title: USC_ChipSeq_MCF-7_H3K27ac_UCDavis

value: USC

value: Farnham - University of Southern California

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

value: No special treatment or protocol applies

tag: antibody

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.

value: UCDavis

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: UW_ChipSeq_H7-hESC_Input_diffProtA_14d

status: Public on Jun 07 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

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

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: undifferentiated embryonic stem cells

value: inner cell mass

value: U

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage:mesoderm

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion

value: Bowtie 0.12.7


title: UW_ChipSeq_SK-N-SH_RA_Input

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

value: F

value: Bowtie 0.12.5


title: UW_ChipSeq_H7-hESC_H3K4me3_diffProtA_14d

value: in vitro differentiated cells

value: cardiac mesoderm

value: UW

value: Stamatoyannopoulous - University of Washington

value: undifferentiated embryonic stem cells

tag: cell sex

tag: antibody

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: Millipore

tag: antibody vendorid

tag: controlid

tag: replicate


title: UW_ChipSeq_HCF_H3K4me3

source_name: HCF

tag: lab

tag: lab description

tag: datatype

value: HCF

value: cardiac fibroblasts

value: normal

value: mesoderm

value: U

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: Bowtie 0.12.7


title: UW_ChipSeq_SAEC_Input

source_name: SAEC

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: SAEC

tag: cell organism

value: human

tag: cell description

value: small airway epithelial cells

tag: cell karyotype

value: endoderm

value: Input

tag: antibody description

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

tag: labexpid

tag: labversion

value: Bowtie 0.12.5


title: UW_ChipSeq_H7-hESC_H3K36me3_diffProtA_5d

value: UW

value: Stamatoyannopoulous - University of Washington

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm

tag: controlid


title: UW_ChipSeq_GM12865_Input

status: Public on Jun 08 2012

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

value: normal

value: mesoderm

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: UW_ChipSeq_HCF_Input

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: HCF

tag: cell organism

value: human

tag: cell description

value: cardiac fibroblasts

tag: cell karyotype

value: U

value: Input

tag: antibody description

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

tag: labexpid

tag: labversion

value: Bowtie 0.12.7


title: UW_ChipSeq_HCM_Input

source_name: HCM

value: UW

value: Stamatoyannopoulous - University of Washington

value: HCM

value: cardiac myocytes

tag: cell lineage

tag: cell sex

tag: antibody

tag: controlid


title: UW_ChipSeq_HCM_H3K4me3

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: normal

value: mesoderm

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: Millipore

tag: antibody vendorid

tag: treatment


title: UW_ChipSeq_H7-hESC_H3K36me3_diffProtA_2d

value: in vitro differentiated cells

value: cardiac mesoderm

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: undifferentiated embryonic stem cells

value: inner cell mass

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage:mesoderm

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: UW_ChipSeq_HCPEpiC_H3K4me3

source_name: HCPEpiC

value: UW

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: HCPEpiC

value: human

value: choroid plexus epithelial cells

tag: cell karyotype

tag: cell lineage

value: ectoderm

tag: cell sex

value: U

tag: antibody

value: No special treatment or protocol applies

tag: controlid

tag: labexpid

tag: labversion

value: Bowtie 0.12.7


title: UW_ChipSeq_HCFaa_Input

source_name: HCFaa

tag: lab

tag: lab description

tag: datatype

value: Chromatin IP Sequencing

value: HCFaa

value: cardiac fibroblasts- adult atrial

value: normal

value: mesoderm

value: F

value: Input

tag: antibody description

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


title: UW_ChipSeq_H7-hESC_H3K27me3_diffProtA_14d

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype description

tag: cell

tag: cell organism

value: undifferentiated embryonic stem cells

value: inner cell mass

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage:mesoderm

value: std

value: Standard input signal for most experiments.


title: UW_ChipSeq_H7-hESC_H3K4me3_diffProtA_5d

value: in vitro differentiated cells

value: cardiac mesoderm

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell description

tag: cell lineage

tag: cell sex

value: U

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm

tag: control

tag: control description

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_HCPEpiC_Input

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: HCPEpiC

value: choroid plexus epithelial cells

tag: cell karyotype

value: normal

value: ectoderm

tag: antibody

value: Input

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

value: No special treatment or protocol applies

tag: controlid

tag: labexpid

tag: labversion


title: UW_ChipSeq_HCT-116_H3K4me3

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

value: colorectal carcinoma (PMID:7214343)

value: cancer

value: endoderm

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.


title: UW_ChipSeq_Monocytes-CD14+_RO01746_H3K27me3

value: UW

value: Chromatin IP Sequencing

value: human

tag: cell description

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

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: rabbit polyclonal. Antibody Target:H3K27me3

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

tag: treatment

tag: treatment description

tag: control

tag: control description

value: Bowtie 0.12.7


title: UW_ChipSeq_K562_H3K4me3_ZNF_knockout_4C50_C4

tag: lab

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

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 karyotype

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: beta-globin LCR deletion (18Kb), homozygous (Stam)

tag: controlid

tag: replicate


title: UW_ChipSeq_K562_H3K36me3

tag: datatype description

tag: cell

tag: cell organism

value: cancer

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

value: Abcam

value: No special treatment or protocol applies

value: std

tag: labexpid

tag: labversion

value: Bowtie 0.12.5


title: UW_ChipSeq_K562_H3K4me3_ZNF_knockout_A4.1-C6

value: UW

value: Chromatin IP Sequencing

value: human

tag: cell description

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: off-target control (Stam)

value: Standard input signal for most experiments.


title: UW_ChipSeq_NHEK_H3K27me3

source_name: NHEK

tag: lab

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: ChipSeq

value: NHEK

value: epidermal keratinocytes

tag: cell karyotype

value: normal

value: ectoderm

value: U

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27me3

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

tag: control

tag: control description


title: UW_ChipSeq_K562_H3K4me3_ZNF_knockout_2C10_C5

value: UW

tag: datatype description

tag: cell

tag: cell organism

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

value: cancer

tag: 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: beta-globin LCR deletion (18Kb), homozygous (Stam)

value: std

tag: controlid

value: Bowtie 0.12.7

tag: replicate


title: LU185_mRNA

city: Rochester

first: Krishna

middle: R

last: Kalari

state: MN

address: 200 1st ST SW

department: Department of Biomedical Statistics and Informatics

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
LU185_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm

molecule: polyA RNA

source_name: Lung adenocarcinoma sample

growth_protocol: All cell lines were grown under conditions recommended by ATCC and RNA and DNA were extracted from mid log phase populations of low passage number cultures.

