description:
design description: Bisulfite-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A04698) using Illumina HiSeq 2000
library name: A04698
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 231-688 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 99.4
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 12
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM941747_UCSF-UBC.Brain_Germinal_Matrix.Bisulfite-Seq.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A04698-1.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Germinal Matrix Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13770
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BGM BS 02 98
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,295,657,686
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.58
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Brain

tag: histological type

value: Germinal matrix tissue

tag: is tumor

value: primary tissue

value: brain (germinal matrix) tissue


title: Duke_Combined_Medullo_wgEncodeOpenChromSynth

status: Public on Sep 12 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Medullo

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

tag: lab

value: Duke

tag: lab description

value: Crawford - Duke University

tag: datatype

value: Combined

tag: datatype description

value: Multi-assay Synthesis

tag: cell

value: Medullo

tag: cell organism

value: human

tag: cell description

value: medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997)

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: U

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: composite

value: wgEncodeOpenChromSynth

tag: labversion


title: Duke_Combined_Urothelia_UT189_wgEncodeOpenChromSynth

source_name: Urothelia

value: Urothelia

value: primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene

value: normal

value: F

value: UT189 E.Coli treatment 1 hour, followed by 24 hour incubation


title: Duke_Combined_GM12891_wgEncodeOpenChromSynth

value: Duke

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: mesoderm

value: M


title: Duke_Combined_HeLa-S3_IFNa4h_wgEncodeOpenChromSynth

value: Crawford - Duke University

value: Combined

value: Multi-assay Synthesis

value: cervical carcinoma

value: 4 hours of 500 U/ml Interferon alpha (Crawford)


title: Duke_Combined_GM12892_wgEncodeOpenChromSynth

value: human


title: Duke_Combined_NHEK_wgEncodeOpenChromSynth

source_name: NHEK

value: NHEK

value: epidermal keratinocytes

value: ectoderm

value: U

value: No special treatment or protocol applies


status: Public on Sep 13 2012

city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: Bisulfite-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A13819) using Illumina HiSeq 2000
library name: A13819
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 200-400 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 147-400 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 98.5
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM941746_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Bisulfite-Seq.HuFNSC02.A13819.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A13819-1.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13771
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: NGED BS 02 19
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 Library A13819 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 694,237,331
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.63
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Brain

value: Ganglionic eminence neurosphere culture

value: No

value: primary cell culture

tag: cell type


title: Duke_Combined_Gliobla_wgEncodeOpenChromSynth

source_name: Gliobla

tag: lab

value: Duke

tag: lab description

value: Gliobla

value: glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID:7252524)

value: cancer

value: wgEncodeOpenChromSynth


title: Duke_Combined_HTR8svn_wgEncodeOpenChromSynth

value: Crawford - Duke University

tag: datatype

value: Combined

tag: datatype description

value: Multi-assay Synthesis

value: trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo

value: normal

value: F


title: BT-474 TFAP2C

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description: BT-474 TFAP2C

data_processing:
Raw sequences generated from Illumina/Solexa sequencer were aligned using ELAND software to NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3' end of each read was extended 250 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format.
Genome_build: hg18

source_name: BT-474, TFAP2C ChIP

growth_protocol: The human breast cancer cell lines MCF-7, BT-474, MDA-MB-453 and SKBR-3 were obtained from the American Type Culture Collection (ATCC). All cell lines were grown in appropriate medium at 37°C in a humidified 5% CO2 incubator.

