title: Bernstein_K562_H3K4me1

value: immortalized cell line

tag: line

value: human

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

tag: cell lineage

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: antibody vendorname

tag: control description

tag: controlid


title: Bernstein_HMEC_H3K9ac

status: Public on Jun 02 2011

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone

molecule: genomic DNA

organism: Homo sapiens

source_name: HMEC

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

tag: cell description

value: mammary epithelial cells

tag: cell karyotype

value: normal

value: ectoderm

tag: cell sex

value: U

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

tag: antibody targetdescription

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

value: abcam

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

value: Standard input signal for most experiments.

tag: replicate

tag: softwareversion


title: Bernstein_NH-A_H3K4me3

source_name: NH-A

value: human

value: astrocytes (also called Astrocy)

tag: cell lineage

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: antibody vendorname

value: 1)abcam; 2)Millipore

tag: control description

tag: controlid


title: Bernstein_NHDF-Ad_CTCF

source_name: NHDF-Ad

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: adult dermal fibroblasts

value: mesoderm

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: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HepG2_H3K27ac

value: immortalized cell line

tag: line

value: Chromatin IP Sequencing

tag: cell organism

tag: cell description

value: hepatocellular carcinoma

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody

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

value: No special treatment or protocol applies


title: Bernstein_HUVEC_H3K27ac

source_name: HUVEC

value: primary cell

value: endothelial cell of umbilical vein

value: human

value: umbilical vein endothelial cells

tag: antibody targetdescription

tag: antibody vendorid

tag: treatment

tag: treatment description

tag: control

value: std

value: Standard input signal for most experiments.


title: Bernstein_HUVEC_H3K4me1

value: Broad

value: Bernstein - Broad Institute

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 vendorname

tag: control description

tag: replicate

tag: softwareversion


title: Bernstein_GM12878_Control

value: immortalized cell line

tag: lab

tag: lab description

tag: datatype

value: Chromatin IP Sequencing

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

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: Input

tag: antibody description

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

tag: controlid


title: Bernstein_HeLa-S3_H4K20me1

tag: datatype description

tag: cell organism

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H4K20me1

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

value: abcam

value: No special treatment or protocol applies


title: Bernstein_HSMMtube_H3K4me3

source_name: HSMMtube

value: in vitro differentiated cells

value: myotube

value: human

tag: cell description

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell sex

value: U

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody

tag: antibody targetdescription

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

value: 1)abcam; 2)Millipore

tag: antibody vendorid

tag: treatment

value: std

value: Standard input signal for most experiments.


title: Bernstein_NHEK_H3K4me2

source_name: NHEK

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

value: epidermal keratinocytes

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

tag: treatment description

tag: control

tag: control description

tag: replicate

tag: softwareversion


title: Bernstein_NHDF-Ad_H3K36me3

tag: lab

tag: lab description

tag: datatype

value: adult dermal fibroblasts

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

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.

value: abcam

value: No special treatment or protocol applies

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HepG2_H3K4me3

value: immortalized cell line

tag: line

tag: datatype description

tag: cell organism

value: human

tag: cell description

value: hepatocellular carcinoma

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: 1)abcam; 2)Millipore

value: std

tag: controlid


title: Bernstein_HeLa-S3_H3K27ac

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

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

tag: antibody vendorname

tag: antibody vendorid

tag: treatment

tag: treatment description

value: Standard input signal for most experiments.


title: Bernstein_Osteobl_H3K9me3

source_name: Osteobl

value: primary cell

value: osteoblast

tag: lab

value: osteoblasts (NHOst)

value: mesoderm

tag: cell sex

value: U

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

tag: antibody

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: control

tag: control description

tag: replicate

tag: softwareversion


title: Bernstein_HepG2_Control

value: immortalized cell line

tag: line

tag: lab description

tag: datatype

tag: datatype description

value: human

value: hepatocellular carcinoma

value: Input

tag: antibody description

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

value: No special treatment or protocol applies


title: Bernstein_HeLa-S3_H3K4me3

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

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

value: 1)abcam; 2)Millipore

value: std

tag: controlid


title: Bernstein_HUVEC_H3K4me2

tag: cell description

value: umbilical vein endothelial cells

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

tag: antibody vendorid

tag: treatment

tag: treatment description

value: Standard input signal for most experiments.

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HSMM_H4K20me1

source_name: HSMM

tag: lab

value: human

value: skeletal muscle myoblasts

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

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: control

tag: control description

tag: replicate


title: Bernstein_NH-A_H3K27me3

value: primary cell

value: astrocyte

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: astrocytes (also called Astrocy)

tag: cell karyotype

value: normal

value: ectoderm

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody

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

value: No special treatment or protocol applies

tag: softwareversion


title: Bernstein_NHEK_H3K27ac

value: keratinocyte

tag: cell organism

value: human

tag: cell description

value: epidermal keratinocytes

value: U

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

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

tag: antibody vendorname

value: std

value: Standard input signal for most experiments.

tag: controlid


title: Bernstein_K562_H4K20me1

tag: lab

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

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

tag: cell lineage

value: mesoderm

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: antibody vendorid

tag: treatment

tag: treatment description


title: Bernstein_Osteobl_H3K36me3

value: primary cell

value: osteoblast

tag: lab description

value: Chromatin IP Sequencing

value: osteoblasts (NHOst)

tag: cell sex

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.

value: No special treatment or protocol applies

tag: control

tag: control description

tag: replicate


title: Bernstein_NHEK_Pol2(b)

tag: datatype

tag: datatype description

value: human

value: epidermal keratinocytes

value: U

value: mouse monoclonal, clone CTD4H8. Antibody Target:POL2B

value: RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation.

value: Covance

value: std

tag: softwareversion


title: Bernstein_HeLa-S3_H3K79me2

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

tag: cell organism

tag: antibody antibodydescription

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

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

value: Active Motif

value: Standard input signal for most experiments.


title: Bernstein_HSMMtube_H3K36me3

value: in vitro differentiated cells

value: myotube

value: Chromatin IP Sequencing

tag: cell description

value: skeletal muscle myotubes differentiated from the HSMM cell line

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody

tag: antibody targetdescription

tag: antibody vendorname

value: abcam


title: Bernstein_HMEC_H3K27me3

tag: lab

value: human

value: mammary epithelial cells

tag: cell karyotype

value: normal

tag: cell lineage

value: ectoderm

value: U

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: antibody vendorid

value: No special treatment or protocol applies

tag: controlid

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_NHEK_H3K9ac

value: Broad

tag: lab description

value: Bernstein - Broad Institute

value: ChipSeq

value: epidermal keratinocytes

tag: cell sex

value: rabbit polyclonal. Antibody Target:H3K9ac

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

tag: treatment

tag: treatment description

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: Bernstein_Osteobl_H3K27ac

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: osteoblasts (NHOst)

value: mesoderm

tag: antibody antibodydescription

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: replicate

tag: softwareversion


title: Bernstein_GM12878_H3K9me3

tag: lab

tag: cell description

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

tag: cell karyotype

value: normal

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: No special treatment or protocol applies


title: Bernstein_HUVEC_H3K27me3

value: Broad

tag: lab description

value: Bernstein - Broad Institute

value: ChipSeq

value: umbilical vein endothelial cells

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: antibody vendorid

tag: controlid

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_NH-A_H3K4me1

value: Chromatin IP Sequencing

value: human

value: astrocytes (also called Astrocy)

tag: cell lineage

value: ectoderm

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: treatment

tag: treatment description

tag: control

value: std

value: Standard input signal for most experiments.