extract_protocol: Total RNA extraction was performed using Exiqon's miRCURY RNA Isolation Kit. Long-read mRNA-seq cDNA libraries were prepared from 1ug of total RNA using a modification of the Illumina mRNA-seq protocol.  Briefly, mRNA was resolved using poly-dT oligonucleotides attached to magnetic beads, fragmented using divalent cations under elevated temperatures, and converted to cDNA using random primers. After conversion of the cleaved fragments into cDNA, the cDNA underwent blunt end repair, addition of an 'A' base to the 3' blunt ends, and ligation of adapter molecules which will be used for PCR amplification, bridge amplification, and sequencing. The cDNA library was resolved by gel electrophoresis using conventional Illumina protocols except that we cut from the gel those cDNA fragments in the range of 300-400bp. The increased fragment length is necessary to accommodate paired end sequence analysis. The gel purified cDNA fragments were amplified by PCR and sequenced using the Illumina Cluster Station and Genome Analyzer. Paired-end sequence analysis (51 cycles/end) was carried out using sequencing primers that correspond to either end of the bridge-amplified cDNA fragments so as to obtain 50nt of sequence from either end of every cDNA fragment.

tag: kras status

value: KRAS mutant ©

tag: cell type

value: Lung adenocarcinoma

tag: passages

value: ATCC low passage


title: UW_ChipSeq_GM12864_H3K4me3

tag: lab

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

tag: cell lineage

value: mesoderm

tag: cell sex

value: M

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion


title: UW_ChipSeq_HMF_Input

source_name: HMF

value: UW

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: HMF

tag: cell organism

value: mammary fibroblasts

value: F

tag: antibody

value: Input

tag: antibody description

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

tag: control

tag: control description


title: UW_ChipSeq_K562_Input

tag: lab

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: std

tag: controlid

value: Bowtie 0.12.5

tag: replicate


title: UW_ChipSeq_HepG2_Input

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: hepatocellular carcinoma

value: endoderm

tag: cell sex

tag: treatment

tag: treatment description

tag: labexpid


title: UW_ChipSeq_GM12865_H3K4me3

tag: lab description

tag: datatype

tag: datatype description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

value: normal

value: mesoderm

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: Millipore

tag: antibody vendorid

value: No special treatment or protocol applies

value: Standard input signal for most experiments.

tag: labversion

value: Bowtie 0.12.7


title: UW_ChipSeq_HCFaa_H3K4me3

tag: lab

value: UW

tag: cell

value: HCFaa

tag: cell organism

tag: cell description

value: cardiac fibroblasts- adult atrial

value: F

tag: antibody

tag: control

value: std

tag: control description


title: UW_ChipSeq_HBMEC_Input

source_name: HBMEC

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: Chromatin IP Sequencing

value: HBMEC

value: human

value: brain microvascular endothelial cells

tag: cell karyotype

tag: cell lineage

tag: cell sex

value: U

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description

tag: controlid

tag: replicate


title: UW_ChipSeq_HPAF_H3K4me3

source_name: HPAF

tag: lab description

tag: datatype

tag: datatype description

value: HPAF

value: pulmonary artery fibroblasts

value: normal

value: mesoderm

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: Millipore

tag: antibody vendorid

value: No special treatment or protocol applies

tag: labexpid


title: UW_ChipSeq_HEEpiC_Input

source_name: HEEpiC

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: cell

value: HEEpiC

tag: cell organism

tag: cell description

value: esophageal epithelial cells

value: endoderm

tag: antibody

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labversion

value: Bowtie 0.12.7


title: UW_ChipSeq_HMF_H3K4me3

value: ChipSeq

value: Chromatin IP Sequencing

value: HMF

value: human

value: mammary fibroblasts

tag: cell sex

value: F

tag: treatment

tag: treatment description

tag: controlid

tag: replicate


title: UW_ChipSeq_HCT-116_Input

tag: lab description

tag: datatype

tag: datatype description

value: colorectal carcinoma (PMID:7214343)

tag: cell karyotype

value: cancer

tag: cell lineage

value: M

value: Input

tag: antibody description

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


title: UW_ChipSeq_HFF-Myc_Input

source_name: HFF-Myc

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: cell

value: HFF-Myc

tag: cell organism

value: foreskin fibroblast cells expressing canine cMyc

value: normal

value: fibroblast

value: No special treatment or protocol applies

tag: labexpid


title: UW_ChipSeq_LNCaP_Input

source_name: LNCaP

value: ChipSeq

value: Chromatin IP Sequencing

value: LNCaP

tag: cell description

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: endoderm

tag: antibody

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: Bowtie 0.12.7


title: UW_ChipSeq_HEEpiC_H3K4me3

value: HEEpiC

value: human

value: esophageal epithelial cells

tag: cell sex

value: U

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: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

tag: labversion


title: UW_ChipSeq_HEK293_H3K4me3

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: embryonic kidney, cells contain Adenovirus 5 DNA (PMID:11967234)

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: controlid

tag: replicate


title: UW_ChipSeq_HPAF_Input

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: HPAF

tag: cell organism

tag: cell description

value: pulmonary artery fibroblasts

tag: antibody

value: Input

tag: antibody description

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

value: No special treatment or protocol applies

tag: control

tag: labexpid


title: UW_ChipSeq_K562_H3K4me3_ZNF_knockout_P5

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: cancer

tag: cell sex

value: F

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: treatment

tag: treatment description

value: Parental K562 (Stam)

value: std

tag: control description

value: Standard input signal for most experiments.

value: Bowtie 0.12.7


title: UW_ChipSeq_BE2_C_Input

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.

