title: CTCF_peaks

first: Ali

last: Torkamani

address: 3344 North Torrey Pines Court Suite 300

institute: TSRI

data_processing: Alignment: The Bowtie algorithm was used to map experimental and input control fastaq tags to the mm9 genome.  Duplicated reads were removed prior to mapping. All valid alignments were reported using the most exhaustive search settings with a maximum of two mismatches allowed within the seed region of each tag. Tags mapping uniquely to the genome, defined as reads where the best alignment score occurs at only a single locus in the mm9 genome, were extended 300 bp upstream or downstream from the alignment start site, depending upon the strand orientation of the mapping. All reads mapping with their best alignment score at multiple sites in the genome were discarded unless all of those sites resided within LINE elements, Ig regions or TCR regions.

source_name: CTCF ChIP

growth_protocol: Bone marrow cells were isolated from 4- to 8-wk-old Rag1−/− mice and were enriched for CD19+ cells with MACS microbeads.

extract_protocol: B6 Rag1−/− pro-B cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Subsequently, the lysates were sonicated using a Diagenode Biorupter. The chromatin solution was precleared with salmon sperm DNA-protein A agarose beads. The lysate was immunoprecipitated with antibodies against CTCF (Millipore 07-729) and Rad21 (Millipore #ab992). Immune complexes were isolated with protein A agarose beads.  Following elution, chromatin-antibody complexes and input DNA were reverse crosslinked by heating at 65°C overnight.  The DNA was purified using the Qiagen DNA purification kit. The sequencing libraries were prepared using 10 ng double-stranded cDNA prepared by ChIP (pull-down and input). ChIP DNA samples ends were repaired using recommended Illumina protocol including T4 DNA polymerase, Klenow Large Fragment, and T4 polynucleotide kinase. DNA products were purified using DNA Clean&Concentrator™-5 Kit (Zymo Research). Next, DNA ends were A-tailed with Klenow (3’→5’ exo-) at 37C for 30 min. DNA products were again purified using the DNA Clean&Concentrator™-5 Kit. Next, Illumina Paired End-adapter oligonucleotides, at 0.33 μM concentration, were ligated to the A-tailed cDNA ends with T4 DNA ligase. DNA products were purified using DNA Clean&Concentrator™-5 Kit. The DNA library products were then separated on a 2% agarose gel and products corresponding to a size of approximately 200-250 bases were removed from the gel and cleaned using the Agencourt SPRI system (Beckman). The DNA material was PCR amplified with Phusion™ Polymerase (Finnzymes) with 0.6 μM PCR primers PE 1.0 and PE 2.0 (Illumina) for 15 cycles. The amplified DNA products were further purified on 2% agarose gel, excised, and isolated again using Zymoclean™Gel DNA recovery kit. The purified DNA library was quantitated using the Qubit quantitation platform (Invitrogen) and sized using the 2100 Bioanalyzer (Agilent). DNA products were then denatured in 0.1N NaOH and diluted to a final concentration of 10 pM before being loaded onto the Illumina paired-end flow-cell for massively parallel sequencing by synthesis on the Illumina GAIIx.

value: bone marrow

value: CD19+Rag1−/− pro-B

tag: antibody

value: CTCF (Millipore 07-729)


title: ALI-D21, donor 3

status: Public on Jun 07 2011

type: SRA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: MicroRNA expression data

library_source: transcriptomic

data_processing: Data analysis was performed using rna2map software provide by SOLiD™ Software Development Community (http://solidsoftwaretools.com/gf/). This tool allows to identifies reads as miRNAs among a reference set miRNAs: here xtr mirbase_v14. Parameters of identification has been set as follows: 1 color mismatch in the miRNAs seed (first 18 bases) and 2 color mismatchs in the extension step. Following identification of miRNAs, a normalization to 1000000 miRNAs count was performed. See supplementary series file for original (unrounded) counts and miRNA names.

molecule: total RNA

organism: Homo sapiens

source_name: Human nasal epithelial cells

growth_protocol: Dissociated cells from nasal polyps were seed on collagen-type IV coated permeable supports for differentiation.

extract_protocol: SREK was performed according to the manufacturer’s protocol (Ambion, Inc, Austin, TX).

treatment_protocol: At confluency (day 7 after seeding), cultures cells were switched in air-liquid interface (ALI) in the differentiating medium.

tag: tissue

value: human nasal mucosa

tag: differentiation step

value: Terminal mucociliary differentiation

tag: rin number

tag: bank concentration (µg/µl)

tag: amount used (ng)


title: Rad21_peaks

city: La Jolla

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Rad21 ChIP

tag: strain

tag: genotype/variation

value: Rad21 (Millipore #ab992)


title: XEN_11_5b

description: MicroRNA expression data

organism: Xenopus laevis

source_name: epidermal explants at stage 11.6

growth_protocol: Eggs obtained from NASCO females were fertilized in vitro, dejellied, embryos were grown in culture medium until stage 11.5 or 26.

treatment_protocol: Epidermal explants (at stage 11.5 and 26) were dissected and frozed.

value: epidermic embryo

tag: developmental stage

value: Gastrula Stage 11.5

value: Non ciliated


title: XEN_26b

description: MicroRNA expression data

source_name: epidermal explants at stage 27

value: Tailbud Stage 26

value: Ciliated


title: Columnar cells, donor 3

description: Columnar ciliated cells

source_name: Columnar cells

growth_protocol: HAECs were dissociated from nasal polyps for cell sorting by FACSaria.

treatment_protocol: Isolated HAECs were  incubated with both mouse monoclonal anti-CD151-PE (6 µl/106 cells) and monoclonal mouse anti-TF-FITC antibodies (3 µl/106 cells).Bright basal cells (CD151+/TF+) and negative columnar cells (CD151-/TF-) were selected and sorted using the cell sorter’s purity option at a rate of 5,000 events per second. Sorted populations were reanalyzed (3 x 104 events recorded) for purity and viability.

tag: cell type

value: Majority of columnar ciliated cells

tag: bank concentration (ng/µl)


title: XEN_26a

description: MicroRNA expression data

source_name: epidermal explants at stage 26


title: XEN_11_5a

description: MicroRNA expression data

source_name: epidermal explants at stage 11.5


title: Basal cells, donor 2

description: Basal cells

source_name: Basal cells

value: Basal


title: Columnar cells, donor 2

description: Columnar ciliated cells


title: Basal cells, donor 3

description: Basal cells


title: Columnar cells, donor 1

description: Columnar ciliated cells


title: ALI-D14, donor 3

description: MicroRNA expression data

value: Onset of mucociliary differentiation


title: ALI-D21, donor 2

description: MicroRNA expression data


title: ALI-D0, donor 3

description: MicroRNA expression data

value: End of proliferation


title: ALI-D7, donor 3

description: MicroRNA expression data

value: Polarization


title: Adult_Cerebellum_mRNA-Seq

city: Philadelphia

first: Ravi

last: Gupta

state: PA

address: 3601 Spruce Street

department: Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program

institute: The Wistar Institute

description: PolyA-tailed mRNA is purified and converted to cDNA.

data_processing: mRNA-seq alignment: Alignment to genome build mm9 (UCSC) was performed using the Bowtie program.

extract_protocol: Following the ChIP experiment, protein-DNA crosslink was reversed at 65oC for 14 hr and the DNA was purified after RNase and Proteinase K treatment using the Qiagen PCR purification kit. For RNA extraction, we used Tri reagent (Sigma Inc.) to isolate total RNA. Library construction was performed using the mRNA-seq prep kit and ChIP-seq DNA sample prep kit from Illumina Inc. according to manufacturer's instructions. Briefly, mRNA-seq library construction involves purification of polyA RNA, fragmentation of RNA, generation of cDNAs, ligation of adapters, size selection from gel and enrichment by PCR. For the ChIP-seq library constructions, the following multiple steps were followed: DNA-end repair, addition of an A base at the 3-prime end, adapter ligation, purification of ligated products, and enrichment of adapter-ligated fragments.