title: Bernstein_HMEC_H3K4me3

value: primary cell

value: mammary epithelial cell

tag: datatype

tag: datatype description

tag: cell organism

value: mammary epithelial cells

value: normal

tag: cell sex

value: U

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody

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

value: 1)abcam; 2)Millipore

value: No special treatment or protocol applies

tag: control description


title: Bernstein_HeLa-S3_Control

value: immortalized cell line

tag: line

tag: lab

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

value: Input

tag: antibody description

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

tag: replicate


title: Bernstein_NHEK_H3K9me1

tag: lab description

value: human

tag: cell description

value: epidermal keratinocytes

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9me1

tag: antibody targetdescription

value: Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.

tag: softwareversion


title: Bernstein_K562_H3K79me2

tag: datatype

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

tag: cell lineage

value: mesoderm

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

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

value: Active Motif

tag: treatment

tag: treatment description

tag: control

tag: controlid


title: Bernstein_NHLF_H4K20me1

source_name: NHLF

value: Broad

value: Bernstein - Broad Institute

tag: datatype description

tag: cell organism

value: lung fibroblasts

tag: cell karyotype

value: normal

value: endoderm

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: No special treatment or protocol applies

tag: control description

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_K562_Pol2(b)

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell description

value: mouse monoclonal, clone CTD4H8. Antibody Target:POL2B

value: RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation.

value: Covance

tag: replicate


title: Bernstein_NHLF_H3K4me3

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: 1)abcam; 2)Millipore

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.


title: Bernstein_HSMMtube_H4K20me1

value: Broad

value: Bernstein - Broad Institute

tag: datatype

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

value: abcam

tag: treatment

tag: softwareversion


title: Bernstein_HMEC_H3K4me1

value: primary cell

value: mammary epithelial cell

value: ChipSeq

tag: datatype description

tag: cell organism

value: mammary epithelial cells

value: normal

value: ectoderm

value: rabbit polyclonal. Antibody Target:H3K4me1

tag: antibody

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

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: controlid

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HepG2_H3K79me2

tag: lab

tag: lab description

value: Chromatin IP Sequencing

value: human

tag: cell description

value: hepatocellular carcinoma

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

value: std

tag: control description

value: Standard input signal for most experiments.


title: Bernstein_HUVEC_H3K4me3

value: Broad

value: Bernstein - Broad Institute

value: umbilical vein endothelial cells

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: 1)abcam; 2)Millipore

tag: labversion

tag: replicate


title: Bernstein_HUVEC_H4K20me1

tag: datatype

value: ChipSeq

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: antibody vendorid

tag: treatment


title: Bernstein_Osteobl_H3K4me1

value: primary cell

value: osteoblast

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: osteoblasts (NHOst)

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

value: rabbit polyclonal. Antibody Target:H3K4me1

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

value: No special treatment or protocol applies

tag: softwareversion


title: Bernstein_H1-hESC_H3K4me2

growth_protocol: missing

tag: lab

value: Broad

value: Bernstein - Broad Institute

value: embryonic stem cells

value: inner cell mass

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: treatment description

tag: control

value: std

value: Standard input signal for most experiments.

tag: controlid


title: Bernstein_NHEK_CTCF

tag: lab description

value: ChipSeq

tag: cell description

value: epidermal keratinocytes

tag: antibody antibodydescription

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: control description


title: Bernstein_HSMM_H3K36me3

value: primary cell

value: skeletal muscle myoblast

value: Chromatin IP Sequencing

value: human

value: skeletal muscle myoblasts

value: mesoderm

value: U

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody

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: replicate


title: Bernstein_NHLF_H3K36me3

value: Broad

value: Bernstein - Broad Institute

tag: datatype

tag: datatype description

value: lung fibroblasts

tag: cell karyotype

value: normal

value: endoderm

tag: antibody vendorid

tag: treatment

value: No special treatment or protocol applies

value: std


title: Bernstein_HSMMtube_H3K4me2

tag: lab

value: ChipSeq

tag: cell organism

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell lineage

tag: cell sex

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: Standard input signal for most experiments.

tag: softwareversion


title: Bernstein_K562_H3K4me2

tag: lab description

value: Chromatin IP Sequencing

value: human

tag: cell description

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

value: mesoderm

tag: treatment description

tag: control

tag: controlid


title: Bernstein_HMEC_H3K36me3

value: primary cell

value: mammary epithelial cell

value: mammary epithelial cells

value: ectoderm

value: U

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody

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: control description


title: Bernstein_Osteobl_Control

value: Broad

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: osteoblasts (NHOst)

value: Input

tag: antibody description

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

value: No special treatment or protocol applies

value: std

tag: replicate


title: Bernstein_NHLF_CTCF

tag: lab

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: lung fibroblasts

tag: cell karyotype

value: normal

tag: cell lineage

value: endoderm

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: antibody vendorid

tag: treatment

value: Standard input signal for most experiments.


title: Bernstein_H1-hESC_H4K20me1

value: Broad

tag: lab description

tag: cell description

value: embryonic stem cells

value: inner cell mass

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: treatment description

tag: control

tag: softwareversion


title: Bernstein_HepG2_H3K4me2

value: Bernstein - Broad Institute

value: ChipSeq

value: hepatocellular carcinoma

tag: antibody antibodydescription

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: No special treatment or protocol applies

tag: controlid


title: Bernstein_K562_H3K4me3

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: human

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

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: 1)abcam; 2)Millipore

value: std

tag: control description


title: Bernstein_HepG2_H3K36me3

value: immortalized cell line

tag: line

tag: lab

value: Broad

tag: cell organism

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody

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.

value: Standard input signal for most experiments.

tag: replicate


title: Bernstein_NH-A_Control

tag: lab description

value: Bernstein - Broad Institute

value: ChipSeq

value: astrocytes (also called Astrocy)

tag: cell karyotype

value: normal

tag: cell lineage

value: ectoderm

value: Input

tag: antibody description

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

tag: treatment


title: Bernstein_GM12878_H3K9ac

value: Chromatin IP Sequencing

value: human

tag: cell description

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

value: mesoderm

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

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

value: abcam

tag: antibody vendorid

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: labversion

value: Illumina_GA2e and Illumina_GA2x

tag: softwareversion


title: Bernstein_H1-hESC_CTCF

value: Broad

tag: datatype

tag: datatype description

value: embryonic stem cells

value: inner cell mass

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: Bernstein_HSMMtube_H3K27ac

tag: lab

tag: lab description

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell sex

value: U

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: replicate


title: Bernstein_GM12878_H3K36me3

value: human

tag: cell description

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

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: antibody antibodydescription

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.

value: abcam

tag: treatment

value: No special treatment or protocol applies


title: Bernstein_NHDF-Ad_H3K27ac

value: primary cell

value: fibroblast of dermis

value: Broad

value: adult dermal fibroblasts

tag: antibody

tag: antibody vendorid

tag: treatment description

tag: control

value: std

tag: labversion

value: Illumina_GA2e and Illumina_GA2x

tag: softwareversion


title: Bernstein_HMEC_H3K27ac

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mammary epithelial cells

value: ectoderm

value: U

tag: antibody targetdescription

tag: antibody vendorname

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: Bernstein_HSMM_H3K27me3

value: skeletal muscle myoblast

tag: lab

tag: lab description

tag: cell organism

value: human

tag: cell description

value: skeletal muscle myoblasts

value: mesoderm

tag: cell sex

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: replicate


title: Bernstein_HSMMtube_H3K4me1

value: Broad

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell lineage

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: antibody vendorid

tag: treatment

value: No special treatment or protocol applies


title: Bernstein_K562_H3K27me3

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

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

tag: treatment description

tag: control

value: std

tag: softwareversion


title: Bernstein_K562_H3K27ac

value: immortalized cell line

tag: line

tag: datatype

tag: datatype description

value: human

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody

tag: antibody targetdescription

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

value: Standard input signal for most experiments.