tag: cell karyotype

tag: cell lineage

value: ectoderm

value: M

tag: controlid

tag: labversion

tag: replicate


title: UW_ChipSeq_NHLF_Input

source_name: NHLF

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: NHLF

tag: cell organism

tag: cell description

value: lung fibroblasts

value: normal

value: endoderm

value: U

tag: antibody

tag: antibody description

tag: control

tag: labexpid


title: UW_ChipSeq_HPF_H3K4me3

source_name: HPF

value: HPF

value: human

value: pulmonary fibroblasts isolated from lung tissue

tag: cell sex

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: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control description


title: UW_ChipSeq_MCF-7_Input

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: F

value: Input

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

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_HRE_H3K4me3

source_name: HRE

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: HRE

tag: cell organism

tag: cell description

value: renal epithelial cells

value: normal

value: mesoderm

value: U

tag: antibody

tag: control

tag: labexpid

value: Bowtie 0.12.5


title: UW_ChipSeq_NB4_H3K4me3

value: UW

value: Stamatoyannopoulous - University of Washington

value: human

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

tag: cell sex

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: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: UW_ChipSeq_NHEK_Input

tag: lab description

tag: datatype

tag: datatype description

value: NHEK

value: epidermal keratinocytes

tag: cell karyotype

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.

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: UW_ChipSeq_HMEC_H3K27me3

source_name: HMEC

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: HMEC

tag: cell organism

tag: cell description

value: mammary epithelial cells

value: normal

value: U

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27me3

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

tag: control

tag: labversion

tag: replicate


title: UW_ChipSeq_K562_H3K4me3_ZNF_knockout_F4.1-B2

value: UW

value: Stamatoyannopoulous - University of Washington

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: cancer

value: mesoderm

tag: cell sex

value: F

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: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: beta-globin LCR deletion (18Kb), heterozygous (Stam)

tag: labexpid

value: Bowtie 0.12.7


title: UW_ChipSeq_HVMF_H3K4me3

source_name: HVMF

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: HVMF

value: villous mesenchymal fibroblast cells

tag: cell karyotype

value: No special treatment or protocol applies

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: UW_ChipSeq_HRPEpiC_Input

source_name: HRPEpiC

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: cell

value: HRPEpiC

tag: cell organism

value: human

tag: cell description

value: retinal pigment epithelial cells

value: normal

tag: cell lineage

value: ectoderm

value: U

tag: antibody

value: Input

tag: antibody description

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

tag: control


title: UW_ChipSeq_Jurkat_Input

source_name: Jurkat

value: ChipSeq

value: Jurkat

value: T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID:68013)

value: cancer

value: mesoderm

tag: cell sex

value: M

tag: treatment

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_HVMF_Input

value: UW

tag: lab description

tag: datatype

value: Chromatin IP Sequencing

value: HVMF

value: villous mesenchymal fibroblast cells

tag: treatment description

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: labexpid


title: UW_ChipSeq_MCF-7_H3K4me3

value: Stamatoyannopoulous - University of Washington

tag: datatype description

value: human

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: ectoderm

value: F

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: Millipore

tag: antibody vendorid

tag: control description

tag: controlid


title: UW_ChipSeq_HRPEpiC_H3K4me3

tag: lab

value: ChipSeq

tag: cell

value: HRPEpiC

tag: cell organism

tag: cell description

value: retinal pigment epithelial cells

value: normal

tag: cell lineage

value: U

tag: antibody

tag: control


title: UW_ChipSeq_HPF_Input

value: UW

tag: lab description

tag: datatype

value: Chromatin IP Sequencing

value: HPF

value: pulmonary fibroblasts isolated from lung tissue

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

tag: treatment description

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_Jurkat_H3K4me3

value: Stamatoyannopoulous - University of Washington

tag: datatype description

value: Jurkat

value: human

value: T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID:68013)

tag: cell karyotype

value: cancer

value: mesoderm

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: No special treatment or protocol applies

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labexpid


title: UW_ChipSeq_WI-38_H3K4me3

tag: lab

value: UW

value: ChipSeq

tag: cell

tag: cell organism

tag: cell description

value: embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct

value: normal

tag: cell lineage

value: endoderm

value: F

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: control

tag: controlid


title: UW_ChipSeq_SK-N-MC_H3K4me3

source_name: SK-N-MC

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: Chromatin IP Sequencing

value: SK-N-MC

value: human

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

value: ectoderm

tag: cell sex

tag: treatment

tag: treatment description

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_WERI-Rb-1_H3K4me3

tag: datatype description

value: retinoblastoma (PMID:844036)

tag: cell karyotype

value: cancer

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: No special treatment or protocol applies

value: std

tag: control description

value: Standard input signal for most experiments.


title: UW_ChipSeq_NHLF_H3K4me3

tag: lab

value: UW

value: ChipSeq

tag: cell

value: NHLF

tag: cell organism

tag: cell description

value: lung fibroblasts

value: normal

tag: cell lineage

value: endoderm

value: U

tag: antibody

tag: labexpid


title: UW_ChipSeq_PANC-1_H3K4me3

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: Chromatin IP Sequencing

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

tag: cell sex

value: M

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: treatment

tag: treatment description

tag: control

tag: controlid


title: UW_ChipSeq_GM12878_Input

tag: datatype description

value: human

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

tag: cell karyotype

value: mesoderm

value: F

value: Input

tag: antibody description

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

value: No special treatment or protocol applies

tag: labversion

value: Bowtie 0.12.5

tag: replicate


title: UW_ChipSeq_HMEC_Input

tag: lab

value: UW

value: ChipSeq

tag: cell

value: HMEC

tag: cell organism

value: mammary epithelial cells

value: normal

value: ectoderm

value: std

tag: control description

value: Standard input signal for most experiments.


title: UW_ChipSeq_HEK293_Input

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell description

value: embryonic kidney, cells contain Adenovirus 5 DNA (PMID:11967234)

tag: cell lineage

value: U

tag: antibody

tag: labexpid


title: UW_ChipSeq_HRE_Input

tag: lab description

tag: datatype

value: HRE

value: human

value: renal epithelial cells

value: mesoderm

tag: cell sex

tag: treatment


title: UW_ChipSeq_HL-60_Input

tag: datatype description

value: promyelocytic leukemia cells, (PMID:276884)

value: cancer

value: F

value: Input

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

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: controlid

value: Bowtie 0.12.5


title: UW_ChipSeq_NHDF-neo_Input

source_name: NHDF-neo

value: UW

value: ChipSeq

value: NHDF-neo

value: neonatal dermal fibroblasts

tag: cell karyotype

value: normal

tag: antibody description

value: std

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_HeLa-S3_Input

tag: lab

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

value: cervical carcinoma

value: ectoderm

tag: control description

value: Standard input signal for most experiments.