tag: age

value: postnatal day 56

value: adult

value: cerebellum


title: P15_Cerebellum_mRNA-Seq

value: postnatal day 15


title: P5_Cerebellum_mRNA-Seq

value: postnatal day 5


title: ALI-D14, donor 2

description: MicroRNA expression data

value: human nasal mucosa


title: P0_Cerebellum_mRNA-Seq

value: postnatal day 0


title: ALI-D7, donor 2

description: MicroRNA expression data


title: Adult_Cerebellum_Igg_ChIP-Seq

description: Chromatin IP for determining the non-specific background using IgG antibody.

data_processing: The ChIP-Seq data (RNAP2, H3K4me3, H3K27me3, IgG-Control) analysis was comprised of 3 major stages: (i) alignment, (ii) peak identification and (iii) promoter prediction. We used the Bowtie program for alignment of ChIP-Seq data to genome build mm9 (UCSC). Only uniquely mapped reads with up to 2-mismatches were considered for analysis. The significant peak identification was performed using a two-step procedure. In the first step, statistically significant enriched genomic regions (of length = 1000bp) were identified. A region is defined as statistically significant if the difference in the number of reads between experiment (Pol-II, H3K4me3, H3K27me3) and control IgG samples within the region is higher than a given cutoff read count calculated using a p-value of 0.05. Each ChIP-Seq read distribution in the genome can be considered as a Poisson distribution and the difference of two Poisson distributions is given by the Skellam distribution. After identification of enriched regions, the significant enriched peaks in experimental data are identified based on threshold read count obtained from second cut-off p-value <= 0.01.

tag: chip-antibody

value: IgG

tag: antibody vendor

value: Sigma Inc.


title: P5_Cerebellum_Igg_ChIP-Seq


title: P15_Cerebellum_Igg_ChIP-Seq


title: ALI-D0, donor 2

description: MicroRNA expression data


title: ALI-D21, donor 1

description: MicroRNA expression data

value: Terminal mucociliary differentiation


title: Input DNA

source_name: Input DNA

value: bone marrow

value: CD19+Rag1−/− pro-B


title: ALI-D14, donor 1

description: MicroRNA expression data


title: P0_Cerebellum_Igg_ChIP-Seq


title: P15_Cerebellum_H3K27me3_ChIP-Seq

description: Chromatin IP against H3K27me3.

value: Abcam Inc.

tag: antibody catalog #

tag: antibody lot #


title: P0_Cerebellum_H3K27me3_ChIP-Seq

description: Chromatin IP against H3K27me3.


title: Adult_Cerebellum_H3K27me3_ChIP-Seq

description: Chromatin IP against H3K27me3.


title: P5_Cerebellum_H3K27me3_ChIP-Seq

description: Chromatin IP against H3K27me3.


title: Adult_Cerebellum_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II.

value: anti-RNAP-II


title: P15_Cerebellum_H3K4me3_ChIP-Seq

description: Chromatin IP against H3K4me3.


title: Adult_Cerebellum_H3K4me3_ChIP-Seq

description: Chromatin IP against H3K4me3.


title: P5_Cerebellum_H3K4me3_ChIP-Seq

description: Chromatin IP against H3K4me3.


title: P15_Cerebellum_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II.


title: Transcriptome

status: Public on Jun 06 2011

city: Los Angeles

first: Chongyuan

last: Luo

address: 695 Charles E Young Drive South

department: Human Genetics

institute: University of California Los Angeles

description:
Transcriptome
SRX025337
SRA010097

data_processing: The barcodes were decoded allowing zero mismatches. The color-space reads for each barcoded library were aligned to TAIR 8 Arabidopsis thaliana reference genome using Corona Lite 4.2.1 (Life Technologies) allowing 3 colorspace mismatches in the 35 bps reads. For ChIP-seq tags that mapped to more than one position in the genome, the reported position was randomly chosen from up to 1,000 potential matches. For RNA-seq data, only tags mapped to unique location were used for analyses. Tags mapped to an identical genomic position were removed except for one in order to compensate for the potential over-amplification of the library.

organism: Arabidopsis thaliana

source_name: young leaves of 21-28 days old plants

growth_protocol: For plants used for ChIP-seq, Arabidopsis plants were germinated and grown for two weeks in 0.5X MS media solidified with 0.8% agar. Plants used for RNA-seq were grown in soil for 21-28 days.

extract_protocol: For the construction of ChIP library, the purified ChIPed DNA was fragmentated by the Covaris S2 system to ~125 bp-long. After recovering the DNA with ethanol precipitation, samples were treated with DNA End-Repair Kit. End-repaired DNA was then purified with MinElute Reaction Cleanup Kit. Adaptors were synthesized as single-strand oligos (P1 HPLC grade; P2 desalted grade) and annealed in 1X PCR buffer with a thermal cycler. P2 adaptors were resolved on a 3% agarose gel and the dominant 50 bp band was purified. After ligating both P1 and P2 adaptors, a phenol/chloroform extraction followed by ethanol precipitation was performed to remove ligase and salts. The purified DNA was resolved on a 6% native PAGE gel to separate ligation products from adaptors. The gel piece corresponding to where 150-250 bp DNA migrate was sliced and stored frozen. The optimal cycle for library amplification was empirically determined with 1/3 of the gel piece. Library prepared with the rest 2/3 of gel slice was resolved on a 3% agarose gel to recover the 150-250 bp smear. For the construction of RNA-seq libraries, ribosomal RNAs were depleted from the total RNA with two rounds of treatment with the RibominusTM Plant Kit (Invitrogen). RNA-seq fragment libraries were constructed using the SOLiDTM Whole-Transcriptome Analysis Kit following the manufacturerâs protocol. Briefly, the RNA was fragmented using RNase III and subsequently purified using the Qiagen gel extraction minelute kit. The RNA fragments were then ligated to barcoded RNA adaptors supplied in the Whole Transcriptome Kit, and then reverse transcribed. The resulting cDNA was then resolved on a 3% agarose gel, size selected and purified, and then amplified by PCR. The libraries were quantitated using a NanoDrop and pooled.

value: leaves

tag: ecotype

tag: chip antibody


title: ALI-D7, donor 1

description: MicroRNA expression data

tag: tissue


title: Input

description:
input DNA
SRX017605
SRA010097

source_name: aerial tissue of two-week-old plants

value: 2 wk

value: aerial tissue


title: P0_Cerebellum_H3K4me3_ChIP-Seq

description: Chromatin IP against H3K4me3.


title: H3K27me3

description:
Chromatin IP against H3K27me3
SRX017597
SRA010097

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot #


title: H3K27me1

description:
Chromatin IP against H3K27me1
SRX017596
SRA010097


title: P0_Cerebellum_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II.


title: H3

description:
Chromatin IP against H3
SRX017604
SRA010097


title: H3K36me2

description:
Chromatin IP against H3K36me2
SRX017599
SRA010097

value: Abcam


title: ALI-D0, donor 1

description: MicroRNA expression data

tag: differentiation step

value: End of proliferation

tag: rin number

tag: bank concentration (µg/µl)

tag: amount used (ng)


title: H3K36me3

description:
Chromatin IP against H3K36me3
SRX017600
SRA010097


title: H3K4me2

description:
Chromatin IP against H3K4me2
SRX017553
SRA010097


title: H3K9me2

description:
Chromatin IP against H3K9me2
SRX017556
SRA010097


title: H3K9Ac

description:
Chromatin IP against H3K9Ac
SRX017555
SRA010097


title: H3K4me3

description:
Chromatin IP against H3K4me3
SRX017554
SRA010097

value: H3K4me3 (Millipore, cat. # 07-473)


title: H3K18Ac

description:
Chromatin IP against H3K18Ac
SRX017595
SRA010097

value: H3K18Ac (Abcam, cat. # ab1191)


title: P5_Cerebellum_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II.