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HMEC_H3K4me2

tag: lab

value: Broad

tag: lab description

tag: cell organism

value: mammary epithelial cells

tag: cell karyotype

value: normal

value: ectoderm

value: U

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

tag: control description

tag: controlid


title: Bernstein_NHLF_H3K9ac

value: Bernstein - Broad Institute

value: ChipSeq

tag: cell description

value: lung fibroblasts

tag: cell lineage

value: endoderm

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

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

value: abcam

tag: antibody vendorid

tag: treatment

value: No special treatment or protocol applies

tag: replicate


title: Bernstein_HSMMtube_Control

value: in vitro differentiated cells

value: myotube

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: human

value: skeletal muscle myotubes differentiated from the HSMM cell line

value: mesoderm

tag: cell sex

value: Input

tag: antibody description

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

tag: treatment description

tag: control

value: std

value: Standard input signal for most experiments.


title: Bernstein_NHDF-Ad_H3K4me3

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

value: ChipSeq

tag: cell organism

value: adult dermal fibroblasts

value: normal

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

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

value: 1)abcam; 2)Millipore

tag: labversion

value: Illumina_GA2e and Illumina_GA2x

tag: softwareversion


title: Bernstein_NHLF_H3K4me1

value: Chromatin IP Sequencing

tag: cell description

value: lung fibroblasts

tag: cell karyotype

tag: cell lineage

value: endoderm

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: antibody vendorname

value: abcam

value: No special treatment or protocol applies

tag: control description

tag: controlid


title: Bernstein_HMEC_H4K20me1

tag: datatype

tag: datatype description

value: human

value: mammary epithelial cells

value: ectoderm

value: U

tag: antibody antibodydescription

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 vendorid

tag: treatment

value: std

value: Standard input signal for most experiments.

tag: replicate


title: Bernstein_HepG2_CTCF

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

value: ChipSeq

value: hepatocellular carcinoma

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: treatment description

tag: control


title: Bernstein_NHLF_H3K27ac

value: primary cell

value: fibroblast of lung

value: Chromatin IP Sequencing

tag: cell organism

value: lung fibroblasts

value: normal

value: endoderm

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody

tag: antibody targetdescription

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

value: abcam

tag: softwareversion


title: Bernstein_GM12878_H4K20me1

value: human

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: mesoderm

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

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HSMMtube_H3K9ac

value: Broad

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell sex

value: U

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

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

tag: control description

tag: controlid


title: Bernstein_H1-hESC_H3K4me3

tag: lab

tag: lab description

value: Chromatin IP Sequencing

value: embryonic stem cells

value: inner cell mass

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: 1)abcam; 2)Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

tag: replicate


title: MitoPLD-/- 10 dpp small RNA

status: Public on Jun 01 2011

city: NewHaven

first: Toshiaki

last: Watanabe

state: CT

address: 10 Amistad

institute: Yale University

description: small RNA cloning by length

library_source: transcriptomic

data_processing: small RNAs were mapped to the genome (UCSC 2007, mm9), and mapped sequences were annotated.

molecule: total RNA

organism: Mus musculus

source_name: 10 dpp testes

extract_protocol: small RNA ranging from 20 nt to 40 nt were gel purified. Libraries are prepared according to small RNA Sample prep kit (Illumina).

tag: genotype/variation

value: MitoPLD-/-


title: Mili-/- E16.5 small RNA

description: small RNA cloning by length

source_name: E16.5 testes

tag: development stage

tag: tissue type

value: testes

value: Mili-/-

tag: strain


title: Miwi2-/- E16.5 small RNA

description: small RNA cloning by length


title: Bernstein_HepG2_H3K9ac

tag: cell organism

value: human

tag: cell description

value: hepatocellular carcinoma

tag: antibody targetdescription

tag: antibody vendorname

value: abcam

value: No special treatment or protocol applies

tag: control

value: std

value: Standard input signal for most experiments.

tag: softwareversion


title: Bernstein_HSMM_H3K4me3

value: primary cell

value: skeletal muscle myoblast

value: Broad

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: skeletal muscle myoblasts

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: antibody antibodydescription

tag: antibody

tag: control description

tag: controlid


title: MK_SCL

city: Cambridge

first: Samuel

middle: David

last: Foster

state: Cambridgeshire

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

department: Department of Haematology

country: United Kingdom

institute: Cambridge Institute for Medical Research

description: Chromatin IP against SCL

data_processing:
Processed Alignment: Sequence reads were mapped to the human (March, 2006) genome using Mapping and Assembly with Quality (Maq; http://maq.sourceforge.net/) using the standard settings. Column headings can be found in the linked Readme file.
The .bedgraph files were created using an in house script and show the sequence read denisty across the hg18 human genome.

source_name: Megakaryocytes

growth_protocol: Cultures were started with ≥98% pure cord blood CD34-positive cells isolated by magnetic cell sorting (Myltenyi Biotec, Surrey, United Kingdom) according to the manufacturer’s instructions. Cells were seeded at 1 x 10^5 cells/mL in 12 wells plates in CellGro SCGM medium (CellGenix, Freiburg, Germany) in the presence of 100 ng/mL TPO (CellGenix) and 10 ng/m IL1β (Miltenyi Biotec). Cells were incubated for 10 days at 37º C and 5% CO2. When cell numbers reached an estimate of ~2 – 2.5 x 10^6/mL before day 5, cells were split 1:2 by addition of 1 mL fresh medium containing growth factors and transfer of 1 mL to a new well. After day 5 extra medium containing growth factors was added to the well without transfer of cells.

extract_protocol:
ChIP assays were performed as previously described (Forsberg et al., 2000). Briefly, cells were fixed with 0.4% (for GATA2, FLI1 and SCL) or 1% (for GATA1 and RUNX1) formaldehyde. ChIP was performed on 9.4 - 12.6 x 106 cells using polyclonal antibodies:
anti-GATA1 (ab11963, Abcam), anti-GATA2 (clone H-116, Santa Cruz), anti-RUNX1 (ab23980, Abcam), anti-FLI1 (ab15289, Abcam) or anti-TAL1 antibody (clone C-21, Santa Cruz). As a control non-specific Rabbit IgG (I5006; Sigma Aldrich) was used.
Chromatin was fixed in 0.4% (for GATA2, FLI1 and SCL) or 1% (for GATA1 and RUNX1) formaldehyde, sheared to 200-500 bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: cell type

value: megakaryocytes cultured from cord blood CD34-positive cells

tag: chip antibody

value: SCL


title: MK_rIgG

description: Chromatin IP against rabbit-IgG

value: Rabbit-IgG


title: MK_GATA1

description: Chromatin IP against GATA1


title: MK_FLI1

description: Chromatin IP against FLI1


title: sRNA from tomato fruit 5 days post breaker

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

institute: University of East Anglia

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 5 days post breaker

data_processing: Removed adaptors. Sequences without adapters were discarded. Mapped sequences to BAC release v405 from http://sgn.cornell.edu

organism: Solanum lycopersicum

source_name: breaker +5 days fruit

growth_protocol: Plants were grown in pots with soil in a growth chamber having a photoperiod of 16/8h day/night, a thermoperiod 23/ 18ºC  day/night and humidity of 40%.