extract_protocol: One hundred million cells were cross-linked for 10 min at 37°C using 0.7% formaldehyde, 0.125 M glycine. Cells were washed twice with PBS, re-suspended in lysis buffer and incubated for 5 minutes. Cells were collected by centrifugation and cell pellets were frozen in liquid nitrogen and stored at minus 80°C. Cell pellets were thawed in lysis buffer, collected by centrifugation and cell nuclei were re-suspended in RIPA buffer. Chromatin was sonicated using conditions determined empirically for MCF-7 cells to achieve an optimal fragment length between 100 to 400 bp. After sonication, samples were centrifuged at 20,000 × g for 10 min at 4°C. The supernatant containing cross-linked DNA/histones was diluted with IP dilution buffer to 2 mg/ml. Half of the sample was immunoprecipitated with 10 μg of TFAP2C monoclonal antibody SC-12762 (Santa Cruz Biotechnology, Santa Cruz, CA), which was previously shown to be specific for TFAP2C without cross-reactivity to TFAP2A, and half with control nonspecific IgG (Upstate, Waltham, MA) with the addition of Dynal sheep anti-mouse Dynabeads and allowed to recognize their antigens overnight at 4°C with rotation. Protein/antibody/DNA complexes were collected magnetically, followed by washing and elution. Protein/DNA cross-links were reversed using 200 mmol/L NaCl at 65°C overnight. DNA was treated with Proteinase K and RNase A and was recovered with the QIAquick PCR Kit (Qiagen) according to the manufacturer's suggested protocol. Purified DNA was quantified by using a NanoDrop ND-1000 (NanoDrop, Wilmington, DE).

tag: cell line

tag: chip antibody

value: TFAP2C monoclonal antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog #


title: MDA-MB-453 TFAP2C

description: MDA-MB-453 TFAP2C

source_name: MDA-MB-453, TFAP2C ChIP


title: Duke_Combined_PanIslets_wgEncodeOpenChromSynth

source_name: PanIslets

tag: cell

value: PanIslets

tag: cell organism

value: human

tag: cell description

value: pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005)

tag: cell karyotype

tag: cell lineage

value: endoderm

tag: cell sex

value: M

value: No special treatment or protocol applies


title: Duke_Combined_HepG2_wgEncodeOpenChromSynth

value: Duke

value: hepatocellular carcinoma

tag: treatment

tag: treatment description

tag: composite

tag: labversion


title: Duke_Combined_H1-hESC_wgEncodeOpenChromSynth

growth_protocol: missing

tag: lab

tag: lab description

value: embryonic stem cells

value: inner cell mass

value: wgEncodeOpenChromSynth


title: Duke_Combined_GM19239_wgEncodeOpenChromSynth

value: Crawford - Duke University

tag: datatype

value: Combined

tag: datatype description

value: Multi-assay Synthesis

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

value: mesoderm


title: Duke_Combined_K562_wgEncodeOpenChromSynth

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

value: cancer

value: F


title: MCF-7 TFAP2C

description: MCF-7 TFAP2C

source_name: MCF-7, TFAP2C ChIP

tag: cell line

tag: chip antibody

value: TFAP2C monoclonal antibody

value: Santa Cruz


title: Duke_Combined_HUVEC_wgEncodeOpenChromSynth

source_name: HUVEC

value: HUVEC

value: human

value: umbilical vein endothelial cells

value: normal

value: U


title: Duke_Combined_HeLa-S3_wgEncodeOpenChromSynth

value: Duke

value: cervical carcinoma

value: ectoderm

value: No special treatment or protocol applies


title: Six2 ChIP-seq JP484_ChIPSeq

status: Public on Sep 11 2012

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Six2 ChIP-seq

data_processing:
Basecalling performed using GAPipeline 1.3 for JP332-1-s8.txt, JP332-3-s1.txt, JP332-3-s2.txt, JP336-2-s3.txt, JP336-2-s4.txt, JP336-3-s2.txt, JP336-3-s6.txt, JP356-2-s6.txt, JP356-2-s7.txt, JP386-1-s1.txt, JP386-1-s2.txt, JP388-1-s3.txt, JP388-1-s4.txt
Basecalling performed using CASAVA 1.6 for JP332-4-s1.txt, JP336-4-s2.txt, JP356-3-s5.txt, JP331_s1.txt, JP334_s2.txt, JP355-s3.txt, JP483-s6.txt, JP484-1-s7.txt, JP484-2-s7.txt
ChIP-seq reads were trimmed to the first 25 bases
ChIP-seq reads were mapped to mm9 genome using seqmap 1.0.8 using default parameters and allowing up to 2 mismatches
Peaks were called using an iterative two-sample peak caller (Ma and Wong 2011)
Genome_build: mm9
Supplementary_files_format_and_content: bed file of called peak regions

organism: Mus musculus

source_name: fresh Six2-expressing cells

growth_protocol: For Six2 ChIP, freshly FACS isolated Six2+ cells were used. For b-catenin ChIP, FACS isolated Six2+ cells were aggregated by centrifugation at 850g for 5min and incubated in 10%FBS/DMEM containing 4uM BIO for 24hrs.