tag: strain

value: postnatal day 5

value: cerebellum


title: Stam_H7-hESC_1

status: Public on Jun 03 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

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

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:H7-hESC_Stam_protocol.pdf

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

tag: cell

tag: cell organism

value: Human

tag: cell description

value: Undifferentiated human embryonic stem cells

tag: cell karyotype

value: unknown

tag: cell sex

value: U

tag: replicate


title: Stam_HepG2_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HepG2_protocol.pdf

value: liver carcinoma

value: cancer

tag: cell lineage

value: endoderm

value: M


title: Stam_HepG2_1


title: Stam_K562_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

value: leukemia

value: "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: F


title: Stam_HRPEpiC_1

source_name: HRPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRPEpiC_Stam_protocol.pdf

value: HRPEpiC

value: Human Retinal Pigment Epithelial Cells

value: ectoderm


title: Stam_HMEC_1

source_name: HMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HMEC_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HMEC_Crawford_protocol.pdf UW_Stam:HMEC_Stam_protocol.pdf

value: HMEC

value: Human Mammary Epithelial Cells


title: Stam_HAEpiC_1

source_name: HAEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAEpiC_Stam_protocol.pdf

value: HAEpiC

value: Human Amniotic Epithelial Cells


title: Stam_HMVEC-LLy_2

source_name: HMVEC-LLy

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-LLy_Stam_protocol.pdf

value: HMVEC-LLy

value: Human

value: Normal Human Lymphatic Microvascular Endothelial Cells, Lung-Derived


title: Stam_HPdLF_1

source_name: HPdLF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPdLF_Stam_protocol.pdf

value: HPdLF

value: Normal Human Periodontal Ligament Fibroblasts


title: Stam_AG10803_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG10803_Stam_protocol.pdf

value: Adult human abdominal skin fibroblasts

value: mesoderm


title: Stam_GM06990_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

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

value: normal


title: Stam_HL-60_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HL-60_Stam_protocol.pdf

value: Human promyelocytic leukemia cells. (PMID:276884)

value: cancer

value: F


title: Stam_HNPCEpiC_1

source_name: HNPCEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HNPCEpiC_Stam_protocol.pdf

value: HNPCEpiC

value: Human Non-Pigment Ciliary Epithelial Cells

value: U


title: Stam_HRPEpiC_2

value: HRPEpiC

value: Human Retinal Pigment Epithelial Cells

value: ectoderm


title: Stam_AG09319_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09319_Stam_protocol.pdf

value: Human

value: Adult human gum tissue fibroblasts


title: Stam_HMF_1

source_name: HMF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMF_Stam_protocol.pdf

value: HMF

value: human mammary fibroblasts


title: Stam_GM12878_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/GM12878_protocol.pdf

value: immortalized cell line

tag: line

value: lymphoblastoid

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus


title: Stam_HA-sp_2

source_name: HA-sp

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HA-sp_Stam_protocol.pdf

value: HA-sp

value: human

value: Human astrocytes spinal cord

value: Normal

value: Astrocytic


title: Stam_AG09309_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09309_Stam_protocol.pdf

value: Adult human toe fibroblast

value: mesoderm

value: F


title: Stam_SAEC_2

source_name: SAEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SAEC_Stam_protocol.pdf

value: SAEC

value: Small Airway Epithelial Cells

value: normal

value: U


title: Stam_NHLF_1

source_name: NHLF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:NHLF_Bernstein_protocol.pdf UW_Stam:NHLF_Stam_protocol.pdf

value: NHLF

value: Human

value: Normal Human Lung Fibroblasts


title: Stam_WI-38_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:WI38_Stam_protocol.pdf

value: Embryonic Lung Fibroblast Cells, hTERT immortalized, includes Raf1 construct

value: Normal (RAF)

value: Fibroblast


title: Stam_HMVEC-dNeo_1

source_name: HMVEC-dNeo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-dNeo_Stam_protocol.pdf

value: HMVEC-dNeo

value: Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived

value: M


title: Stam_HIPEpiC_2

source_name: HIPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HIPEpiC_Stam_protocol.pdf

value: HIPEpiC

value: Human Iris Pigment Epithelial Cells

value: ectoderm


title: Stam_WERI-Rb-1_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:WERI-Rb-1_Stam_protocol.pdf

value: retinoblastoma (PMID:844036)

value: F


title: Stam_SAEC_1

value: SAEC

value: Small Airway Epithelial Cells


title: Stam_H7-hESC_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:H7-hESC_Stam_protocol.pdf

value: Undifferentiated human embryonic stem cells

value: unknown

value: U


title: Stam_HMVEC-dBl-Ad_1

source_name: HMVEC-dBl-Ad

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-dBl-Ad_Stam_protocol.pdf

value: HMVEC-dBl-Ad

value: Human

value: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: Stam_HMVEC-dNeo_2


title: Stam_CMK_1

source_name: CMK

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:CMK_Stam_protocol.pdf

value: CMK

value: human acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID:3016165)


title: Stam_HRGEC_2

source_name: HRGEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRGEC_Stam_protocol.pdf

value: HRGEC

value: human

value: Human Renal Glomerular Endothelial Cells

value: Normal

value: Endothelial


title: Stam_BE2_C_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:BE2-C_Myers_protocol.pdf

value: Human neuroblastoma

value: ectoderm

value: M


title: Stam_HPAF_2

source_name: HPAF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPAF_Stam_protocol.pdf

value: HPAF

value: Human Pulmonary Artery Fibroblasts


title: Stam_HFF-Myc_2

source_name: HFF-Myc

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HFFMyc_Stam_protocol.pdf

value: HFF-Myc

value: Human Foreskin Fibroblast Cells Expressing Canine cMyc

value: Normal (cMyc)

value: Fibroblast


title: Stam_NB4_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NB4_protocol.pdf UW_Stam:NB4_Stam_protocol.pdf

value: Human

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

value: cancer

value: U


title: Stam_HFF_1

source_name: HFF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HFF_Stam_protocol.pdf

value: HFF

value: human

value: Human Foreskin Fibroblast


title: Stam_LNCaP_2

source_name: LNCaP

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:LNCaP_Crawford_protocol.pdf Yale_TFBS(Farnham):LNCaP_protocol.pdf UW_Stam:LNCaP_Stam_protocol.pdf

value: LNCaP

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


title: Stam_HCPEpiC_2

source_name: HCPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCPEpiC_Stam_protocol.pdf

value: HCPEpiC

value: Human Choroid Plexus Epithelial Cells


title: Stam_HA-h_1

source_name: HA-h

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAh_Stam_protocol.pdf

value: HA-h

value: Human Astrocytes-hippocampal

value: Normal

value: Astrocytic


title: Stam_HL-60_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HL-60_Stam_protocol.pdf

value: Human promyelocytic leukemia cells. (PMID:276884)

value: F


title: Stam_SKMC_1

source_name: SKMC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SkMC_Stam_protocol.pdf