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom fruit 5 days post breaker

tag: developmental stage

value: fruit 5 days post breaker stage

tag: cultivar

value: Micro-Tom

tag: tissue

value: fruit


title: MK_GATA2

description: Chromatin IP against GATA2


title: MK_RUNX1

description: Chromatin IP against RUNX1


title: JMM-cel-014_fem-1_AD_5'INDEP-3

first: Jay

last: Maniar

address: 300 Pasteur Dr L302

department: Genetics

institute: Stanford University

description: barcode: AAGA

data_processing: Raw data only (no processing performed).

organism: Caenorhabditis elegans

source_name: Adult hermaphrodite

extract_protocol: Small RNAs were size-selected (Ambion - miRvana).  We then captured the 3' end (IDT-Linker-1 or IDT-Linker-2).  These 3'-captured small RNAs were then further size selected and treated first with antarctic phosphatase and T4 polynucleotide kinase.  Subsequently, these treated RNAs were ligated to a barcoded 5' adapter, reverse transcribed, amplified and sequenced.

tag: genotype

tag: strain

tag: rna-seq method


title: JMM-cel-013_fem-1_AD_5'INDEP-2

description: barcode: TGAA


title: JMM-cel-006_ego-1_fem-1_L4_5'INDEP-2

description: barcode: CAAT

source_name: L4 hermaphrodite


title: JMM-cel-005_ego-1_fem-1_L4_5'INDEP-1

description: barcode: CAAT


title: JMM-cel-010_ego-1_fem-1_AD_5'INDEP-2

description: barcode: AAGA


title: JMM-cel-008_fem-1_L4_5'INDEP-2

description: barcode: ATAC


title: JMM-cel-003_fem-1_L3_5'INDEP-1

description: barcode: GCAG

source_name: L3 hermaphrodite


title: JMM-cel-007_fem-1_L4_5'INDEP-1

description: barcode: TTCT


title: JMM-cel-001_ego-1_fem-1_L3_5'INDEP-1

description: barcode: TTCT


title: JMM-cel-004_fem-1_L3_5'INDEP-2

description: barcode: GCAG


title: JMM-cel-037_fem-1_AD_5'DEP-3

description: barcode: AAGA

extract_protocol: Small RNAs were size-selected (Ambion - miRvana).  We then captured the 3' end (IDT-Linker-1 or IDT-Linker-2).  These 3'-captured small RNAs were then further size selected.  Subsequently, size-selected linkered RNAs were ligated to a barcoded 5' adapter, reverse transcribed, amplified and sequenced.


title: JMM-cel-038_fem-1_AD_5'DEP-4

description: barcode: AAGA


title: JMM-cel-002_ego-1_fem-1_L3_5'INDEP-2

description: barcode: ATAC


title: JMM-cel-036_fem-1_AD_5'DEP-2

description: barcode: ACTT


title: JMM-cel-035_fem-1_AD_5'DEP-1

description: barcode: ACTT


title: JMM-cel-034_ego-1_fem-1_AD_5'DEP-4

description: barcode: TGAA


title: JMM-cel-032_ego-1_fem-1_AD_5'DEP-2

description: barcode: TATG


title: JMM-cel-031_ego-1_fem-1_AD_5'DEP-1

description: barcode: TATG


title: JMM-cel-033_ego-1_fem-1_AD_5'DEP-3

description: barcode: TGAA


title: JMM-cel-030_fem-1_AD_mRNA-4

description: barcode: ATAC

molecule: polyA RNA

extract_protocol: High molecular weight RNA (Ambion - miRvana) was polyA+ selected (Ambion - PolyApurist).  We then fragmented the polyA with RNA fragmentation reagents (Ambion) and treated the RNA with T4 polynucleotide kinase.  These treated RNAs were then ligated to a 3' adapter (IDT-Linker-1 or IDT-Linker-2).  These 3'-captured fragmented RNAs were size selected and ligated to a barcoded 5' adapter, reverse transcribed, amplified and sequenced.

value: mRNAseq


title: JMM-cel-028_fem-1_AD_mRNA-2

description: barcode: TTCT


title: sRNA from tomato fruit 7 days post breaker

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom 7 days post breaker

source_name: breaker +7 days fruit

growth_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom fruit 7 days post breaker

extract_protocol: Plants were grown in pots with soil in a growth chamber having a photoperiod of 16/8h day/night, a thermoperiod 23/ 18ºC  day/night and humidity of 40%.

value: fruit 7 days post breaker stage


title: JMM-cel-027_fem-1_AD_mRNA-1

description: barcode: CAAT


title: JMM-cel-026_ego-1_fem-1_AD_mRNA-4

description: barcode: GCAG


title: JMM-cel-024_ego-1_fem-1_AD_mRNA-2

description: barcode: GCAG


title: JMM-cel-022_fem-1_L4_mRNA-2

description: barcode: TATG


title: JMM-cel-021_fem-1_L4_mRNA-1

description: barcode: TTCT


title: JMM-cel-023_ego-1_fem-1_AD_mRNA-1

description: barcode: ATAC


title: JMM-cel-019_ego-1_fem-1_L4_mRNA-1

description: barcode: ATAC


title: sRNA from tomato fruit 5mm to 7mm in diameter

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 5mm to 7mm in diameter

source_name: 5-7mm fruit

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom fruit 5mm to 7mm in diameter

value: 5-7mm diameter fruit


title: JMM-cel-016_ego-1_fem-1_L3_mRNA-2

description: barcode: TATG


title: JMM-cel-015_ego-1_fem-1_L3_mRNA-1

description: barcode: AAGA


title: JMM-cel-025_ego-1_fem-1_AD_mRNA-3

description: barcode: GCAG


title: JMM-cel-017_fem-1_L3_mRNA-1

description: barcode: ACTT


title: JMM-cel-018_fem-1_L3_mRNA-2

description: barcode: ACTT


title: MBD-HG-3

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description: MBD-biotin based CPG methylated DNA affinity Capture

data_processing:
Illimina Pipeline 1.4
Alignment with bwa  0.5.7 against the hg18 genome
Differential Peak calling with MACS 1.3.7.1 between treatment and control (HG v LG). Input DNA not used directly in peak generation. Results (*peaks.bed files) are linked to Series entry.

source_name: Methyl Miner_CpGSeq_HG

growth_protocol: Primary HAECs (human aortic endothelial cells), purchased from Lonza (Walkersville, MD, USA), were cultured in EBM-2 medium (Lonza) containing EGM-2 growth factors and supplements (Lonza) and 10% fetal bovine serum (Gibco).

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. 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: Glucose response was analyzed in cells treated 48 hours with medium containing 30 mM high glucose (HG) or 5.5 mM low glucose (LG).

value: primary Human Aortic Endothelial cells (HAEC)

tag: passages

value: 3 to 6

value: MBD-Biotin Protein (Invitrogen ME10025)

tag: treatment

value: HG (repeat 3)


title: MBD-HG-2

value: HG (repeat 2)


title: MBD-HG-1

value: HG (repeat 1)


title: HAEC-Input-R2

description: input DNA not used directly in peak generation

source_name: input DNA


title: MitoPLD-/- E16.5 small RNA

description: small RNA cloning by length

tag: genotype/variation

value: MitoPLD-/-


title: sRNA from tomato mature green fruit

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from tomato mature green fruit

source_name: mature green fruit

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom mature green fruit

value: mature green fruit


title: JMM-cel-029_fem-1_AD_mRNA-3

description: barcode: ATAC


title: MBD-LG-2

source_name: Methyl Miner_CpGSeq_LG

value: LG (repeat 2)


title: HAEC-HG-H3Ac-R3

description: Chromatin IP against H3K9/K14ac


title: HAEC-HG-H3Ac-R2

description: Chromatin IP against H3K9/K14ac


title: MBD-LG-1

value: LG (repeat 1)