title: UW_ChipSeq_HA-sp_Input

source_name: HA-sp

value: HA-sp

tag: cell description

value: astrocytes spinal cord

tag: cell lineage

value: U

tag: antibody

value: Input

tag: labexpid


title: UW_ChipSeq_NB4_Input

value: UW

tag: lab description

tag: datatype

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

value: cancer

value: mesoderm

tag: cell sex

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

tag: treatment

value: No special treatment or protocol applies


title: UW_ChipSeq_PANC-1_Input

value: ChipSeq

tag: datatype description

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: endoderm

value: M

tag: treatment description

tag: control

value: std

tag: controlid

value: Bowtie 0.12.7


title: UW_ChipSeq_HA-sp_H3K4me3

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

value: human

tag: cell karyotype

value: normal

value: ectoderm

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: Millipore

tag: antibody vendorid

value: Standard input signal for most experiments.

tag: labversion

tag: replicate


title: UW_ChipSeq_HAc_H3K4me3

source_name: HAc

tag: lab

value: UW

tag: cell

value: HAc

tag: cell organism

tag: cell description

value: astrocytes-cerebellar

tag: cell lineage

value: U

tag: antibody

tag: control description


title: UW_ChipSeq_NHDF-neo_H3K4me3

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: NHDF-neo

value: neonatal dermal fibroblasts

value: mesoderm

tag: cell sex

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid


title: UW_ChipSeq_WI-38_Input

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

value: embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct

tag: cell karyotype

value: endoderm

value: F

value: Input

tag: antibody description

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

tag: control

value: std

tag: controlid

value: Bowtie 0.12.7


title: UW_ChipSeq_GM06990_Input

tag: lab

value: UW

tag: cell

value: human

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

value: normal

value: Standard input signal for most experiments.

tag: labversion

value: Bowtie 0.12.5

tag: replicate


title: UW_ChipSeq_BE2_C_H3K4me3

value: ChipSeq

tag: cell organism

tag: cell description

value: neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.

value: cancer

tag: cell lineage

value: ectoderm

value: M

tag: antibody

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: Millipore

tag: antibody vendorid


title: UW_ChipSeq_A549_Input

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

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

value: endoderm

tag: cell sex

value: Input

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

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control description

tag: labexpid


title: UW_ChipSeq_Caco-2_Input

tag: lab

value: UW

tag: cell

value: human

tag: cell karyotype

tag: antibody description

tag: control

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: replicate


title: UW_ChipSeq_LNCaP_H3K4me3

value: ChipSeq

value: LNCaP

tag: cell organism

tag: cell description

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: cancer

tag: cell lineage

tag: antibody

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: Bowtie 0.12.7


title: UW_ChipSeq_HepG2_H3K27me3

tag: lab description

tag: datatype

tag: datatype description

value: hepatocellular carcinoma

tag: cell sex

value: M

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: treatment

tag: treatment description

tag: control description

tag: labexpid

value: Bowtie 0.12.5


title: UW_ChipSeq_HUVEC_H3K36me3

source_name: HUVEC

tag: lab

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell

value: HUVEC

value: umbilical vein endothelial cells

tag: cell karyotype

value: normal

value: mesoderm

value: U

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

tag: control

tag: controlid

tag: labversion

tag: replicate


title: UW_ChipSeq_HRE_H3K36me3

value: UW

value: ChipSeq

value: HRE

tag: cell organism

value: human

tag: cell description

value: renal epithelial cells

tag: cell lineage

tag: antibody

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.


title: UW_ChipSeq_HFF-Myc_H3K4me3

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: HFF-Myc

value: foreskin fibroblast cells expressing canine cMyc

value: fibroblast

tag: cell sex

value: M

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: Bowtie 0.12.7


title: UW_ChipSeq_K562_H3K27me3

tag: lab

value: UW

value: ChipSeq

tag: cell

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

tag: cell karyotype

value: cancer

value: mesoderm

value: F

value: rabbit polyclonal. Antibody Target:H3K27me3

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

tag: control

tag: control description

tag: controlid

tag: labexpid

value: Bowtie 0.12.5


title: UW_ChipSeq_HeLa-S3_H3K36me3

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

value: cervical carcinoma

tag: cell lineage

value: ectoderm

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: labversion

tag: replicate


title: UW_ChipSeq_HAc_Input

value: UW

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: HAc

value: astrocytes-cerebellar

value: normal

tag: cell sex

value: U

value: Input

tag: antibody description

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

value: Bowtie 0.12.7


title: UW_ChipSeq_CD20+_RO01778_H3K4me3

value: primary cell

value: B cell

tag: lab

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell

value: human

value: B cells, caucasian, draw number 1, newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: mesoderm

value: F

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: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description


title: UW_ChipSeq_HUVEC_Input

value: UW

value: ChipSeq

value: HUVEC

tag: cell organism

tag: cell description

value: umbilical vein endothelial cells

tag: cell lineage

tag: antibody

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

value: Bowtie 0.12.5


title: UW_ChipSeq_Monocytes-CD14+_RO01746_H3K4me3

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

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

value: normal

tag: cell sex

tag: antibody antibodydescription

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_WI-38_Input_4OHTAM_20nM_72hr

tag: lab

value: Chromatin IP Sequencing

tag: cell

value: human

value: embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct

tag: cell karyotype

value: endoderm

value: Input

tag: antibody description

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

tag: treatment

value: 72 hours with 20 nM 4-hydroxytamoxifen (Stam)