value: SKMC

value: Human

value: Human Skeletal Muscle Cells

value: unknown

value: mesoderm


title: Stam_HMVEC-dLy-Ad_2

source_name: HMVEC-dLy-Ad

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-dLy-Ad_Stam_protocol.pdf

value: HMVEC-dLy-Ad

value: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: Stam_AG04449_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04449_Stam_protocol.pdf

value: Fetal buttock/thigh fibroblast

value: M


title: Stam_BJ_2

source_name: BJ

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:BJ-tert_Stam_protocol.pdf

value: BJ

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

value: normal


title: Stam_HCT-116_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:HCT-116_protocol.pdf UW_Stam:HCT116_Stam_protocol.pdf

value: immortalized cell line

value: colorectal carcinoma (PMID:7214343)

value: cancer

value: endoderm


title: Stam_HIPEpiC_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HIPEpiC_Stam_protocol.pdf

value: HIPEpiC

value: Human Iris Pigment Epithelial Cells

value: ectoderm

value: U


title: Stam_Th1_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: Human

value: primary human Th1 T cells

value: unknown


title: Stam_HAc_1

source_name: HAc

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAc_Stam_protocol.pdf

value: HAc

value: human

value: Human Astrocytes-cerebellar

value: Normal

value: Astrocytic


title: Stam_Caco-2_2

value: M


title: Stam_MCF-7_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:MCF-7_Crawford_protocol.pdf Yale_TFBS(Farnham):MCF-7_Farnham_protocol.pdf UW_Stam:Stam_15_protocols.pdf

value: immortalized cell line

value: mammary gland, adenocarcinoma. (PMID:4357757)

value: F


title: Stam_H1-hESC_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/H1_ES_protocol.pdf

value: stem cell

value: Human Embryonic Stem Cells

value: normal

value: embryonic stem cells


title: Stam_NH-A_2

source_name: NH-A

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad:NH-A_Bernstein_protocol.pdf UW_Stam: NH-A_Stam_protocol.pdf

value: primary cell

value: astrocyte

value: NH-A

value: normal human astrocytes

value: U


title: Stam_HAEpiC_2

source_name: HAEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAEpiC_Stam_protocol.pdf

value: HAEpiC

value: Human

value: Human Amniotic Epithelial Cells


title: Stam_HEEpiC_1

source_name: HEEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HEEpiC_Stam_protocol.pdf

value: HEEpiC

value: Human Esophageal Epithelial Cells

value: endoderm


title: Stam_HMVEC-dLy-Ad_1

value: HMVEC-dLy-Ad

value: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: Stam_AG10803_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG10803_Stam_protocol.pdf

value: Adult human abdominal skin fibroblasts

value: mesoderm

value: M


title: Stam_AoAF_1

source_name: AoAF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AoAF_Stam_protocol.pdf

value: AoAF

value: Normal Human Aortic Adventitial Fibroblast Cells

value: F


title: Stam_A549_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:A549_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:A549_Crawford_protocol.pdf UW_Stam:A549_Stam_protocol.pdf

value: epithelial cell line "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, derived from a lung carcinoma tissue. (PMID:175022)

value: cancer


title: Stam_SK-N-SH_RA_2

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

value: ectoderm


title: Stam_HCFaa_2

source_name: HCFaa

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCFaa_Stam_protocol.pdf

value: HCFaa

value: Human

value: Human Cardiac Fibroblasts-Adult Atrial


title: Stam_HGF_1

source_name: HGF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HGF_Stam_protocol.pdf

value: HGF

value: Human Gingival Fibroblasts

value: normal

value: U


title: Stam_MCF-7_1

value: mammary gland, adenocarcinoma. (PMID:4357757)


title: Stam_HMVEC-dLy-Neo_1

source_name: HMVEC-dLy-Neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-dLy-Neo_Stam_protocol.pdf

value: HMVEC-dLy-Neo

value: Normal Neonatal Human Lymphatic Microvascular Endothelial Cells, Dermal-Derived


title: Stam_HGF_2


title: Stam_HUVEC_1

source_name: HUVEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HUVEC_protocol.pdf

value: HUVEC

value: Human Umbilical Vein Endothelial Cell

value: mesoderm


title: Stam_HPF_1

source_name: HPF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPF_Stam_protocol.pdf

value: HPF

value: Human Pulmonary Fibroblasts isolated from lung tissue


title: Stam_HMVEC-dLy-Neo_2

value: M


title: Stam_HFF_2

source_name: HFF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HFF_Stam_protocol.pdf

value: HFF

value: human

value: Human Foreskin Fibroblast

value: Normal

value: Fibroblast


title: Stam_HMVEC-dBl-Neo_1

source_name: HMVEC-dBl-Neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-dBl-Neo_Stam_protocol.pdf

value: HMVEC-dBl-Neo

value: Human

value: Normal Neonatal Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: Stam_HCF_1

source_name: HCF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCF_Stam_protocol.pdf

value: HCF

value: Human Cardiac Fibroblasts

value: U


title: Stam_HCPEpiC_1

source_name: HCPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCPEpiC_Stam_protocol.pdf

value: HCPEpiC

value: Human Choroid Plexus Epithelial Cells


title: Stam_NHDF-Ad_1

source_name: NHDF-Ad

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:NHDF-Ad_Stam_protocol.pdf Broad_Histone:NHDF-Ad_Bernstein_protocol.pdf

value: NHDF-Ad

value: Adult Normal Human Dermal Fibroblasts

value: F


title: Stam_K562_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

value: leukemia

value: cancer

value: "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


title: Stam_LNCaP_1

source_name: LNCaP

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:LNCaP_Crawford_protocol.pdf Yale_TFBS(Farnham):LNCaP_protocol.pdf UW_Stam:LNCaP_Stam_protocol.pdf

value: LNCaP

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

value: M


title: Stam_AG04450_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04450_Stam_protocol.pdf

value: Human

value: Fetal lung fibroblast

value: mesoderm


title: Stam_AG04449_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04449_Stam_protocol.pdf

value: Fetal buttock/thigh fibroblast


title: Stam_HSMM_1

source_name: HSMM

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HSMM_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HSMM_HSMMtube_Crawford_protocol.pdf

value: HSMM

value: Normal Human Skeletal Muscle Myoblasts

value: normal

value: U


title: Stam_HeLa-S3_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf

value: immortalized cell line

value: cervical carcinoma

value: ectoderm


title: Stam_SK-N-SH_RA_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

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

value: cancer

value: F


title: Stam_GM12865_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12865_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown


title: Stam_NHEK_2

source_name: NHEK

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Keratinocyte_protocol.pdf

value: NHEK

value: Normal Human Epidermal Keratinocytes


title: Stam_HRCEpiC_2

source_name: HRCEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRCEpiC_Stam_protocol.pdf

value: HRCEpiC

value: Human

value: Human Renal Cortical Epithelial cells (normal)


title: Stam_HPAF_1

source_name: HPAF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPAF_Stam_protocol.pdf

value: HPAF

value: Human Pulmonary Artery Fibroblasts


title: Stam_HBMEC_2

source_name: HBMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HBMEC_Myers_protocol.pdf

value: HBMEC

value: Human Brain Microvascular Endothelial Cells


title: Stam_SK-N-MC_2

source_name: SK-N-MC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:SK-N-MC_protocol.pdf

value: SK-N-MC

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.)