title: HAEC-LG-H3Ac-R1

description: Chromatin IP against H3K9/K14ac


title: sRNA from tomato fruit 11mm to 14mm in diameter

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 11mm to 14mm in diameter

source_name: 11-14mm fruit

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom fruit 11mm to 14mm in diameter

value: 11-14mm diameter fruit


title: HAEC-LG-H3Ac-R2

description: Chromatin IP against H3K9/K14ac


title: sRNA from tomato fruit 1mm to 3mm in diameter

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 1mm to 3mm in diameter

source_name: 1-3mm fruit

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom fruit 1mm to 3mm in diameter

value: 1-3mm diameter fruit


title: sRNA from tomato breaker stage fruit

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from tomato breaker stage fruit

source_name: breaker stage fruit

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom breaker stage fruit

value: breaker stage fruit

value: Micro-Tom


title: HAEC-LG-H3Ac-R3

description: Chromatin IP against H3K9/K14ac

value: LG (repeat 3)


title: MBD-LG-3


title: total amplified RNA, 2-to-4 cells Ler/Col embryos, sample # LerCol_7

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

country: Switzerland

institute: MWSchmid GmbH

description: linear amplified

data_processing:
50 base reads generated by SOLiD v3 were aligned to the TAIR8.0 version of the Arabidopsis Col genome using the SOLiD™ System Analysis Pipeline Tool (Corona Lite 4.0r2.0, Applied Biosystems, USA), allowing up to 4 color-space mismatches with the additional rule “count valid adjacent errors as single errors”. For transcriptome profiles, reads were excluded if they mapped to more than one genomic position, mapped at splice junctions or were partially overlapping. Consequently, full-length reads uniquely mapping inside a transcript were taken.
Processed data file contains transcript coverage, read count (full-length), transcript type

organism: Arabidopsis thaliana

source_name: embryos (dissected)

growth_protocol: Plants were grown under 16h light.

extract_protocol: 1-RNA extraction: PicoPure RNA Isolation Kit (Arcturus). 2-RNA amplification: WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, USA) producing single-stranded cDNA. 3- Second strand synthesis: poly-A tails added using Terminal Transferase (New England Biolabs, USA) in presence of dATPs (1 PCR cycle using Ex Taq Polymerase , (TaKaRa, Japan), and oligo(dT)12-18   primers (Invitrogen).  4-Library preparation:  from 500 ng ds cDNA, Covaris S2 system (Covaris, Inc.),  sheared into 80–130 bp   fragments , DNA ends were repaired and ligated to SOLiD P1 and P2 adaptors, followed by enrichment by PCR (7 cycles) and a size selection on gel

tag: Stage

value: 2-to-4 cells embryo stage with suspensor (partial)

tag: maternal strain

value: Landsberg erecta (Ler)

tag: maternal genotype/variation

value: wildtype

tag: paternal strain

value: Columbia_0 (Col0)

tag: paternal genotype/variation


title: total amplified RNA, globular Ler/Col embryos, sample # LerCol_4

description: linear amplified

value: globular embryo stage with suspensor (partial)


title: JMM-cel-011_ego-1_fem-1_AD_5'INDEP-3

description: barcode: TGAA


title: Smoker with Lung Cancer (C_NuGEN)

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

description: Prototype NuGEN Ovation RNA-seq Protocol, 36 bp single end sequencing

data_processing: Reads were aligned to human genome build 19 using Tophat software v1.0.14 with mammalian defaults with the exception of specifying a maximum of 10 multi-reads.  Gene expression measurements (RPKM, reads per kilobase per million reads) were calculated based on the alignments using Scripture software's score function.  The annotation file used by Scripture software was based on Ensembl v59 (n=49,702 genes) where the union set of transcripts mapping to a single gene was used to summarize gene-level expression.  The FWER corrected p-value for the observed read count across the transcript (Scripture software) was used to decide if a gene confidently expressed in a sample (p-value < 0.05 were designated as present).

source_name: Large airway epithelial cells

extract_protocol: Standard Illumina mRNA-seq Protocol (Paired end 75 bp reads, fragments were 300bp, 2 50 bp adapter sequences, 2 75 bp reads, and a 50 bp insert (sd= 50bp) or prototype NuGEN Ovation RNA-seq protocol (36 bp single end reads)

value: large airway epithelial cells

tag: gender

value: 2 Male, 1 Female

tag: average age

tag: smoking status

value: 2 Former, 1 Current

tag: packyears

tag: lung cancer

value: 3 Yes


title: Healthy smoker (S_NuGEN)

tag: cell type

value: 1 Male, 2 Female

value: 3 Current

value: 3 No


title: Smoker without Lung Cancer (NC_NuGEN)


title: Healthy non-smoker (NS_NuGEN)

value: 3 Female

value: 3 Never


title: Smoker without Lung Cancer (NC_Illumina)

description: Standard Illumina mRNA-seq Protocol, 75 bp paired-end sequencing


title: total amplified RNA, 2-to-4 cells Ler/Col embryos, sample # KypCol_11

description: linear amplified


title: IgG_control

status: Public on May 31 2011

first: Kinyui Alice

last: LO

address: 77 Massachusetts Ave.

department: Biological Engineering

institute: MIT

description: control DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI36/hg18(March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Unique sequences from each ChIP-seq experiment were extended 200 base pairs in a strand specific manner and allocated to 25-basepairs bins.  Peaks calling was done using a p-value threshold of 10-9 compared to a Poissonian background. An empirical background model was obtained from a mock immunoprecipitation experiment using IgG.  We eliminated any peaks that did not have at least three-fold higher ChIP-seq density in the specific immunoprecipitated sample compared to the non-specific IgG sample, normalized for the total number of reads sequenced.

source_name: Adipocytes

growth_protocol: Human mesenchymal stem cells were purchased from Lonza and cultured in growth medium kit (PT3001).  Cells were seeded at a density of 5000 cells/cm2.  At confluence, the cells were differentiated into adipocytes using the adipogenic differentiation kit (Lonza PT3004).  The total differentiation process took 19 days, with 14 days of induction and 5 days of maintenance.  All media were from Lonza, except that the insulin concentration (in both induction and maintenance media) was adjusted to 120 pM.

extract_protocol: Cells were lysed and chromatin was sonicated.The sonicated chromatin was incubated with  antibody-coupled beads overnight. The beads were then washed and the chromatin was eluted, reverse-crosslinked at 65°C overnight, treated with RNase and Proteinase K and extracted with phenol-chloroform.  The DNA was ethanol precipitated, purified and subjected to sequencing preparation using the Illumina sample preparation protocol.  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 PCR amplified with Illumina primers for 15 cycles and library fragments around 200-300bp were cut from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Sequencing was done using the Illumina Genome Analyzer II.

treatment_protocol: Mature adipocytes were subjected to 1% formaldehyde cross-linking for 10 minutes at room temperature and neutralized with 0.125M glycine for 5 minutes.  Cells were then  treated with Accutase and scraped.  The preparation was centrifuged for 25 minutes at 15°C at 3500 rpm.  The adipocytes, which formed a white layer (anti-pellet) at the meniscus, were harvested and snap-frozen in liquid nitrogen.