title: UW_ChipSeq_Monocytes-CD14+_RO01746_Input

value: UW

value: ChipSeq

tag: cell organism

tag: cell description

tag: cell lineage

value: mesoderm

value: F

tag: antibody

tag: treatment description


title: UW_ChipSeq_SAEC_H3K36me3

source_name: SAEC

tag: lab description

value: SAEC

value: small airway epithelial cells

value: U

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid


title: UW_ChipSeq_GM12875_H3K4me3

tag: lab

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

value: normal

tag: cell sex

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: Millipore

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: UW_ChipSeq_SK-N-MC_Input

value: UW

value: ChipSeq

value: SK-N-MC

tag: cell organism

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

value: F

tag: antibody

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description


title: UW_ChipSeq_HFF_Input

source_name: HFF

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

value: HFF

value: foreskin fibroblast

value: M

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid


title: UW_ChipSeq_HL-60_H3K4me3

tag: lab

value: UW

tag: datatype

tag: datatype description

tag: cell

value: human

value: promyelocytic leukemia cells, (PMID:276884)

value: mesoderm

tag: cell sex

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: Millipore

tag: antibody vendorid

value: Bowtie 0.12.5


title: UW_ChipSeq_BJ_Input

source_name: BJ

value: ChipSeq

value: BJ

tag: cell organism

tag: cell description

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

tag: cell karyotype

value: normal

tag: antibody

value: Input

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

tag: labversion

tag: replicate


title: UW_ChipSeq_HFF_H3K4me3

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

value: HFF

value: foreskin fibroblast

value: M

tag: antibody antibodydescription

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: control description

value: Bowtie 0.12.7


title: UW_ChipSeq_A549_H3K4me3

value: immortalized cell line

tag: lab

value: UW

tag: datatype

tag: datatype description

tag: line

value: human

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

value: cancer

tag: cell lineage

value: endoderm

value: rabbit polyclonal. Antibody Target:H3K4me3

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid


title: UW_ChipSeq_GM12866_H3K4me3

value: ChipSeq

tag: cell

tag: cell organism

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed.

tag: cell karyotype

value: normal

value: mesoderm

tag: cell sex

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid


title: UW_ChipSeq_WI-38_H3K4me3_4OHTAM_20nM_72hr

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

value: embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct

value: F

tag: antibody

tag: antibody antibodydescription

tag: treatment

tag: treatment description

value: 72 hours with 20 nM 4-hydroxytamoxifen (Stam)

tag: control

tag: labversion

tag: replicate


title: UW_ChipSeq_SKMC_H3K4me3

source_name: SKMC

tag: lab

value: UW

tag: datatype

tag: datatype description

value: SKMC

value: human

value: skeletal muscle cells

tag: cell lineage

value: U

value: No special treatment or protocol applies

tag: control description

tag: controlid

tag: labexpid

value: Bowtie 0.12.7


title: UW_ChipSeq_RPTEC_Input

source_name: RPTEC

value: ChipSeq

tag: cell

value: RPTEC

tag: cell organism

tag: cell description

value: renal proximal tubule epithelial cells

tag: cell karyotype

tag: cell sex

value: Input

tag: antibody description

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

value: std

value: Standard input signal for most experiments.


title: UW_ChipSeq_GM12878_H3K36me3

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

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

value: normal

value: mesoderm

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: treatment

tag: treatment description

value: Bowtie 0.12.5


title: UW_ChipSeq_HepG2_H3K36me3

tag: lab

value: UW

tag: datatype

tag: datatype description

value: human

value: hepatocellular carcinoma

value: cancer

tag: cell lineage

value: endoderm

value: M

value: No special treatment or protocol applies

tag: control

tag: control description

tag: labversion

tag: replicate


title: UW_ChipSeq_SK-N-SH_RA_H3K27me3

value: ChipSeq

tag: cell

tag: cell organism

tag: cell description

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

tag: cell karyotype

value: ectoderm

tag: cell sex

value: F

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

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid


title: UW_ChipSeq_RPTEC_H3K4me3

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

value: RPTEC

value: renal proximal tubule epithelial cells

value: normal

value: U

tag: antibody

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

tag: antibody vendorid

tag: treatment

value: Bowtie 0.12.7


title: UW_ChipSeq_GM06990_H3K36me3

tag: lab

value: UW

tag: datatype

value: ChipSeq

tag: datatype description

value: human

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

tag: cell lineage

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: control description

value: Bowtie 0.12.5


title: UW_ChipSeq_BJ_H3K36me3

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell

value: BJ

tag: cell organism

tag: cell description

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

tag: cell karyotype

tag: cell sex

value: M

value: std

value: Standard input signal for most experiments.

tag: labversion

tag: replicate


title: UW_ChipSeq_HeLa-S3_H3K27me3

value: UW

tag: lab description

value: cervical carcinoma

value: cancer

value: ectoderm

value: F

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: controlid

tag: labexpid


title: UW_ChipSeq_SK-N-SH_RA_H3K36me3

tag: lab

tag: datatype

value: ChipSeq

tag: datatype description

value: human

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

tag: cell lineage

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: UW_ChipSeq_SK-N-SH_RA_H3K4me3

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

tag: cell karyotype

tag: cell sex

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: control

value: std

tag: control description

value: Bowtie 0.12.5


title: UW_ChipSeq_Caco-2_H3K27me3

value: UW

tag: lab description

value: cancer

value: endoderm

value: M

tag: antibody

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

value: Standard input signal for most experiments.

tag: labversion

tag: replicate


title: UW_ChipSeq_SAEC_H3K27me3

tag: lab

tag: datatype

value: ChipSeq

tag: datatype description

value: SAEC

value: human

value: small airway epithelial cells

value: normal

tag: cell lineage

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

tag: controlid

tag: labexpid


title: UW_ChipSeq_Caco-2_H3K36me3

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

tag: cell karyotype

tag: cell sex

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: UW_ChipSeq_CD20+_RO01794_H3K4me3

value: UW

tag: lab description

value: B cells, African American, draw number 1, newly promoted to tier 2:not in 2011 analysis

value: mesoderm

value: F

tag: antibody

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

tag: control

value: std

tag: control description

value: Bowtie 0.12.7


title: UW_ChipSeq_SAEC_H3K4me3

tag: lab

tag: datatype

value: ChipSeq

tag: datatype description

value: SAEC

value: human

value: small airway epithelial cells

value: normal

tag: cell lineage

value: endoderm

value: U

tag: antibody vendorid

value: Standard input signal for most experiments.