title: Stam_HSMM_2

value: HSMM

value: Normal Human Skeletal Muscle Myoblasts

value: normal

value: mesoderm

value: U


title: Stam_HMEC_2

source_name: HMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HMEC_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HMEC_Crawford_protocol.pdf UW_Stam:HMEC_Stam_protocol.pdf

value: HMEC

value: Human Mammary Epithelial Cells


title: Stam_AG09309_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09309_Stam_protocol.pdf

value: Adult human toe fibroblast

value: F


title: Stam_NHEK_1

value: NHEK

value: Human

value: Normal Human Epidermal Keratinocytes

value: ectoderm


title: Stam_HNPCEpiC_2

source_name: HNPCEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HNPCEpiC_Stam_protocol.pdf

value: HNPCEpiC

value: Human Non-Pigment Ciliary Epithelial Cells


title: Stam_HRCEpiC_1

value: HRCEpiC

value: Human Renal Cortical Epithelial cells (normal)


title: Stam_HRE_2

source_name: HRE

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRE_Stam_protocol.pdf

value: HRE

value: Human Renal Epithelial cells (normal)


title: Stam_NHDF-neo_2

source_name: NHDF-neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:NHDF-neo_Stam_protocol.pdf

value: NHDF-neo

value: Neonatal Human Dermal Fibroblasts


title: Stam_HConF_1

source_name: HConF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HConF_Stam_protocol.pdf

value: HConF

value: Human Conjunctival Fibroblast

value: U


title: Stam_HMVEC-LBl_1

source_name: HMVEC-LBl

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-Lbl_Stam_protocol.pdf

value: HMVEC-LBl

value: Normal Human Blood Microvascular Endothelial Cells, Lung-Derived


title: Stam_RPTEC_1

source_name: RPTEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:RPTEC_Stam_protocol.pdf

value: RPTEC

value: Renal Proximal Tubule Epithelial Cells


title: Stam_NH-A_1

source_name: NH-A

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad:NH-A_Bernstein_protocol.pdf UW_Stam: NH-A_Stam_protocol.pdf

value: NH-A

value: Human

value: normal human astrocytes


title: Stam_RPTEC_2


title: Stam_HCF_2

source_name: HCF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCF_Stam_protocol.pdf

value: HCF

value: Human Cardiac Fibroblasts

value: mesoderm


title: Stam_GM06990_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

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

value: normal

value: F


title: Stam_HAc_2

source_name: HAc

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAc_Stam_protocol.pdf

value: HAc

value: human

value: Human Astrocytes-cerebellar

value: Normal

value: Astrocytic


title: Stam_HA-h_2

source_name: HA-h

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAh_Stam_protocol.pdf

value: HA-h

value: Human Astrocytes-hippocampal

value: U


title: Stam_NHLF_2

source_name: NHLF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:NHLF_Bernstein_protocol.pdf UW_Stam:NHLF_Stam_protocol.pdf

value: NHLF

value: Normal Human Lung Fibroblasts


title: Stam_AG09319_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09319_Stam_protocol.pdf

value: Human

value: Adult human gum tissue fibroblasts


title: Stam_HEEpiC_2

source_name: HEEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HEEpiC_Stam_protocol.pdf

value: HEEpiC

value: Human Esophageal Epithelial Cells

value: endoderm


title: Stam_HSMMtube_1

source_name: HSMMtube

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HSMMtube_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HSMM_HSMMtube_Crawford_protocol.pdf

value: HSMMtube

value: Normal Human Skeletal Muscle Myotubes

value: normal

value: mesoderm


title: Stam_HPdLF_2

source_name: HPdLF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPdLF_Stam_protocol.pdf

value: HPdLF

value: Normal Human Periodontal Ligament Fibroblasts

value: M


title: Stam_NB4_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NB4_protocol.pdf UW_Stam:NB4_Stam_protocol.pdf

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

value: cancer


title: Stam_HMF_2

source_name: HMF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMF_Stam_protocol.pdf

value: HMF

value: human mammary fibroblasts

value: F


title: Stam_HRE_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRE_Stam_protocol.pdf

value: HRE

value: Human

value: Human Renal Epithelial cells (normal)

value: U


title: Stam_HVMF_1

source_name: HVMF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HVMF_Stam_protocol.pdf

value: HVMF

value: Human Villous Mesenchymal Fibroblast Cells


title: Stam_HUVEC_2

source_name: HUVEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HUVEC_protocol.pdf

value: HUVEC

value: Human Umbilical Vein Endothelial Cell


title: Stam_WI-38_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:WI38_Stam_protocol.pdf

value: human

value: Embryonic Lung Fibroblast Cells, hTERT immortalized, includes Raf1 construct

value: Normal (RAF)

value: Fibroblast


title: Stam_GM12864_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12864_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: M


title: Stam_HFF-Myc_1

source_name: HFF-Myc

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HFFMyc_Stam_protocol.pdf

value: HFF-Myc

value: Human Foreskin Fibroblast Cells Expressing Canine cMyc

value: Normal (cMyc)


title: Stam_HMVEC-dBl-Ad_2

source_name: HMVEC-dBl-Ad

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-dBl-Ad_Stam_protocol.pdf

value: HMVEC-dBl-Ad

value: Human

value: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived

value: F


title: Stam_HA-sp_1

source_name: HA-sp

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HA-sp_Stam_protocol.pdf

value: HA-sp

value: Human astrocytes spinal cord

value: Normal

value: Astrocytic

value: U


title: Stam_SK-N-MC_1

source_name: SK-N-MC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:SK-N-MC_protocol.pdf

value: SK-N-MC

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: cancer

value: ectoderm


title: Stam_HMVEC-dBl-Neo_2

source_name: HMVEC-dBl-Neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-dBl-Neo_Stam_protocol.pdf

value: HMVEC-dBl-Neo

value: Normal Neonatal Human Blood Microvascular Endothelial Cells, Dermal-Derived

value: M


title: Stam_PANC-1_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:PANC-1_Myers_protocol.pdf UW_Stam:PANC-1_Stam_protocol.pdf

value: immortalized cell line

value: pancreatic carcinoma. (PMID:1140870)


title: Stam_BJ_1

source_name: BJ

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:BJ-tert_Stam_protocol.pdf

value: BJ

value: Human

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

value: normal

value: mesoderm


title: Stam_HCM_1

source_name: HCM

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCM_Stam_protocol.pdf

value: HCM

value: Human Cardiac Myocytes


title: Stam_PANC-1_1


title: Stam_AG04450_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04450_Stam_protocol.pdf

value: Fetal lung fibroblast


title: Stam_Monocytes-CD14+_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:MonoCD14_Stam_protocol.pdf

value: human

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis product

value: Normal

value: Monocytic

value: F


title: Stam_NHDF-Ad_2

source_name: NHDF-Ad

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:NHDF-Ad_Stam_protocol.pdf Broad_Histone:NHDF-Ad_Bernstein_protocol.pdf

value: NHDF-Ad

value: Adult Normal Human Dermal Fibroblasts


title: Stam_GM12865_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12865_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown


title: Stam_HBMEC_1

source_name: HBMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HBMEC_Myers_protocol.pdf

value: HBMEC

value: Human Brain Microvascular Endothelial Cells

value: U


title: Stam_BE2_C_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:BE2-C_Myers_protocol.pdf

value: Human

value: Human neuroblastoma

value: ectoderm

value: M


title: Stam_HeLa-S3_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf

value: cervical carcinoma

value: cancer


title: Stam_A549_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:A549_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:A549_Crawford_protocol.pdf UW_Stam:A549_Stam_protocol.pdf

value: epithelial cell line "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, derived from a lung carcinoma tissue. (PMID:175022)

value: endoderm


title: Stam_HMVEC-LLy_1

source_name: HMVEC-LLy

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-LLy_Stam_protocol.pdf

value: HMVEC-LLy

value: Normal Human Lymphatic Microvascular Endothelial Cells, Lung-Derived


title: Stam_AoAF_2

source_name: AoAF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AoAF_Stam_protocol.pdf

value: AoAF

value: Normal Human Aortic Adventitial Fibroblast Cells

value: F


title: Stam_HPF_2

source_name: HPF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPF_Stam_protocol.pdf

value: HPF

value: Human Pulmonary Fibroblasts isolated from lung tissue


title: Stam_Th2_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Th2_Stam_protocol.pdf

value: Primary human Th2 T cells

value: unknown

value: mesoderm


title: Stam_Caco-2_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: Human


title: Stam_Jurkat_1

source_name: Jurkat

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Jurkat_protocol.pdf UW_Stam:Jurkat_Stam_protocol.pdf