extract_protocol: library construction was performed using a ChIP-seq sample preparation kit (Illumina) following the instructions from the manufacturer. In brief, DNA ends were repaired, A-tailed and ligated with adapters. 250-500 bp of DNA were gel-purified and amplified with 18 cycles of PCR.

treatment_protocol: 4uM BIO in DMSO was added in culture.

tag: strain

value: mixed background

tag: developmental stage

value: kidney

tag: cell type

value: nephron progenitor

tag: genotype

value: transgenic Six2GFPcre-positive


title: beta-catenin ChIP-seq JP336_ChIPSeq

description: beta-catenin ChIP-seq

source_name: BIO-treated Six2-expressing cells

value: beta-catenin

value: 4uM BIO


title: KO mRNA Alkbh1-/-

city: Oslo

first: Jonas

last: Paulsen

state: Foreign

address: Montebello

department: Radium Hospital

country: Norway

institute: Oslo University Hospital

description: Alkbh1-null mice were previously generated by targeted deletion of exon 6, and heterozygous were backcrossed onto a C57/BL6 background (Nordstrand et al., 2010). Large RNAs >200 nt were isolated from pachytene cells using the mirVana miRNA Isolation Kit (Ambion) in line with the manufacturer’s protocol. Any DNA remnants were removed from the RNA using TURBO DNase (Ambion) before mRNA isolation was performed. One µg RNA from wild-type and 1.6 µg RNA from Alkbh1-/- were diluted to 50 µL, and mRNA was isolated using the Sera-Mag® Magnetic Oligo(dT) Particles (Thermo Scientific part#1004815) according to the manufacturer’s protocol. From here, the mRNA-Seq Sample Preparation Guide (Illumina part # 1004898, Rev D September 2009) was used to perform ligation of 5’ and 3’ adapters to the cDNA and purification of the ligation product. cDNA template was enriched by PCR amplification (15 cycles) using the mRNA Seq 8 Sample Prep Kit (RS-100-0801, Illumina). Finally, the mRNA library (230-233 bp) was sequenced (75 bp Paired-End Read) using the Illumina Genome Analyzer ΙΙx (GAΙΙx).

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.3
The smallRNA reads consisting solely of adapter sequences were removed. The remaining smallRNA reads were aligned to the reference genome (mm9) using Novoalign (http:/ /www.novocraft.com/), with settings allowing maximum one mismatch, and automatic adapter trimming. For reads that had a best hit to fewer than six positions in the genome, all positions were considered, the rest were considered to have an unknown location. Known piRNA clusters were downloaded from piRNABank  and from piRNAdb (http://kbrb.ioz.ac.cn/piRNA). All non-overlapping clusters from these two sources were considered for annotation.
For the mRNA-samples mapping of sequence reads to the genome was done using TopHat. The output from TopHat was then converted to BED-format using a script from Ensembl (ftp://193.62.203.113/pub/ensembl-functgenomics/scripts/miscellaneous/sam2bed.pl). These reads were then intersected with all known mouse genes from Ensembl using intersectBed. Similar to the analysis of the piRNAs, reads were counted for each annotated gene. Reads that were annotated to multiple genes were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: bed-files contain name and position of the identified piRNA-clusters and the corresponding expression score for each cluster. The expression score was generated by summing the number of mapped reads for each cluster intersected with intersectBed. Reads that mapped to several positions, were divided between them such that fractions were used instead of full counts. The mRNA_table.txt file contains Ensembl gene-ID and number of reads in the knock-out and wildtype sample respectively

molecule: total RNA

source_name: Pachytene, Testes

extract_protocol: Total RNA was isolated using the Fast RNA Pro Green Kit (MP Biomedicals) according to the manufacturer’s protocol.