tag: labversion

value: Bowtie 0.12.5

tag: replicate


title: UW_ChipSeq_HeLa-S3_H3K4me3

value: UW

value: Stamatoyannopoulous - University of Washington

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: cervical carcinoma

tag: cell karyotype

value: cancer

value: ectoderm

tag: cell sex

value: Millipore

value: No special treatment or protocol applies

tag: controlid

tag: labexpid


title: UW_ChipSeq_CD20+_RO01778_Input

value: primary cell

value: B cell

tag: lab description

value: ChipSeq

value: B cells, caucasian, draw number 1, newly promoted to tier 2:not in 2011 analysis

value: mesoderm

value: F

tag: antibody

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description

value: std

value: Bowtie 0.12.7


title: UW_ChipSeq_CD20+_RO01794_Input

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: human

value: B cells, African American, draw number 1, newly promoted to tier 2:not in 2011 analysis

value: normal

tag: control

tag: control description

value: Standard input signal for most experiments.


title: UW_ChipSeq_BJ_H3K27me3

value: Chromatin IP Sequencing

tag: cell

value: BJ

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: No special treatment or protocol applies

tag: labversion

value: Bowtie 0.12.5

tag: replicate


title: UW_ChipSeq_H7-hESC_Input_diffProtA_5d

tag: lab description

value: ChipSeq

tag: cell organism

tag: cell description

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

tag: cell sex

value: U

value: Input

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

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm

value: std

tag: controlid

tag: labexpid


title: UW_ChipSeq_H7-hESC_Input_diffProtA_9d

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: human

tag: antibody

tag: antibody description

tag: treatment

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage:mesoderm

value: Standard input signal for most experiments.

value: Bowtie 0.12.7


title: UW_ChipSeq_H7-hESC_H3K36me3_diffProtA_9d

tag: cell

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control

tag: control description


title: UW_ChipSeq_H7-hESC_H3K4me3_diffProtA_2d

value: in vitro differentiated cells

value: cardiac mesoderm

tag: lab description

value: ChipSeq

tag: cell organism

tag: cell description

value: undifferentiated embryonic stem cells

tag: cell lineage

tag: cell sex

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage:mesoderm

tag: labversion

tag: replicate


title: UW_ChipSeq_GM12878_H3K27me3

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

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

tag: cell karyotype

value: normal

value: mesoderm

value: F

tag: antibody

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: No special treatment or protocol applies

value: std

tag: controlid

tag: labexpid

value: Bowtie 0.12.5


title: UW_ChipSeq_H7-hESC_Input_diffProtA_2d

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

value: inner cell mass

value: U

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description

value: Standard input signal for most experiments.

value: Bowtie 0.12.7


title: UW_ChipSeq_GM06990_H3K27me3

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: cell organism

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

value: normal

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control

tag: control description


title: UW_ChipSeq_GM12878_H3K4me3

tag: lab

tag: datatype

tag: datatype description

tag: cell description

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

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: No special treatment or protocol applies

tag: labversion

tag: replicate


title: UW_ChipSeq_AG04449_H3K4me3

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

value: fetal buttock/thigh fibroblast

tag: cell karyotype

value: M

tag: antibody

tag: treatment

tag: treatment description

value: std

tag: controlid

tag: labexpid


title: UW_ChipSeq_H7-hESC_Input

value: UW

tag: lab description

tag: cell organism

value: undifferentiated embryonic stem cells

value: inner cell mass

value: U

value: Input

tag: antibody description

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

tag: control

value: Standard input signal for most experiments.

value: Bowtie 0.12.5


title: UW_ChipSeq_H7-hESC_H3K4me3

tag: lab

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control description


title: UW_ChipSeq_H7-hESC_H3K36me3

value: ChipSeq

tag: cell

tag: cell description

tag: cell lineage

tag: cell sex

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

value: No special treatment or protocol applies

tag: labversion

tag: replicate


title: UW_ChipSeq_GM06990_H3K4me3

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

value: human

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

tag: cell karyotype

value: normal

value: mesoderm

value: F

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

tag: treatment

tag: treatment description

value: std

tag: controlid

tag: labexpid


title: UW_ChipSeq_HUVEC_H3K4me3

tag: lab

value: UW

tag: datatype

tag: datatype description

value: HUVEC

value: umbilical vein endothelial cells

value: U

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: control

value: Standard input signal for most experiments.

value: Bowtie 0.12.5


title: UW_ChipSeq_H7-hESC_H3K27me3

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

tag: cell

tag: cell description

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

tag: cell sex

tag: antibody

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: control description


title: UW_ChipSeq_BJ_H3K4me3

tag: lab description

value: Chromatin IP Sequencing

value: BJ

tag: cell organism

value: human

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

tag: cell karyotype

value: normal

value: M

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labversion

tag: replicate


title: UW_ChipSeq_AG04449_Input

tag: lab

value: UW

tag: datatype

tag: datatype description

value: fetal buttock/thigh fibroblast

value: Input

tag: antibody description

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

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

value: Bowtie 0.12.7


title: UW_ChipSeq_HepG2_H3K4me3

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

tag: cell

tag: cell description

value: hepatocellular carcinoma

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

tag: antibody antibodydescription

tag: antibody targetdescription

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

tag: antibody vendorname

tag: control

value: Bowtie 0.12.5


title: UW_ChipSeq_AG04450_H3K4me3

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: fetal lung fibroblast

tag: cell karyotype

value: normal

value: M

tag: antibody

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

tag: control description


title: UW_ChipSeq_HUVEC_H3K27me3

tag: lab

value: UW

tag: datatype

tag: datatype description

value: HUVEC

value: umbilical vein endothelial cells

value: mesoderm

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: No special treatment or protocol applies

tag: controlid

tag: labexpid

tag: labversion

tag: replicate


title: UW_ChipSeq_NHEK_H3K36me3

source_name: NHEK

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

tag: cell

value: NHEK

tag: cell description

value: epidermal keratinocytes

tag: cell lineage

value: ectoderm

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

value: std

value: Standard input signal for most experiments.