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)


title: Stam_HRGEC_1

source_name: HRGEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRGEC_Stam_protocol.pdf

value: HRGEC

value: human

value: Human Renal Glomerular Endothelial Cells

value: Normal

value: Endothelial

value: U


title: Stam_GM12878_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/GM12878_protocol.pdf

value: lymphoblastoid

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus


title: Stam_WERI-Rb-1_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:WERI-Rb-1_Stam_protocol.pdf

value: retinoblastoma (PMID:844036)

value: F


title: Stam_HConF_2

source_name: HConF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HConF_Stam_protocol.pdf

value: HConF

value: Human Conjunctival Fibroblast


title: Stam_SKMC_2

source_name: SKMC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SkMC_Stam_protocol.pdf

value: SKMC

value: Human Skeletal Muscle Cells

value: unknown

value: mesoderm


title: AP-2γ ChIP sequencing in E2 (estradiol) treated MCF-7 cells

city: Singapore

first: SI KEE

last: TAN

address: 60 Biopolis Street #02-01 Genome

department: Cancer biology and Pharmacology

country: Singapore

institute: Genomic Institute of Singapore

description: AP-2γ ChIP sequencing, after E2 (estradiol) treatment

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer II Pipeline. In-house (Genome Institute of Singapore) BATMAN program was used for mapping the sequence tags to the reference genome hg18. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.
Peak calling: Binding peaks were determined using in-house Control based ChIPSeq Analysis Tools (CCAT) program with reference to a set of input reads as negative control. Peaks with a stringent cut-off of FDR 0.005 were considered. See 'significant.peak' files.
CCAT file format: chromosome, peakcenter, regionstart, regionend, tagcount, bgcount, zscore, fdr

source_name: MCF-7 breast cancer cells

growth_protocol: MCF-7 breast cancer cells were maintained in DMEM (Invitrogen/Gibco) supplemented with 5% fetal bovine serum (FBS), penicillin, streptomycin, and gentamycin in a 37°C incubator with 5% CO2. Prior to 17 beta-estradiol (“estrogen/E2”, Sigma) stimulation, ~4 millions cells were seeded into 150mm dish and starved with phenol red-free DMEM/F12 containing 5% charcoal stripped FBS (Hyclone) with penicillin, streptomycin and gentamycin for 96 hours to 80% confluence.

extract_protocol: All DNA samples were processed as per the Illumina Solexa ChIP-seq sample processing methods.  5 to10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An A base was added to the polished DNA fragments followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification with Pfx DNA polymerase (Invitrogen) and Illumina primers. 200-300 bp size fractions were selectively isolated from the 2% ultra low range agarose gel and eluted by Qiagen gel extraction kit. The extracted DNA was quantified using Agilent bioanalyzer and subjected to Solexa sequencing according to the manufacturer’s instruction.

treatment_protocol: Hormone-depleted cells were treated with E2 to a final concentration of 100 nM for 45 mins before the ChIP procedure.  Cells treated with an equal volume vehicle, ETOH (ethanol) for 45 min are used as controls

tag: cell line

value: MCF-7 breast cancer cell line

tag: agent

value: estradiol

tag: antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody batch/lot#

tag: antibody catalog#


title: Stam_HVMF_2

source_name: HVMF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HVMF_Stam_protocol.pdf

value: HVMF

value: Human

value: Human Villous Mesenchymal Fibroblast Cells


title: AP-2γ ChIP sequencing in ETOH (ethanol) treated MCF-7 cells

description: AP-2γ ChIP sequencing, after ETOH (ethanol) treatment

value: ethanol


title: Stam_Jurkat_2

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: M


title: FoxA1 ChIP sequencing in E2 (estradiol) treated MCF-7 cells

description: FoxA1 ChIP sequencing, after E2 (estradiol) treatment

value: Abcam


title: FoxA1 ChIP sequencing in ETOH (ethanol) treated MCF-7 cells

description: FoxA1 ChIP sequencing, after ETOH (ethanol) treatment


title: Bernstein_K562_H2A.Z

status: Public on Jun 02 2011

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

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

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

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

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: 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: controlid

tag: softwareversion


title: Bernstein_HSMM_H3K9ac

source_name: HSMM

tag: cell organism

tag: cell description

value: skeletal muscle myoblasts

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

value: rabbit polyclonal. Antibody Target:H3K9ac

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

value: abcam

tag: replicate


title: Bernstein_K562_H3K9me3

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

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

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


title: Bernstein_HeLa-S3_CTCF

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: human

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

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


title: Stam_HCM_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCM_Stam_protocol.pdf

tag: cell

value: HCM

value: Human

value: Human Cardiac Myocytes


title: Bernstein_HepG2_H2A.Z

value: hepatocellular carcinoma

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

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.


title: Stam_HMVEC-LBl_2

source_name: HMVEC-LBl

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMVEC-Lbl_Stam_protocol.pdf

value: HMVEC-LBl

value: Normal Human Blood Microvascular Endothelial Cells, Lung-Derived

value: F


title: Bernstein_GM12878_H3K4me1

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

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

tag: cell karyotype

value: normal

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K4me1

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

value: abcam

tag: control

tag: control description

tag: controlid

tag: softwareversion


title: Bernstein_GM12878_H2A.Z

tag: cell organism

value: human

tag: cell description

tag: cell lineage

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

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

value: Millipore

tag: replicate


title: Bernstein_HeLa-S3_Pol2(b)

tag: lab

tag: lab description

tag: datatype

tag: datatype description

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

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

value: Covance

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.


title: Stam_HCFaa_1

source_name: HCFaa

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCFaa_Stam_protocol.pdf

tag: cell

value: HCFaa

value: Human

value: Human Cardiac Fibroblasts-Adult Atrial

tag: cell sex

value: F


title: Bernstein_H1-hESC_H3K9ac

growth_protocol: missing

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

value: embryonic stem cells

value: inner cell mass

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

tag: antibody targetdescription

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

tag: antibody vendorname

tag: antibody vendorid

tag: treatment


title: Bernstein_NHDF-Ad_H3K4me2

value: human

value: adult dermal fibroblasts

tag: cell karyotype

value: normal

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K4me2

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

value: abcam

tag: treatment description

tag: control

tag: control description

tag: controlid


title: Stam_HCT-116_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:HCT-116_protocol.pdf UW_Stam:HCT116_Stam_protocol.pdf

tag: cell organism

value: Human

tag: cell description

value: colorectal carcinoma (PMID:7214343)

value: cancer

tag: cell lineage

value: endoderm

value: M

tag: replicate


title: Bernstein_HeLa-S3_H3K9ac

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: softwareversion


title: Bernstein_HUVEC_H3K36me3

source_name: HUVEC

value: human

value: umbilical vein endothelial cells

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

tag: antibody vendorname

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_NHDF-Ad_Control

value: adult dermal fibroblasts

tag: cell karyotype

value: normal

value: mesoderm

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: Bernstein_HUVEC_Pol2(b)

value: Broad

tag: cell organism

tag: cell description

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

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

value: Covance

tag: antibody vendorid

tag: control

tag: control description

tag: controlid


title: Bernstein_HSMMtube_H2A.Z

source_name: HSMMtube

tag: lab

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell lineage

tag: cell sex

value: U

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

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

value: Millipore

value: No special treatment or protocol applies

tag: replicate


title: Bernstein_HSMM_H3K79me2

value: human

value: skeletal muscle myoblasts

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

tag: antibody vendorname

value: Active Motif

value: std

value: Standard input signal for most experiments.

