag: passage

tag: line

value: HUES64 derived CD184+

value: in vitro culture

tag: batch

value: BioSAli 396

value: Cell Line

value: differentiated

value: Male

value: Harvard

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


description:
design description: MRE-Seq analysis of foreskin keratinocyte from skin03 (A13914) using Illumina HiSeq 2000
library name: A13914
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 156-400 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM958169_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13914-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13774
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,051,340
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.17
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

ANALYSIS FILE NAME: GSM958169_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13914-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13777
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFK MRE 03 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,051,340
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.17
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

extract_protocol: library construction protocol: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Keratinocyte

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin keratinocyte


title: Man1

description: Sequenced reads were generated from outer edge of mantle in Crassostrea gigas, this part of tissue is along the edge of shells and is thought to be rich of sensory elements, as well as responsible for the extension of shell.

source_name: outer edge of mantle

tag: developmental stage

value: adult

tag: tissue

value: outer edge of mantle

tag: exptl group

value: tissue


title: Bisulfite-Seq analysis of WGBS_Lib 16 derived from human Mobilized CD34 cells; WGBS_Lib 16

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 16
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11651
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916052_BI.Mobilized_CD34_Primary_Cells.Bisulfite-Seq.RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 16.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Mobilized CD34 Primary Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13767
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: MCD34 BS 49 16
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Bisulfite-Seq Donor RO 01549 Library WGBS_Lib 16 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,042,902,089
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.49
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD34+ cells from cord blood; WGBS_Lib 16

tag: sample alias

tag: sample common name

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: 33 years

value: Female

value: Caucasian

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n


title: Fgo

description: Sequenced reads were generated from female gonad in Crassostrea gigas. The individual whose organs are isolated and sampled respectively is a female.The gonad is full of eggs as oyster has millions of eggs in the gland at mature season, while the gland tissue maybe only take up very few part.

source_name: female gonad

value: female gonad


title: CLB-GA neuroblastoma cell line

description: MBD2 captured genomic DNA after shearing (MethylCollector, ActiveMotif)

source_name: CLB-GA neuroblastoma cell line

tag: mycn

value: not amplified


description:
design description: MRE-Seq analysis of foreskin melanocyte from skin03 (A13915) using Illumina HiSeq 2000
library name: A13915
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 159-394 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM958170_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MRE-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13915-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13772
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,738,118
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 96.23
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.55

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

ANALYSIS FILE NAME: GSM958170_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MRE-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13915-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13775
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFM MRE 03 15
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin03 Library A13915 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,738,118
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 96.23
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.55

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

value: male

value: Penis

value: Melanocyte

value: No

value: primary cell culture

value: foreskin melanocyte


title: Gil

description: Sequenced reads were generated from gill in Crassostrea gigas.

source_name: gill

value: adult

value: gill

value: tissue


title: Bisulfite-Seq analysis of WGBS_Lib 10 derived from human hippocampus middle cells; WGBS_Lib 10

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 10
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11649
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916050_BI.Brain_Hippocampus_Middle.Bisulfite-Seq.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 10.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Hippocampus Middle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Brain Hippocampus Middle, Donor 150 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13766
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BHM BS 50 10
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,406,121,847
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.01
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; WGBS_Lib 10

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD present

tag: molecule

value: genomic DNA

tag: disease

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 73.0 Years

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


description:
design description: MRE-Seq analysis of foreskin fibroblast from skin03 (A13913) using Illumina HiSeq 2000
library name: A13913
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 160-390 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM958171_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MRE-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13913-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13773
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,601,225
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 97.71
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM958171_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MRE-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13913-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13776
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFF MRE 03 13
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin03 Library A13913 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,601,225
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 97.71
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

value: male

value: Penis

value: Fibroblast

value: No

value: primary cell culture

value: foreskin fibroblast


title: NOMe-seq IMR90

status: Public on Sep 12 2012

city: Chicagp

first: Yaping

last: Liu

state: IL

address: 303 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

description: M.CviPI treated following bisulfite-convertion of genomic DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
IMR90 reads were mapped to hg18 whole genome using MAQ-0.7.1 with parameters -c; GBM reads were mapped to hg19 whole genome using BSMAP-2.01 with parameters -z 64 -p 11 -s 18 -v 10 -q 2
BisSNP-0.70 were used to do base quality recalibration and indel realignment with dbSNP135, 1000G_phase1 for known SNP and indels file, duplicated reads were marked by MarkDuplicates.jar in Picard
BisSNP-0.70 were used to call genotype and DNA methylation with dbSNP135 known SNPs file and parameters, -mmq 30 -mbq 5 -minConv 1 -stand_call_conf 20
DNA methylation information were extracted into wig file at GCH, HCG sites with at least 1 C or T reads
Genome_build: hg18(IMR90), hg19(2 GBMs)
Supplementary_files_format_and_content: wig files, DNA methylation information were extracted into wig file at GCH, HCG sites with at least 1 C or T reads

source_name: lung fibroblast

growth_protocol: Cells were isolated and cultured as described (PMID 14645703)

extract_protocol: Following trypsinization, 2 million cells were washed with 1xPBS and nuclei were extracted in 10mM Tris (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1mM EDTA, 0.5% NP-40 on ice for 10 minutes followed by centrifugation at 3000 rpm 4°C for 5 minutes. Nuclei were treated with M.CviPI  and DNA was extracted and fragmented (~150bp) using Covaris.  5ug DNA was end-repaired (EpiCentre) and A’s were added to the 3’ ends using Klenow. Methylated adaptors (Illumina ME-100-0010) were ligated and no more than 6 cycles of PCR was performed.  DNA was run on a 2% agarose gel and fragments between 200-500 were size selected and purified. Clustering and sequencing was performed on an Illumina HiSeq according to the manufacturer's recommendations.

tag: cell line

value: lung fiboblast cells


title: NOMe-seq GBM248

source_name: glioblastoma cells

value: Primary culture

value: glioblastoma


title: NOMe-seq GBM157


title: Duke_Combined_GM18507_wgEncodeOpenChromSynth

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=wgEncodeOpenChromSynth

tag: lab

value: Duke

tag: lab description

value: Crawford - Duke University

tag: datatype

value: Combined

tag: datatype description

value: Multi-assay Synthesis

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell lineage

value: mesoderm

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: composite

value: wgEncodeOpenChromSynth

tag: labversion