title: UW_ChipSeq_AG10803_Input

value: UW

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell

value: M

tag: antibody

value: Input

tag: antibody description

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

tag: treatment

tag: control

value: Bowtie 0.12.7


title: UW_ChipSeq_NHEK_H3K4me3

tag: lab

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell karyotype

value: normal

value: U

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: antibody vendorid

tag: treatment description

value: No special treatment or protocol applies

tag: control description

tag: controlid

value: Bowtie 0.12.5


title: UW_ChipSeq_AG10803_H3K4me3

value: UW

tag: cell

tag: cell description

tag: cell sex

tag: antibody antibodydescription

value: std

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion

tag: replicate


title: UW_ChipSeq_H7-hESC_H3K4me3_diffProtA_9d

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

tag: antibody

tag: antibody targetdescription

tag: antibody vendorname

tag: treatment

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage:mesoderm


title: UW_ChipSeq_AG09309_Input

tag: lab

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell

value: F

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: Bowtie 0.12.7


title: UW_ChipSeq_AG09319_H3K4me3

value: ChipSeq

tag: cell

tag: cell description

value: gum tissue fibroblasts from apparently heathly 24 year old

tag: cell karyotype

value: normal

tag: cell sex

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: Millipore

tag: antibody vendorid

tag: control description

tag: controlid


title: UW_ChipSeq_K562_H3K4me3

value: UW

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

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

value: cancer

tag: cell lineage

value: mesoderm

tag: antibody

tag: antibody targetdescription

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion

value: Bowtie 0.12.5

tag: replicate


title: UW_ChipSeq_AoAF_Input

source_name: AoAF

tag: lab

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: AoAF

value: human

value: aortic adventitial fibroblast cells

value: F

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description

tag: control


title: UW_ChipSeq_HBMEC_H3K4me3

source_name: HBMEC

value: ChipSeq

tag: cell

value: HBMEC

tag: cell description

value: brain microvascular endothelial cells

tag: cell karyotype

value: normal

tag: cell sex

value: U

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.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control description

value: Bowtie 0.12.7


title: UW_ChipSeq_SKMC_Input

value: UW

tag: lab description

value: Chromatin IP Sequencing

value: SKMC

tag: cell organism

value: skeletal muscle cells

tag: cell lineage

value: mesoderm

tag: antibody

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion


title: UW_ChipSeq_Caco-2_H3K4me3

tag: lab

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: ChipSeq

tag: datatype description

value: human

value: cancer

value: endoderm

value: M

tag: antibody targetdescription

tag: treatment

tag: treatment description

value: Bowtie 0.12.5

tag: replicate


title: UW_ChipSeq_HMEC_H3K4me3

source_name: HMEC

tag: cell

value: HMEC

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:H3K4me3

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

tag: antibody vendorname

value: Millipore

tag: control


title: UW_ChipSeq_HRE_H3K27me3

source_name: HRE

value: UW

tag: lab description

value: Chromatin IP Sequencing

value: HRE

tag: cell organism

value: renal epithelial cells

tag: cell lineage

value: mesoderm

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27me3

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

tag: antibody vendorid

value: No special treatment or protocol applies

value: std

tag: control description

tag: controlid


title: Cl8-PolII_ChipSeq_Input extraction1_seq1 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: input DNA

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  WIG Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

organism: Drosophila melanogaster

growth_protocol: Growth of modENCODE cell lines for large scale chromatin extract preparation from asynchronous cultures.

extract_protocol:
Cross linking and chromatin extraction protocol for Drosophila ChIP experiments.
Chromatin IP of a chromatin extract with an antibody.
Generation of a genomic library suitable for Illumina sequencing, using the standard Illumina protocol.  This includes a 150-200bp size selection step.
Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).

tag: cell line

tag: tissue

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: Sex

value: Male


title: Cl8-ORC_ChIP-Seq_IP4 extraction4_seq1 aliquote 1

description: ChIP DNA; Antibody information listed below: official name: dORC2;target name: Drosophila ORC2p;host: Rabbit;antigen: purified full length protein;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Stephen P. Bell MIT;reference: Austin et al 1999;input DNA

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.


title: Cl8-PolII_ChipSeq_IP1 extraction1_seq1 aliquote 1

description: ChIP DNA; Antibody information listed below: official name: Anti-RNA polymerase II clone CTD4H8;target name: RNA polymerase II;host: Mouse;antigen: unknown;clonal: Monoclonal;purified: Protein A/G;company: Upstate-Millipore;catalog: 05-623;short description: Anti-RNA polymerase II clone CTD4H8. Peptide containing 10 repeats of YSPT[pS]PS corresponding to the carboxyl-terminal domain of RNA polymerase II. Purified mouse IgG1 in buffer containing 0.02 M phosphate buffer pH 7.6 0.25 M NaCl and 0.1% Sodium Azide before the addition of glycerol to 30%.;input DNA


title: UW_ChipSeq_AG09319_Input

tag: lab

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

value: human

tag: cell description

value: gum tissue fibroblasts from apparently heathly 24 year old

value: normal

value: F

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion

value: Bowtie 0.12.7

tag: replicate


title: Cl8-ORC_ChIP-Seq_IP3 extraction3_seq1 aliquote 1


title: Cl8-ORC_ChIP-Seq_IP2 extraction2_seq1 aliquote 1


title: Cl8-ORC_ChIP-Seq_Input extraction1_seq1 aliquote 1

description: input DNA


title: Cl8-ORC_ChIP-Seq_IP1 extraction1_seq1 aliquote 1


title: UW_ChipSeq_AG09309_H3K4me3

value: UW

tag: lab description

value: Chromatin IP Sequencing

tag: cell organism

value: adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell

tag: cell sex

tag: antibody

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: Millipore

tag: antibody vendorid

tag: control

tag: control description


title: UW_ChipSeq_AoAF_H3K4me3

tag: lab

tag: datatype

tag: datatype description

tag: cell

value: AoAF

tag: cell description

value: aortic adventitial fibroblast cells

tag: cell karyotype

tag: cell lineage

value: mesoderm

value: No special treatment or protocol applies

value: std

tag: controlid


title: Stat3 (Dex+LIF)