tag: softwareversion


title: Stam_NHDF-neo_1

source_name: NHDF-neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:NHDF-neo_Stam_protocol.pdf

tag: cell

value: NHDF-neo

tag: cell organism

value: Human

value: Neonatal Human Dermal Fibroblasts

value: mesoderm


title: Bernstein_Osteobl_CTCF

source_name: Osteobl

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: osteoblasts (NHOst)

value: Rabbit polyclonal. Antibody Target:CTCF

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

tag: antibody vendorid

tag: treatment

tag: treatment description


title: Bernstein_NHEK_Control

source_name: NHEK

value: primary cell

value: keratinocyte

tag: lab

value: human

value: epidermal keratinocytes

value: U

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: control description

tag: controlid


title: Bernstein_HSMMtube_CTCF

tag: lab description

tag: datatype

tag: datatype description

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell lineage

tag: cell sex

value: Millipore

value: std

value: Standard input signal for most experiments.

tag: replicate


title: Bernstein_HeLa-S3_H3K4me2

value: Broad

value: Bernstein - Broad Institute

value: ChipSeq

tag: cell organism

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me2

tag: antibody targetdescription

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

tag: antibody vendorname

value: abcam

tag: softwareversion


title: Bernstein_NHLF_Control

source_name: NHLF

value: primary cell

value: fibroblast of lung

tag: lab

value: Chromatin IP Sequencing

tag: cell description

value: lung fibroblasts

tag: cell karyotype

value: normal

value: endoderm

tag: treatment

tag: treatment description


title: Bernstein_HUVEC_H3K9ac

value: human

value: umbilical vein endothelial cells

value: rabbit polyclonal. Antibody Target:H3K9ac

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

tag: antibody vendorid

value: No special treatment or protocol applies

tag: control

tag: control description

tag: controlid

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_Osteobl_H2A.Z

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

tag: datatype description

value: osteoblasts (NHOst)

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

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

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

value: Millipore

value: std

value: Standard input signal for most experiments.


title: Bernstein_GM12878_H3K79me2

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

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

value: normal

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

tag: antibody vendorname

value: Active Motif

tag: replicate


title: Bernstein_K562_Control

value: immortalized cell line

tag: line

tag: lab

value: Broad

value: human

tag: cell description

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

tag: antibody

value: Input

tag: antibody description

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: Bernstein_Osteobl_H3K4me2

value: Bernstein - Broad Institute

value: osteoblasts (NHOst)

value: mesoderm

value: U

value: rabbit polyclonal. Antibody Target:H3K4me2

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

value: abcam

tag: antibody vendorid

tag: treatment description

tag: control

tag: control description

tag: controlid

tag: softwareversion


title: Bernstein_NHEK_H4K20me1

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

value: epidermal keratinocytes

tag: cell sex

value: rabbit polyclonal. Antibody Target:H4K20me1

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

value: std

value: Standard input signal for most experiments.


title: Bernstein_HSMMtube_H3K79me2

value: Broad

value: human

value: skeletal muscle myotubes differentiated from the HSMM cell line

tag: cell lineage

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

tag: antibody vendorname

value: Active Motif

tag: replicate


title: Bernstein_K562_H3K9ac

tag: lab

value: Bernstein - Broad Institute

tag: cell description

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

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K9ac

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

tag: treatment

value: No special treatment or protocol applies

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HSMM_H3K9me3

value: primary cell

value: skeletal muscle myoblast

value: ChipSeq

value: Chromatin IP Sequencing

value: skeletal muscle myoblasts

value: U

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

tag: antibody

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

value: abcam

tag: antibody vendorid

tag: treatment description

tag: control

tag: control description


title: Bernstein_HSMM_H2A.Z

value: Broad

tag: lab description

tag: datatype

tag: datatype description

value: human

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

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

value: Millipore

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: softwareversion


title: Bernstein_HMEC_CTCF

source_name: HMEC

value: Bernstein - Broad Institute

tag: cell organism

value: mammary epithelial cells

tag: cell karyotype

value: normal

tag: cell lineage

value: ectoderm

tag: cell sex

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

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

value: No special treatment or protocol applies


title: Bernstein_NHEK_H3K36me3

value: primary cell

value: keratinocyte

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell description

value: epidermal keratinocytes

value: U

value: rabbit polyclonal. Antibody Target:H3K36me3

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

tag: antibody vendorname

tag: treatment

tag: replicate


title: Bernstein_H1-hESC_Control

value: Broad

value: human

value: embryonic stem cells

value: inner cell mass

tag: antibody

value: Input

tag: antibody description

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

tag: treatment description

tag: control

value: std

tag: control description


title: Bernstein_GM12878_H3K27ac

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

tag: datatype description

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

value: normal

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K27ac

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

value: abcam

tag: antibody vendorid

value: Standard input signal for most experiments.

tag: controlid

tag: softwareversion


title: Bernstein_NHEK_H3K4me3

value: primary cell

value: keratinocyte

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: epidermal keratinocytes

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.

value: 1)abcam; 2)Millipore

value: No special treatment or protocol applies


title: Bernstein_K562_H3K9me1

tag: lab

value: Broad

value: Bernstein - Broad Institute

value: human

tag: cell description

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

tag: cell lineage

value: rabbit polyclonal. Antibody Target:H3K9me1

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

tag: antibody vendorname

tag: treatment

value: std

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_GM12878_H3K4me2

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

tag: cell karyotype

value: normal

value: mesoderm

value: rabbit polyclonal. Antibody Target:H3K4me2

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

value: abcam

tag: treatment description

tag: control

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: Bernstein_K562_CTCF

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Rabbit polyclonal. Antibody Target:CTCF

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

value: Millipore

tag: antibody vendorid

tag: controlid


title: Bernstein_HSMM_H3K4me2

value: Broad

value: Bernstein - Broad Institute

tag: cell organism

value: human

value: skeletal muscle myoblasts

tag: cell sex

value: U

tag: antibody antibodydescription

tag: antibody targetdescription

value: No special treatment or protocol applies

tag: softwareversion


title: Bernstein_H1-hESC_H3K36me3

value: stem cell

tag: line

tag: lab

tag: cell description

value: embryonic stem cells

tag: cell lineage

value: inner cell mass

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody

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

tag: antibody vendorname

tag: treatment

value: std


title: Bernstein_H1-hESC_H3K4me1

tag: lab description

value: ChipSeq

value: rabbit polyclonal. Antibody Target:H3K4me1

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

value: abcam

tag: treatment description

tag: control

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: small RNAs from Heliconius melpomene rosina

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

country: United Kingdom

institute: University of East Anglia

description: Total endogenous small RNAs from from Heliconius melpomene rosina

data_processing:
Removed adaptors using a custom Perl script. This required an exact match to the first 8 bases of the 3' adaptor sequence. Sequences without adaptor matches were discarded.
No genome sequence to map to as it isn't sequenced yet (as of July 2010). We did have around 2.5Mb of BAC sequence that we mapped sequences to and this was used in part of the analysis. The main comparisons were between the abundances of conserved miRNAs in the two samples and this was done using the miRProf tool  (http://srna-tools.cmp.uea.ac.uk/animal/cgi-bin/srna-tools.cgi?rm=input_form&tool=mirprof) [PMID:18713789].