value: Fully differentiated

value: Mesenchymal stem cells-derived adipocytes

value: less than 7

tag: chip antibody

value: IgG Control

tag: vendor

value: Santa Cruz Biotechnology

tag: catalogue number

tag: lot number


title: HSF1_ChIPSeq

description: Chromatin IP against HSF-1

tag: strain

tag: passages


title: C/EBPa_ChIPSeq

description: Chromatin IP against C/EBPα

value: C/EBPα


title: sRNA from open flower

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from open flower

source_name: Open flower

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom open flowers

tag: developmental stage

value: open flower

tag: cultivar

value: Micro-Tom

tag: tissue

value: flower


title: E2F4_ChIPSeq

description: Chromatin IP against E2F4


title: Healthy smoker (S_Illumina)

value: large airway epithelial cells


title: RNA_seq_P2N

status: Public on May 28 2011

city: Tao-Yuan

first: Ji-Dung

last: Luo

address: No. 259, Wen-Hwa 1st road, Kwei-Shan

department: Graduate Institute of Biomedical Sciences, Division of Medical Biotechnology

country: Taiwan

institute: Chang Gung University

description: RNA-seq of normal tissue in patient 2 (crc_2_n)

data_processing: Alignment: Sequence reads were obtained and mapped to the human RNA reference sequences, human genomes (hg19), and mitochonerial DNA (rCRS; NC_012920) using Borrow-Wheeler Aligner. All reads mapping with two or fewer mismatches were retained.

source_name: normal tissue

extract_protocol: mRNA was captured by oligo-dT. Synthesis of first strand cDNA was oligo-dT primed synthesis. The second strand cDNA synthesized with random hexamer. Both ends of double strand cDNA were filled and ligated with adaptor.

tag: tissue type

value: normal bowel tissue

tag: disease status

value: stage III colorectal cancer patients


title: RNA_seq_P2T

description: RNA-seq of tumor tissue in patient 2 (crc_2_t)

source_name: colorectal tumor tissue

value: Bowel adenocarcinoma tissue


title: RNA_seq_P1T

description: RNA-seq of tumor tissue in patient 1 (crc_1_t)


title: H3K56ac_ChIPSeq

description: Chromatin IP against H3K56ac

value: Epitomics


title: Healthy non-smoker (NS_Illumina)

tag: gender

value: 3 No


title: HAEC-HG-H3Ac-R1

description: Chromatin IP against H3K9/K14ac

value: primary Human Aortic Endothelial cells (HAEC)

value: 3 to 6

tag: antibody

tag: treatment

value: HG (repeat 1)


title: RNA_seq_P1N

description: RNA-seq of normal tissue in patient 1 (crc_1_n)


title: sRNA from closed bud before flower blooming

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from closed bud before flower blooming

source_name: Closed bud before flower blooming

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom closed bud before flower blooming

value: closed bud before flower blooming

value: closed bud


title: 16C follicle cells replicate 2

status: Public on May 27 2011

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing: mRNA-Seq reads were aligned to BDGP Release 5/DM3 using ELAND, using the first 25 bases of a read as a seed.  Each matched seed was then extended up to 36 bases and scored to break any ties between multi-matches.  For mRNA expression counts, unique reads in the genome that landed within any known exons were counted.  The counts were normalized by the mRNA length to get the final RPKM values (reads per KB per million reads).

organism: Drosophila melanogaster

source_name: Adult Drosophila ovaries

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media

extract_protocol: 250,000 - 900,000 16C follicle cells were resuspended in TRIzol reagent and RNA was prepared as indicated in the manufactures protocol. 100ng of total RNA was used to generate a cDNA library for Illumina based RNA-sequencing with DSN normalization according to the manufactures protocol.

treatment_protocol: Not applicable

value: 16C follicle cells of the ovary

value: TOW OregonR


title: sRNA from tomato fruit 3 days post breaker

description: Total endogenous small RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 3 days post breaker

source_name: breaker +3 days fruit

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom fruit 3 days post breaker

value: fruit 3 days post breaker stage

value: fruit


title: Small RNA from 4 pooled macaque principal and basal cells

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

country: China

institute: PICB

description: Small RNA deep sequencing from 4 pooled macaque principal and basal cells.

data_processing: All multiple reads representing one sequence were collapsed and the adapter sequence at the 3’-end of the sequence reads was trimmed using a custom trimming procedure.

organism: Macaca mulatta

source_name: macaque principal and basal cells of epididymis

extract_protocol: Total RNA was firstly isolated using the Trizol (Invitrogen, USA) protocol and further, low molecular weight RNA with length range from 20 to 40 nt were isolated, ligated to the adapters, amplified, and sequenced following the Small RNA Preparation Protocol (Illumina, USA) with no modifications.

treatment_protocol: All rhesus macaque samples were obtained from the Suzhou Experimental Animal Center (Suzhou, China). All tissues were dissected and frozen in liquid nitrogen within 20 minutes after death. Laser Capture Microdissection (LCM) was used to dissect two types of epididymis cells -- principal/basal cells that contained pilRNA according to in situ hybridization results and peritubular tissue that did not contain pilRNA -- from four adult rhesus macaque epididymis samples.

value: principal and basal cells of epididymis

value: adult

value: male


title: 16C follicle cells replicate 1


title: Negative control L139_EMPTY_96

status: Public on May 25 2011

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

data_processing: Barcodes were removed and reads were aligned using Bowtie.

source_name: Negative control

growth_protocol: ES R1 cells were cultured as previously described (Moliner et al. 2008). MEFs were grown in DMEM with 10% FBS, 1x penicillin/streptomycin, 1x Glutamax and 0.05 mM 2-mercaptoethanol. All reagents were from Invitrogen.

extract_protocol: Custom protocol designed to capture the 5' end of transcripts, and maintain strand-information. See accompanying publication for details.

value: Negative control

tag: well


title: ref6-1_H3K27me3_ChIPseq

first: Falong

last: Lu

state: Massachusetts

address: 200 Longwood Ave, WAB 159

department: Program of Cellular and Molecular Medicine

institute: Boston Children's Hospital / HHMI

description: Chromatin IP against H3K27me3.

data_processing: The reads were aligned to the TAIR9 assembly using the ELAND extended program (Illumina) allowing up to two mismatches. The MASC program was used to shift the reads and convert the data to WIG format. WIG files were visualized with the Integrated Genome Browser (IGB).

source_name: ref6-1, 10DAG seedling

growth_protocol: The seeds of the indicated genotype were surface steriled, planted on an MS plate, and grown at 23°C under long day (16h light, 8h dark) conditions for ten days before harvest.

extract_protocol: Nuclear lysates were clarified from sonicated nuclei, and crosslinked histone-DNA complexes were isolated with antibody. DNA was purified after reverse crosslinking. Libraries were prepared according to Illumina's instructions accompanying the single end DNA Sample Kit (Part# 0801-0303). After adapter ligation, DNA was size-fractionated to obtain 300bp fragments from an agarose gel. The library was PCRed for 18 cycles and gel purified before sequencing.

treatment_protocol: No treatment applied.

tag: ecotype background

value: Col

tag: genotype

value: ref6-1 mutant

value: 10 days after germination (DAG)

value: whole seedling

tag: antibody provider

value: T. Jenuwein


title: Negative control L139_EMPTY_95

tag: cell type


title: Col_H3K27me3_ChIPseq

description: Chromatin IP against H3K27me3.

source_name: Col, 10DAG seedling

value: wild type


title: Small RNA from macaque testis

description: Small RNA deep sequencing from macaque testis.

source_name: macaque testis

treatment_protocol: All rhesus macaque samples were obtained from the Suzhou Experimental Animal Center (Suzhou, China). All tissues were dissected and frozen in liquid nitrogen within 20 minutes after death.

value: testis


title: JMM-cel-020_ego-1_fem-1_L4_mRNA-2

description: barcode: TGAA

source_name: L4 hermaphrodite

extract_protocol: High molecular weight RNA (Ambion - miRvana) was polyA+ selected (Ambion - PolyApurist).  We then fragmented the polyA with RNA fragmentation reagents (Ambion) and treated the RNA with T4 polynucleotide kinase.  These treated RNAs were then ligated to a 3' adapter (IDT-Linker-1 or IDT-Linker-2).  These 3'-captured fragmented RNAs were size selected and ligated to a barcoded 5' adapter, reverse transcribed, amplified and sequenced.