value: Pachytene spermatocytes

tag: tissue

value: Testes

tag: rna subset

value: mRNA


title: HudsonAlpha_GM12878_MethylWgbs (superseded by GSE86765)

description:
****************************
GSM1002650 record metadata submitted on Sep 12 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86765
****************************

data_processing: Previously submitted data files were in error and have been removed. New data files will be added soon.

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

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: MethylWgbs

value: DNA Methyl Whole Genome Bisulfite Seq

tag: labexpid


title: KO TzfpGTi/GTi

description: Tzfp targeted mice were designed by a gene-trap procedure using an embryonic stem (ES) cell clone containing a splice acceptor site from the gene trap vector (Omnibank Gene Trap Vector 76) upstream of exon 1 of the Tzfp gene (Furu and Klungland, in preparation). 50 ng of RNA (<200 nt) was diluted to 5.7 µL, entering the Small RNA Sample Preparation Guide (Illumina Part # 1004239 Rev. B August 2009) at the 5’ adapter ligation step. Subsequently, 3’ adapter ligation and cDNA synthesis followed by PCR amplification (15 cycles) was performed using the Small RNA Sample Prep Kit (FC-102-1009, Illumina) according to manufacturer’s recommendations. Finally, the small RNA library (105-110 bp) was sequenced (36bp Single-End Read) using the Illumina Genome Analyzer ΙΙx (GAΙΙx).

value: TzfpGTi/GTi

value: smallRNA


title: SKBR-3 TFAP2C

description: SKBR-3 TFAP2C

source_name: SKBR-3, TFAP2C ChIP

value: TFAP2C monoclonal antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog #


title: IgG mock control JP386_ChIPSeq

description: IgG mock control

value: rabbit igg

value: mixed background

tag: treatment

value: kidney

value: nephron progenitor

value: transgenic Six2GFPcre-positive


title: total DNA input control for JP336 JP334_ChIPSeq

description: total DNA input control for JP336

tag: chip antibody

value: none (input control)

value: 4uM BIO


title: IgG mock control JP388_ChIPSeq

description: IgG mock control

tag: strain


title: HudsonAlpha_H1-hESC_MethylWgbs (superseded by GSE80911)

description:
****************************
GSM1002649 record metadata submitted on Sep 12 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE80911
****************************

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

value: human

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

tag: datatype

tag: datatype description


title: Six2 ChIP-seq JP356_ChIPSeq

description: Six2 ChIP-seq

tag: developmental stage

tag: cell type

tag: genotype


title: total DNA input control for JP484 JP483_ChIPSeq

description: total DNA input control for JP484


title: KO Alkbh1-/-

description: Alkbh1-null mice were previously generated by targeted deletion of exon 6, and heterozygous were backcrossed onto a C57/BL6 background (Nordstrand et al., 2010). 50 ng of RNA (<200 nt) was diluted to 5.7 µL, entering the Small RNA Sample Preparation Guide (Illumina Part # 1004239 Rev. B August 2009) at the 5’ adapter ligation step. Subsequently, 3’ adapter ligation and cDNA synthesis followed by PCR amplification (15 cycles) was performed using the Small RNA Sample Prep Kit (FC-102-1009, Illumina) according to manufacturer’s recommendations. Finally, the small RNA library (105-110 bp) was sequenced (36bp Single-End Read) using the Illumina Genome Analyzer ΙΙx (GAΙΙx).

value: Pachytene spermatocytes

tag: tissue

value: Testes

tag: rna subset

value: smallRNA


title: WT rep1

description: 50 ng of RNA (<200 nt) was diluted to 5.7 µL, entering the Small RNA Sample Preparation Guide (Illumina Part # 1004239 Rev. B August 2009) at the 5’ adapter ligation step. Subsequently, 3’ adapter ligation and cDNA synthesis followed by PCR amplification (15 cycles) was performed using the Small RNA Sample Prep Kit (FC-102-1009, Illumina) according to manufacturer’s recommendations. Finally, the small RNA library (105-110 bp) was sequenced (36bp Single-End Read) using the Illumina Genome Analyzer ΙΙx (GAΙΙx).