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 36bp reads were mapped to the mm9 mouse genome build using Bowtie with the following parameter: --solexa1.3-qual --best --trim5 1 mm9
To identify binding peaks, we processed the mapped sequence reads with MACS version 1.3.7.1 using matching number of IgG control reads to Stat3 or GR samples. We used the following setting in MACS: --format BOWTIE --wig --tsize 35 --bw 250 --mfold 7 --pvalue 1e-8 --gsize 1870000000
Genome_build: mm9
Supplementary_files_format_and_content: wig files generated by MACS 1.3.7.1 and bed files scores reprensent the Cluster number.

organism: Mus musculus

source_name: AtT-20 corticotroph cells treated with Stat3 (Dex+LIF)

growth_protocol: AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.

extract_protocol: Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific polyclonal antibodies.  Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina GAIIx sequencer following the manufacturer's protocols to obtain 36bp reads.

treatment_protocol: The third day after plating, the treatment agents were added directly into the culture medium (DMEM + 10% FBS) and left for 20min.

tag: cell line

tag: cell type

value: pituitary corticotroph cell

tag: treatment

value: Dex+LIF

tag: chip antibody

value: p-STAT3 (sc-7993) and STAT3 (sc-482x) from SantaCruz


title: Control IgG

source_name: AtT-20 corticotroph cells treated with Control IgG

value: LIF, Dex+LIF, Dex (control pooled from different experiments)

value: rabbit IgG (G2018, Sigma)


title: SunyAlbany_RipSeq_GM12878_ripInput

status: Public on Jun 06 2012

molecule: total RNA

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSunyRipSeq
library_strategy: RIP-Seq
library_selection: RNA binding protein antibody

value: SunyAlbany

tag: lab description

value: Tenenbaum - SUNY at Albany

value: RipSeq

value: RNA IP Sequencing

tag: cell organism

value: human

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

value: normal

tag: cell sex

value: F

tag: antibody

value: ripInput

tag: antibody antibodydescription

value: Total input. Antibody Target:ripInput

tag: antibody targetdescription

value: Total input for comparison for RIP experiments

value: Tenenbaum lab

value: RIP Input

tag: replicate


title: SunyAlbany_RipSeq_K562_ELAVL1

tag: lab

tag: datatype

tag: datatype 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: cancer

value: mesoderm

value: 1) Mouse monocloanal vs HuR, Hel-N1, HuC and HuD of mus, rat, hum and Xenopus origin; 2) Rabbit polyclonal. Raised against synthetic peptide, amino acids 3-19 of HuR. Recommended for detection against ELAV1 in human and mouse origin. Antibody Target:ELAVL1

value: (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens)

tag: antibody vendorname

value: 1) Santa Cruz Biotech; 2) Millipore

tag: antibody vendorid

value: SC-5261; 07-1735 is recommended replacement for AB5831

tag: labversion

value: SC_5261 antibody


title: Cl8-PolII_ChipSeq_IP2 extraction2_seq1 aliquote 1

tag: cell line

tag: tissue

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: Sex

value: Male


title: SunyAlbany_RipSeq_K562_PABPC1

value: SunyAlbany

tag: lab description

value: Tenenbaum - SUNY at Albany

value: RipSeq

value: RNA IP Sequencing

tag: cell

value: human

tag: cell description

tag: cell karyotype

tag: cell lineage

value: F

value: Mouse monoclonal vs PABPC1 of human, mouse, bovine, can, hamster, Xenopus origin. Antibody Target:PABPC1

value: poly(A) binding protein, cytoplasmic 1 (Homo sapiens).

value: Sigma Chemical Co.

value: Sig_P6246 antibody


title: SunyAlbany_RipSeq_K562_ripInput

tag: cell organism

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

value: cancer

value: mesoderm

tag: cell sex

tag: antibody

value: ripInput

tag: antibody antibodydescription

value: Total input. Antibody Target:ripInput

tag: antibody targetdescription

value: Total input for comparison for RIP experiments

value: Tenenbaum lab

value: RIP Input


title: SunyAlbany_RipSeq_GM12878_ELAVL1

tag: lab

value: SunyAlbany

value: Tenenbaum - SUNY at Albany

tag: datatype

tag: datatype description

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

value: normal

value: 1) Mouse monocloanal vs HuR, Hel-N1, HuC and HuD of mus, rat, hum and Xenopus origin; 2) Rabbit polyclonal. Raised against synthetic peptide, amino acids 3-19 of HuR. Recommended for detection against ELAV1 in human and mouse origin. Antibody Target:ELAVL1

value: (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens)

tag: antibody vendorname

value: 1) Santa Cruz Biotech; 2) Millipore

value: SC-5261; 07-1735 is recommended replacement for AB5831

value: SC_5261 antibody

tag: replicate


title: SunyAlbany_RipSeq_GM12878_PABPC1

value: RipSeq

value: RNA IP Sequencing

value: human

value: F

value: Mouse monoclonal vs PABPC1 of human, mouse, bovine, can, hamster, Xenopus origin. Antibody Target:PABPC1

value: poly(A) binding protein, cytoplasmic 1 (Homo sapiens).

value: Sigma Chemical Co.

tag: antibody vendorid

tag: labversion

value: Sig_P6246 antibody


title: GR (Dex+LIF)

source_name: AtT-20 corticotroph cells treated with GR (Dex+LIF)

tag: cell line

tag: cell type

value: pituitary corticotroph cell

tag: treatment

value: Dex+LIF

tag: chip antibody

value: GR (sc-1004) from SantaCruz


title: GR (Dex)

source_name: AtT-20 corticotroph cells treated with GR (Dex)

value: Dex


title: Snyder_ZAG-1_GFP_L4_rep1 extraction1_seq1 aliquote 1

status: Public on Jun 04 2012

description: 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.;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. 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 WS220

organism: Caenorhabditis elegans

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.

tag: strain

value: OP83(official name :OP83 genotype :unc119(ed3);wgIs83(zag-1::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 ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by :R Waterston )

tag: developmental stage

tag: genotype

tag: Sex

value: Hermaphrodite


title: Snyder_ZAG-1_Input_L4_rep2 extraction2_seq1 aliquote 1

description: 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. 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 WS220