tag: rna-seq method

value: mRNAseq


title: Negative control L139_EMPTY_94


title: Small RNA from 4 pooled macaque peritubular tissues

description: Small RNA deep sequencing from 4 pooled macaque peritubular tissues.

source_name: macaque peritubular tissues of epididymis

value: peritubular tissues of epididymis


title: Negative control L139_EMPTY_93


title: Embryonic fibroblast L139_MEF_87

source_name: Embryonic fibroblast

value: Embryonic fibroblast

tag: source cell line


title: Embryonic fibroblast L139_MEF_86


title: Embryonic fibroblast L139_MEF_89


title: Embryonic fibroblast L139_MEF_90


title: Embryonic fibroblast L139_MEF_91


title: Terminator 5'-Phosphate-Dependent Exonuclease and RNA 5' Polyphosphatase prep DvH_LS4D_5RNASeq_PPP

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

description: Mid-log phase DvH in LS4D

data_processing: Reads mapped to genome with Eland by the sequencing center

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: DvH grown in defined lactate/sulfate media

growth_protocol: Experiments were conducted within a Coy anaerobic chamber with an atmosphere of about 2% H2 and 5% CO2, with the

extract_protocol: After sample-specific modifications to the 5' ends, we blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We  size-selected products of 150-500 bases from an agarose gel. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor.  We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).

treatment_protocol: Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyzer; only samples with an RNA integrity number of around 9 or better were used.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads coated with oligonucleotides that hybridize to ribosomal RNA.

tag: media

tag: protocol

value: We used Terminator 5'-Phosphate-Dependent Exonuclease (Epicentre) to try to remove 5'-monophosphate (degraded) transcripts and then converted 5'-triphosphate ends to 5'-monophosphate ends with RNA 5' Polyphosphatase (Epicentre).  Between each enzymatic reaction of this library, RNA was purified using Agencourt RNAClean XP beads. Molecules smaller than 100 nucleotides and unligated adaptors were mostly lost in these clean-up reactions.

tag: strain

value: Hildenborough


title: Embryonic fibroblast L139_MEF_83


title: Embryonic fibroblast L139_MEF_85


title: Tobacco Acid Pyrophophatase prep DvH_LS4D_5RNASeq

description: Mid-log phase DvH in LS4D

value: We converted 5'-triphosphate ends to 5'-monophosphate with Tobacco Acid Pyrophophatase.


title: Embryonic fibroblast L139_MEF_84


title: Embryonic fibroblast L139_MEF_82


title: Small RNA from macaque cortex

description: Small RNA deep sequencing from macaque cortex.

source_name: macaque cortex

value: cortex

tag: developmental stage


title: Embryonic fibroblast L139_MEF_81


title: Embryonic fibroblast L139_MEF_78


title: Embryonic fibroblast L139_MEF_80


title: Embryonic fibroblast L139_MEF_77


title: Embryonic fibroblast L139_MEF_71


title: Small RNA from macaque seminal vesicle

description: Small RNA deep sequencing from macaque seminal vesicle.

source_name: macaque seminal vesicle

tag: tissue

value: seminal vesicle

value: adult


title: Embryonic fibroblast L139_MEF_74


title: Small RNA from macaque epididymis

description: Small RNA deep sequencing from macaque epididymis.

source_name: macaque epididymis

value: epididymis

value: male


title: Small RNA from macaque prostate

description: Small RNA deep sequencing from macaque prostate.

source_name: macaque prostate

value: prostate


title: Embryonic fibroblast L139_MEF_70


title: Embryonic fibroblast L139_MEF_69


title: Embryonic fibroblast L139_MEF_68


title: Embryonic fibroblast L139_MEF_67


title: Embryonic fibroblast L139_MEF_65


title: Embryonic fibroblast L139_MEF_79


title: Embryonic fibroblast L139_MEF_75


title: Embryonic fibroblast L139_MEF_63


title: Embryonic fibroblast L139_MEF_76


title: Embryonic fibroblast L139_MEF_60


title: Embryonic fibroblast L139_MEF_64


title: Embryonic fibroblast L139_MEF_61


title: Embryonic fibroblast L139_MEF_62


title: Embryonic fibroblast L139_MEF_59


title: Embryonic fibroblast L139_MEF_58


title: Embryonic fibroblast L139_MEF_56


title: Embryonic fibroblast L139_MEF_57


title: Embryonic fibroblast L139_MEF_55


title: Embryonic fibroblast L139_MEF_73


title: Embryonic fibroblast L139_MEF_53


title: Embryonic fibroblast L139_MEF_66


title: Embryonic fibroblast L139_MEF_52


title: Smoker with Lung Cancer (C_Illumina)

source_name: Large airway epithelial cells

value: large airway epithelial cells

value: 2 Male, 1 Female

tag: average age

tag: smoking status

value: 2 Former, 1 Current

tag: packyears

tag: lung cancer

value: 3 Yes


title: Embryonic fibroblast L139_MEF_51


title: Embryonic fibroblast L139_MEF_50


title: Embryonic stem cell L139_ESC_48

source_name: Embryonic stem cell

value: Embryonic stem cell


title: Embryonic stem cell L139_ESC_46


title: Embryonic stem cell L139_ESC_45


title: Embryonic stem cell L139_ESC_43


title: Embryonic fibroblast L139_MEF_54


title: Embryonic stem cell L139_ESC_39


title: Embryonic stem cell L139_ESC_41


title: Embryonic stem cell L139_ESC_37


title: Embryonic stem cell L139_ESC_35


title: Embryonic stem cell L139_ESC_38


title: Embryonic stem cell L139_ESC_40


title: Embryonic stem cell L139_ESC_33


title: Embryonic stem cell L139_ESC_32


title: Small RNA from mouse epididymis

description: Small RNA deep sequencing from mouse epididymis.

source_name: mouse epididymis

treatment_protocol: Adult male mice were purchased from the Animal Center of the Chinese Academy of Sciences (Shanghai, China). Experiments were conducted according to a protocol approved by the Institute Animal Care Committee. Mouse epididymis samples were obtained from mice after they were sacrificed, and the samples were frozen immediately in liquid nitrogen.

value: wildtype

tag: gender


title: Embryonic stem cell L139_ESC_42

tag: well


title: Embryonic stem cell L139_ESC_36


title: Embryonic stem cell L139_ESC_34


title: Embryonic stem cell L139_ESC_31


title: Embryonic fibroblast L139_MEF_49


title: Embryonic stem cell L139_ESC_29


title: Embryonic fibroblast L139_MEF_92


title: Embryonic stem cell L139_ESC_28


title: Embryonic stem cell L139_ESC_27


title: Embryonic stem cell L139_ESC_47


title: Embryonic stem cell L139_ESC_44


title: Input control 4

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

description: input DNA

data_processing:
Alignment: Sequence reads were mapped to the WS190 reference sequence using BWA
Summary WIG files: Mapped sequence reads were extended to 200 bp, which was the estimated mean insert size targeted in the size selection step when preparing the libraries. A genomic profile of signal levels was then generated by counting the number of extended sequence reads (i.e. read count) overlapping sampling points spaced at regular 50-bp across the genome.

source_name: L3 embyros

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol: Libraries were prepared according to Illumina's instructions for "Preparing Samples for ChIP Sequencing of DNA", with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase. A's were then added to the 3' ends of the fragments using Kelow fragment (3' 5' exo minus). Paired-end adapters were then ligated onto the ends of the fragments. DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA.

treatment_protocol: Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor. Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.