value: wild type


title: Duke_Combined_GM12878_wgEncodeOpenChromSynth

value: Duke

value: Crawford - Duke University

value: Combined

value: Multi-assay Synthesis

tag: cell

tag: cell organism

tag: cell description

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

tag: cell karyotype

tag: cell lineage

value: mesoderm

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: composite

value: wgEncodeOpenChromSynth

tag: labversion


title: WT mRNA

description: Large RNAs >200 nt were isolated from pachytene cells using the mirVana miRNA Isolation Kit (Ambion) in line with the manufacturer’s protocol. Any DNA remnants were removed from the RNA using TURBO DNase (Ambion) before mRNA isolation was performed. One µg RNA from wild-type and 1.6 µg RNA from Alkbh1-/- were diluted to 50 µL, and mRNA was isolated using the Sera-Mag® Magnetic Oligo(dT) Particles (Thermo Scientific part#1004815) according to the manufacturer’s protocol. From here, the mRNA-Seq Sample Preparation Guide (Illumina part # 1004898, Rev D September 2009) was used to perform ligation of 5’ and 3’ adapters to the cDNA and purification of the ligation product. cDNA template was enriched by PCR amplification (15 cycles) using the mRNA Seq 8 Sample Prep Kit (RS-100-0801, Illumina). Finally, the mRNA library (230-233 bp) was sequenced (75 bp Paired-End Read) using the Illumina Genome Analyzer ΙΙx (GAΙΙx).

value: mRNA


title: total DNA input control for JP356 JP355_ChIPSeq

description: total DNA input control for JP356

tag: chip antibody

value: none (input control)

tag: strain

value: mixed background

tag: treatment

value: kidney

value: nephron progenitor

value: transgenic Six2GFPcre-positive


title: total DNA input control for JP332 JP331_ChIPSeq

description: total DNA input control for JP332

value: 4uM BIO


title: Total RNA from LPS stimulated Dendritic Cells four hour post stimulation

city: Worcester

first: Manuel

last: Garber

state: Massachusetts

address: 55 Lake Ave North Worcester

department: Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

data_processing:
Refseq genes were quantifed using Scripture segmentation program (http://www.broadinstitute.org/software/scripture/) by selecting the constituent exon model
Transcript reconsturction was done using Scripture (http://www.broadinstitute.org/software/scripture/)
Genome Build: mm9

source_name: bone marrow

growth_protocol: Briefly, 6-8 week old female C57BL/6J mice were obtained from the Jackson Laboratories. RPMI medium (Invitrogen) supplemented with 10% heat inactivated FBS (Invitrogen), β-mercaptoethanol (50uM, Invitrogen), L-glutamine (2mM, VWR) penicillin/streptomycin (100U/ml, VWR), MEM non-essential amino acids (1X, VWR), HEPES (10mM, VWR), sodium pyruvate (1mM, VWR), and GM-CSF (20 ng/ml; Peprotech, Rocky Hill, NJ) was used throughout the study. At day 0, bone marrow-derived dendritic cells (BMDCs) were collected from femora and tibiae and plated on twenty (per mouse), 100mm non-tissue culture treated plastic dishes using 10ml medium per plate. At day 2, cells were fed with another 10ml medium per dish. At day 5, cells were harvested from 15ml of the supernatant by spinning at 1400rpm for 5 minutes; pellets were resuspended with 5ml medium and added back to the original dish. Cells were fed with another 5ml medium at day 7.  At Day 8, all non-adherent and loosely bound cells were collected and harvested by centrifugation. Cells were then resuspended with medium, plated at a concentration of 15x106 cells in 10ml medium per 100mm dish. At day 9, cells were stimulated for various time points with LPS (100ng/ml, rough, ultra-pure E. coli K12 strain, Invitrogen).