organism: Heliconius melpomene rosina

source_name: Heliconius melpomene rosina. Collected Gamboa, Panama (09°07'N/79°42'W)

growth_protocol: Collected Gamboa, Panama (09°07'N/79°42'W) and reared in insectaries at the Smithsonian Tropical Research Center, Gamboa, Panama.

extract_protocol: Size fractionated small RNA from total RNA extracts of two different Heliconius melpomene races (Heliconius melpomene melpomene and Heliconius melpomene rosina) were isolated from wing tissue using miRVana kit. 100µg RNA from 11  individuals of different developmental stages was pooled for each race as follows: 4.1% larval stage <1; 2% larval stage 1-1.75; 2.9% larval stage  2-2.5; 22% larval stage 2.75-3; 19% larval stage > 3; 25% early pupae; 25%  mid-melanin pupae. Sequences were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

tag: race

value: Heliconius melpomene rosina

tag: collection location

value: Gamboa, Panama (09°07'N/79°42'W)

tag: tissue

value: wing

tag: developmental stages

value: larval, pupal


title: Bernstein_NHLF_H3K4me2

value: Broad

value: Bernstein - Broad Institute

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: lung fibroblasts

tag: cell karyotype

value: normal

value: endoderm

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me2

tag: antibody targetdescription

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

tag: antibody vendorid

tag: controlid

tag: softwareversion


title: Bernstein_H1-hESC_H3K27ac

value: stem cell

tag: line

tag: lab

tag: lab description

value: ChipSeq

tag: cell description

value: embryonic stem cells

tag: cell lineage

value: inner cell mass

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody

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

tag: antibody vendorname

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: std


title: Bernstein_NH-A_CTCF

source_name: NH-A

value: Broad

tag: datatype

tag: datatype description

value: astrocytes (also called Astrocy)

value: ectoderm

value: Rabbit polyclonal. Antibody Target:CTCF

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

value: Millipore

tag: control

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: Bernstein_HUVEC_CTCF

value: Bernstein - Broad Institute

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: umbilical vein endothelial cells

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorid

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_NH-A_H3K27ac

value: primary cell

value: astrocyte

tag: lab

tag: lab description

value: ChipSeq

tag: cell karyotype

value: normal

value: abcam

tag: controlid

tag: softwareversion


title: small RNAs from Heliconius melpomene melpomene

description: Total endogenous small RNAs from from Heliconius melpomene melpomene

organism: Heliconius melpomene melpomene

source_name: Heliconius melpomene melpomene. Collected in Darien, Panama (09°10'N/78°43'W)

growth_protocol: Collected in Darien, Panama (09°10'N/78°43'W) and reared in insectaries at the Smithsonian Tropical Research Center, Gamboa, Panama.

tag: race

value: Heliconius melpomene melpomene

tag: collection location

value: Darien, Panama (09°10'N/78°43'W)

tag: tissue

value: wing

tag: developmental stages

value: larval, pupal


title: Bernstein_HSMM_H3K4me1

value: Broad

tag: datatype

tag: datatype description

tag: cell description

value: skeletal muscle myoblasts

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: antibody vendorname

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std


title: Bernstein_NHDF-Ad_H3K9ac

source_name: NHDF-Ad

tag: lab

tag: lab description

value: Bernstein - Broad Institute

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: adult dermal fibroblasts

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

tag: antibody targetdescription

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

tag: antibody vendorid

tag: control description

value: Standard input signal for most experiments.

tag: replicate


title: Bernstein_HSMM_CTCF

tag: datatype

value: ChipSeq

value: Rabbit polyclonal. Antibody Target:CTCF

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

value: Millipore

tag: controlid

tag: softwareversion


title: Bernstein_NHLF_H3K27me3

value: primary cell

value: fibroblast of lung

value: Broad

tag: datatype description

tag: cell description

value: lung fibroblasts

tag: cell karyotype

value: normal

tag: cell lineage

value: endoderm

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody

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


title: Bernstein_HeLa-S3_H3K36me3

value: immortalized cell line

tag: line

value: Bernstein - Broad Institute

value: Chromatin IP Sequencing

value: human

value: rabbit polyclonal. Antibody Target:H3K36me3

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

tag: antibody vendorname

value: abcam

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std


title: Bernstein_K562_H3K36me3

tag: lab

tag: lab description

value: ChipSeq

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: mesoderm

tag: antibody antibodydescription

tag: antibody targetdescription

value: Standard input signal for most experiments.


title: Bernstein_NH-A_H3K36me3

value: Broad

tag: datatype

value: astrocytes (also called Astrocy)

value: normal

value: ectoderm

tag: antibody vendorid

tag: control description

tag: controlid

tag: replicate


title: Bernstein_GM12878_H3K4me3

tag: datatype description

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: 1)abcam; 2)Millipore

tag: softwareversion


title: Bernstein_HUVEC_H3K9me1

value: Bernstein - Broad Institute

value: Chromatin IP Sequencing

value: human

value: umbilical vein endothelial cells

value: rabbit polyclonal. Antibody Target:H3K9me1

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

tag: antibody vendorname

tag: treatment

tag: treatment description

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_GM12878_CTCF

tag: lab

tag: lab description

value: ChipSeq

tag: cell organism

value: mesoderm

value: Rabbit polyclonal. Antibody Target:CTCF

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

value: Millipore

value: No special treatment or protocol applies

tag: control

value: std


title: Bernstein_HSMM_H3K27ac

value: Broad

tag: datatype

value: skeletal muscle myoblasts

tag: cell sex

value: U

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

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

value: abcam

tag: antibody vendorid

value: Standard input signal for most experiments.


title: Bernstein_GM12878_H3K27me3

value: immortalized cell line

tag: line

value: Bernstein - Broad Institute

tag: datatype description

value: Chromatin IP Sequencing

value: human

tag: cell description

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

value: normal

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody

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

tag: control description

tag: controlid

tag: replicate


title: Bernstein_NHEK_H3K4me1

value: ChipSeq

value: epidermal keratinocytes

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: antibody vendorname

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: softwareversion


title: Bernstein_NHEK_H3K27me3

value: primary cell

value: keratinocyte

tag: lab

value: Broad

tag: lab description

tag: cell organism

value: U

value: Millipore

tag: control

value: std


title: Bernstein_HepG2_H3K27me3

value: immortalized cell line

value: Bernstein - Broad Institute

tag: datatype

value: Chromatin IP Sequencing

value: hepatocellular carcinoma

tag: antibody antibodydescription

tag: antibody targetdescription

value: Standard input signal for most experiments.

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: Bernstein_HeLa-S3_H3K27me3

tag: line

value: ChipSeq

tag: datatype description

value: human

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


title: Bernstein_NHDF-Ad_H3K27me3

tag: cell description

value: adult dermal fibroblasts

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: No special treatment or protocol applies

tag: control description

tag: controlid


title: Bernstein_HepG2_H4K20me1

value: Broad

value: rabbit polyclonal. Antibody Target:H4K20me1

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

tag: antibody vendorname

value: abcam

tag: treatment

tag: treatment description

tag: replicate

tag: softwareversion


title: Bernstein_HUVEC_Control

tag: lab

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

tag: cell organism

value: umbilical vein endothelial cells

tag: antibody

value: Input

tag: antibody description

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

tag: control

value: std


title: Bernstein_H1-hESC_H3K27me3

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell description

value: embryonic stem cells

value: inner cell mass

tag: antibody antibodydescription

tag: antibody targetdescription

value: Millipore

tag: antibody vendorid

value: Standard input signal for most experiments.