tag: chip antibody


title: Input control 3

description: input DNA


title: DPY-27

description: Chromatin IP against DPY-27


title: Embryonic fibroblast L139_MEF_72


title: Embryonic stem cell L139_ESC_26


title: H3K36me3

description: Chromatin IP against H3K36me3


title: Embryonic stem cell L139_ESC_25


title: H3K9me3

description: Chromatin IP against H3K9me3


title: H3K4me3

description: Chromatin IP against H3K4me3


title: Embryonic stem cell L139_ESC_23


title: Embryonic stem cell L139_ESC_19


title: Embryonic stem cell L139_ESC_22


title: Embryonic stem cell L139_ESC_24


title: Embryonic stem cell L139_ESC_14


title: Embryonic stem cell L139_ESC_15


title: Embryonic stem cell L139_ESC_20


title: Embryonic stem cell L139_ESC_16


title: Embryonic stem cell L139_ESC_21


title: Embryonic stem cell L139_ESC_30


title: Embryonic stem cell L139_ESC_17


title: Embryonic stem cell L139_ESC_13


title: Embryonic stem cell L139_ESC_12


title: Embryonic stem cell L139_ESC_6


title: Embryonic stem cell L139_ESC_9


title: Embryonic stem cell L139_ESC_11


title: Embryonic stem cell L139_ESC_7


title: Embryonic stem cell L139_ESC_8


title: Embryonic stem cell L139_ESC_10


title: Embryonic stem cell L139_ESC_4


title: Embryonic stem cell L139_ESC_5


title: Embryonic stem cell L139_ESC_2


title: Embryonic stem cell L139_ESC_1


title: Input_U2OS stables_ChIP-seq_rep1_lane4

status: Public on May 24 2011

city: Palo Alto

first: Philip

last: Cayting

address: 1501 S California Ave

description:
UCD337
Genomic DNA used as Input for Chromatin IP (U2OS)

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg19 female (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

source_name: Osteosarcoma cell line

growth_protocol: All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)

extract_protocol: Lysates were clarified from sonicated nuclei and protein-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 (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA fragments of ~500 bp were band isolated from an agarose gel. Size-selected DNA was PCR amplified with Illumina primers for 15 cycles and 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.

tag: cell line

tag: genotype/variation

value: stably expressing shKAP1 and FLAG-KAP1 wild type

tag: harvest date


title: FLAG-KAP1 wild type_U2OS stables_ChIP-seq_rep2B_lane7

description:
UCD374
Chromatin IP against FLAG-KAP1 wild type

source_name: Osteosarcome cell line

value: mouse anti-FLAG (Sigma, catalog # F1804)


title: FLAG-KAP1 wild type_U2OS stables_ChIP-seq_rep2A_lane5

description:
UCD341
Chromatin IP against FLAG-KAP1 wild type


title: Input_4_HEK293 stables_ChIP-seq_rep1_lane6

description:
UCD336
Genomic DNA used as Input for Chromatin IP (HEK293)

source_name: Transformed embryonic kidney cell line

value: stably expressing FLAG-KAP1 C-ter PB{delta} mutant


title: Embryonic stem cell L139_ESC_18

tag: cell type


title: Input_3_HEK293 stables_ChIP-seq_rep1_lane5

description:
UCD314
Genomic DNA used as Input for Chromatin IP (HEK293)

value: stably expressing FLAG-KAP1 N-ter RBCC{delta} mutant


title: FLAG-KAP1 wild type_U2OS stables_ChIP-seq_rep1_lane8

description:
UCD340
Chromatin IP against FLAG-KAP1 wild type

value: rabbit anti-KAP1 (Abcam, catalog # ab10483)


title: Input_2_HEK293 stables_ChIP-seq_rep1_lane6

description:
UCD291
Genomic DNA used as Input for Chromatin IP (HEK293)

value: stably expressing FLAG-KAP1 HP1-binding domain mutant


title: Endogenous ELK4_HEK93 cells_ChIP-seq_rep2_lane8

description:
UCD449
Chromatin IP against endogenous ELK4
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)

source_name: Untransformed embryonic kidney cell line

value: original cells (non-transformed) from ATCC

value: rabbit anti-ELK4 (SantaCruz, catalog # sc13030-X)


title: Endogenous KAP1_HEK293 cells_ChIP-seq_rep1_lane3

description:
UCD313A
Chromatin IP against endogenous KAP1
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)


title: Endogenous ELK4_HEK293 cells_ChIP-seq_rep1_lane7

description:
UCD448
Chromatin IP against endogenous ELK4
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)


title: Input_1_HEK293 stables_ChIP-seq_rep1_lane6

description:
UCD283
Genomic DNA used as Input for Chromatin IP (HEK293)

value: stably expressing FLAG-KAP1 wild type


title: FLAG-KAP1 N/C-ter (RBCC+PB){delta}_T -Rex HEK293 stables_ChIP-seq_rep1_lane2

description:
UCD434
Chromatin IP against FLAG-KAP1 N/C-ter (RBCC+PB){delta} mutant
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)

value: stably expressing Tetracycline repressor and  FLAG-KAP1 N/C-ter (RBCC+PB){delta} mutant


title: Endogenous KAP1_HEK293 cells_ChIP-seq_rep1_lane4

description:
UCD313B
Chromatin IP against endogenous KAP1
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)


title: FLAG-KAP1 C-ter PB{delta}_HEK293 stables_ChIP-seq_rep1_lane5

description:
UCD335
Chromatin IP against FLAG-KAP1 C-ter PB{delta} mutant
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)


title: FLAG-KAP1 N-ter RBCC{delta} mut_HEK293 stables_ChIP-seq_rep1_lane2

description:
UCD312
Chromatin IP against FLAG-KAP1 N-ter RBCC{delta} mutant
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)


title: FLAG-KAP1 HP1BDmut_HEK293 stables_ChIP-seq_rep1_lane4

description:
UCD334
Chromatin IP against FLAG-KAP1 HP1-binding domain mutant
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)


title: Embryonic stem cell L139_ESC_3

tag: source cell line


title: Snyder_NHR-28_Input_L3 extraction2_seq2 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: OP317(official name :OP317 genotype :unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by :R Waterston )

tag: genotype

tag: Sex

value: Hermaphrodite


title: Snyder_R02D3.7_GFP_L2_rep2 extraction4_seq4 aliquote 1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

tag: strain

value: OP218(official name :OP218 genotype :unc-119(ed3); wgIs218(R02D3.7:TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by : )


title: FLAG-KAP1 wild type_HEK293 stables_ChIP-seq_rep1_lane3,6,7

description:
UCD281
Chromatin IP against FLAG-KAP1 wild type
Input used to score all the HEK293 ChIP-seq samples was the combined HEK293 input from the 4 transformed cell lines (HEK293 + FLAG-WT-KAP1, HEK293 + FLAG-M2-KAP1, HEK293 + FLAG-dRBCC-KAP1, HEK293 + FLAG-dPB-KAP1)


title: Snyder_NHR-28_GFP_L3_rep1 extraction3_seq3 aliquote 1

tag: developmental stage


title: Snyder_NHR-28_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_NHR-28_GFP_L3_rep2 extraction4_seq4 aliquote 1


title: Snyder_ALY-2_GFP_L1_rep2 extraction4_seq4 aliquote 1

value: OP217(official name :OP217 genotype :unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross :3 transgene :aly-2 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by :Mihail Sarov )

value: fed L1

tag: transgene


title: Snyder_R02D3.7_Input_L2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ALY-2_GFP_L1_rep1 extraction3_seq3 aliquote 1


title: Snyder_R02D3.7_GFP_L2_rep1 extraction3_seq3 aliquote 1


title: Snyder_ALY-2_Input_L1 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;