extract_protocol: Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen), and sample quality was tested on a 2100 Bioanalyzer (Agilent). We prepared the RNA-A+-Seq libraries using the ‘dUTP second strand (strand specific) protocol as described in (Levine et al 2010). Briefly, extracts were treated with DNase (Ambion 2238). Polyadenylated RNAs were selected using Ambion's MicroPoly(A)Purist kit (AM1919M) and RNA integrity confirmed using Bioanalyzer (Agilent). RNA was fragmented by incubation in RNA fragmentation buffer (Affymetrix) at 80 degrees for 4 minutes. Fragmented RNA was mixed with 3 μg random hexamers (Invitrogen), incubated at 70 °C for 10 min, and placed on ice briefly before starting cDNA synthesis. We synthesized first-strand cDNA with this RNA primer mix by adding 4 μl 5× first-strand buffer, 2 μl 100 mM DTT, 1 μl 10 mM dNTPs, 4 μg of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55 °C. We synthesized second-strand cDNA by adding 4 μl of 5× first-strand buffer, 2 μl of 100 mM DTT, 4 μl of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 μl of 5× second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16 °C for 2 h. cDNA was eluted using the Qiagen MiniElute kit with 30 μl of the manufacturer's EB buffer. DNA ends were repaired using dNTPs and T4 polymerase (NEB), followed by purification using the MiniElute kit. Adenine was added to the 3′ end of the DNA fragments using dATP and Klenow exonuclease (NEB; M0212S) to allow adaptor ligation, and fragments were purified using MiniElute. Adaptors were ligated and incubated for 15 min at room temperature (25 °C). Phenol/chloroform/isoamyl alcohol (Invitrogen 15593-031); extraction followed to remove the DNA ligase. The pellet was then resuspended in 10 μl EB buffer. The sample was run on a 3% agarose gel (Nusieve 3:1 agarose, Lonza) and a 160–380 base pair fragment was cut out and extracted. PCR was performed with Phusion High-Fidelity DNA Polymerase with the manufacturer's GC buffer (New England Biolabs) and 2 M betaine (Sigma). PCR conditions were 30 s at 98 °C; 16 cycles of 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C; 5 min at 72 °C; forever at 4 °C. Products were run on a polyacrylamide gel for 60 min at 120 V. The PCR products were cleaned up with Agencourt AMPure XP magnetic beads (A63880) to completely remove primers and the product was submitted for Illumina sequencing.

value: LPS

tag: time

value: 4 h

value: bone marrow-derived dendritic cells


title: Total RNA from LPS stimulated Dendritic Cells one hour post stimulation

value: 1 h


title: ChIP-Seq of Rel 120 min post LPS stimulation paired-end

data_processing:
Peaks were called using the ChIP-Seq module of the Scripture segmentation program (http://www.broadinstitute.org/software/scripture/)
Genome Build: mm9

extract_protocol: Solid-phase reversible immobilization (SPRI) cleanup steps were performed using the Bravo liquid handling platform (Agilent) using a modified version of (Fisher et al., 2011). 120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a 96-well magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Sample concentrations were measured and 5 µl was used for ChIP-String enrichment validation.

value: Rel

value: 120 min


title: ChIP-Seq of Relb 120 min post LPS stimulation paired-end

value: Relb


title: ChIP-Seq of Stat2 30 min post LPS stimulation

value: 30 min

tag: chip antibody manufacturer 1

value: Abcam

tag: chip antibody catalog number 1

tag: chip antibody manufacturer 2

value: Santa Cruz

tag: chip antibody catalog number 2


title: ChIP-Seq of Stat2 60 min post LPS stimulation

tag: cell type

value: 60 min


title: WT rep2

value: Pachytene spermatocytes

tag: genotype

value: wild type

tag: tissue

value: Testes

tag: rna subset

value: smallRNA


title: ChIP-Seq of Stat1 60 min post LPS stimulation

value: Bethyl


title: ChIP-Seq of Stat2 0 min post LPS stimulation

value: 0 min


title: ChIP-Seq of Stat1 120 min post LPS stimulation

value: LPS


title: ChIP-Seq of Nfkb1 60 min post LPS stimulation

tag: chip antibody manufacturer

tag: chip antibody catalog number


title: ChIP-Seq of Nfkb1 30 min post LPS stimulation


title: ChIP-Seq of Stat2 120 min post LPS stimulation


title: ChIP-Seq of Irf4 60 min post LPS stimulation


title: ChIP-Seq of Irf4 0 min post LPS stimulation


title: ChIP-Seq of Irf2 60 min post LPS stimulation


title: ChIP-Seq of Nfkb1 0 min post LPS stimulation


title: ChIP-Seq of Irf4 120 min post LPS stimulation


title: ChIP-Seq of Egr1 60 min post LPS stimulation


title: ChIP-Seq of Irf2 0 min post LPS stimulation


title: ChIP-Seq of Stat1 0 min post LPS stimulation


title: Total RNA from LPS stimulated Dendritic Cells six hour post stimulation

value: 6 h


title: ChIP-Seq of Irf2 120 min post LPS stimulation

value: bone marrow-derived dendritic cells


title: ChIP-Seq of Irf2 30 min post LPS stimulation


title: Total RNA from LPS stimulated Dendritic Cells two hour post stimulation

value: 2 h


title: ChIP-Seq of Egr1 30 min post LPS stimulation


title: ChIP-Seq of Egr1 0 min post LPS stimulation


title: ChIP-Seq of Nfkb1 120 min post LPS stimulation


title: ChIP-Seq of Irf4 30 min post LPS stimulation


title: ChIP-Seq of Cebpb 30 min post LPS stimulation

value: Cebpb


title: ChIP-Seq of Cebpb 60 min post LPS stimulation


title: ChIP-Seq of Egr1 120 min post LPS stimulation

value: 120 min


title: ChIP-Seq of Rel 30 min post LPS stimulation

value: Rel


title: ChIP-Seq of Cebpb 0 min post LPS stimulation


title: ChIP-Seq of Cebpb 120 min post LPS stimulation


title: ChIP-Seq of Rel 60 min post LPS stimulation


title: ChIP-Seq of Rel 0 min post LPS stimulation


title: ChIP-Seq of Rel 120 min post LPS stimulation single


title: ChIP-Seq of Atf3 60 min post LPS stimulation


title: ChIP-Seq of Atf3 30 min post LPS stimulation

value: 30 min


title: ChIP-Seq of Atf3 120 min post LPS stimulation

value: Abcam


title: ChIP-Seq of Atf3 0 min post LPS stimulation

value: Santa Cruz


title: ChIP-Seq of WCE 30 min post LPS stimulation


title: ChIP-Seq of WCE 0 min post LPS stimulation


title: ChIP-Seq of WCE 120 min post LPS stimulation


title: ChIP-Seq of Runx1 0 min post LPS stimulation


title: ChIP-Seq of Runx1 120 min post LPS stimulation


title: ChIP-Seq of WCE 60 min post LPS stimulation

value: 60 min


title: ChIP-Seq of Stat3 0 min post LPS stimulation


title: ChIP-Seq of Stat3 60 min post LPS stimulation


title: ChIP-Seq of Stat3 30 min post LPS stimulation


title: ChIP-Seq of Stat3 120 min post LPS stimulation


title: ChIP-Seq of Runx1 60 min post LPS stimulation


title: ChIP-Seq of Rela 60 min post LPS stimulation

value: Rela


title: ChIP-Seq of Atf4 120 min post LPS stimulation


title: ChIP-Seq of Rela 0 min post LPS stimulation


title: ChIP-Seq of Relb 30 min post LPS stimulation

value: Relb


title: ChIP-Seq of Rela 120 min post LPS stimulation


title: ChIP-Seq of Relb 120 min post LPS stimulation single


title: ChIP-Seq of Relb 60 min post LPS stimulation


title: ChIP-Seq of Rela 30 min post LPS stimulation


title: ChIP-Seq of Relb 0 min post LPS stimulation


title: ChIP-Seq of Pol-II 0 min post LPS stimulation

value: Pol-II

value: Covance


title: ChIP-Seq of Pol-II 15 min post LPS stimulation

value: 15 min


title: ChIP-Seq of PU1 30 min post LPS stimulation


title: ChIP-Seq of Pol-II 30 min post LPS stimulation


title: ChIP-Seq of Pol-II 60 min post LPS stimulation


title: ChIP-Seq of PU1 120 min post LPS stimulation


title: ChIP-Seq of Maff 60 min post LPS stimulation

value: Maff


title: ChIP-Seq of PU1 0 min post LPS stimulation

value: LPS

value: 0 min


title: ChIP-Seq of PU1 60 min post LPS stimulation

value: bone marrow-derived dendritic cells


title: ChIP-Seq of Maff 30 min post LPS stimulation


title: ChIP-Seq of Maff 120 min post LPS stimulation


title: ChIP-Seq of Egr2 0 min post LPS stimulation


title: ChIP-Seq of Egr2 60 min post LPS stimulation


title: ChIP-Seq of K4me3 60 min post LPS stimulation

value: Millipore


title: ChIP-Seq of Egr2 30 min post LPS stimulation


title: ChIP-Seq of Maff 0 min post LPS stimulation


title: ChIP-Seq of K4me3 120 min post LPS stimulation


title: ChIP-Seq of K4me3 0 min post LPS stimulation


title: ChIP-Seq of K4me1 240 min post LPS stimulation

value: 240 min


title: ChIP-Seq of K4me1 0 min post LPS stimulation


title: ChIP-Seq of K4me1 120 min post LPS stimulation

value: 120 min


title: ChIP-Seq of K27Ac 60 min post LPS stimulation


title: ChIP-Seq of K27Ac 30 min post LPS stimulation


title: ChIP-Seq of K27Ac 120 min post LPS stimulation


title: ChIP-Seq of K27Ac 0 min post LPS stimulation


title: ChIP-Seq of Junb 60 min post LPS stimulation

value: Junb


title: ChIP-Seq of Stat1 30 min post LPS stimulation

value: 30 min

value: Bethyl


title: ChIP-Seq of Junb 0 min post LPS stimulation

value: Abcam

value: Santa Cruz


title: ChIP-Seq of Junb 120 min post LPS stimulation


title: ChIP-Seq of Junb 30 min post LPS stimulation


title: ChIP-Seq of Irf1 60 min post LPS stimulation

value: 60 min


title: ChIP-Seq of Irf1 0 min post LPS stimulation


title: ChIP-Seq of Hif1a 60 min post LPS stimulation


title: ChIP-Seq of Egr2 120 min post LPS stimulation


title: ChIP-Seq of Irf1 120 min post LPS stimulation


title: ChIP-Seq of Irf1 30 min post LPS stimulation


title: ChIP-Seq of Hif1a 120 min post LPS stimulation


title: ChIP-Seq of Hif1a 30 min post LPS stimulation


title: ChIP-Seq of K4me3 30 min post LPS stimulation


title: ChIP-Seq of Hif1a 0 min post LPS stimulation


title: ChIP-Seq of Ets2 60 min post LPS stimulation


title: ChIP-Seq of Ets2 30 min post LPS stimulation


title: ChIP-Seq of E2f4 60 min post LPS stimulation


title: ChIP-Seq of Ets2 0 min post LPS stimulation


title: ChIP-Seq of Ets2 120 min post LPS stimulation


title: ChIP-Seq of E2f1 60 min post LPS stimulation


title: ChIP-Seq of E2f4 0 min post LPS stimulation


title: ChIP-Seq of E2f1 30 min post LPS stimulation


title: ChIP-Seq of Ctcf 30 min post LPS stimulation

value: Ctcf

value: Upstate


title: ChIP-Seq of Ctcf 60 min post LPS stimulation


title: ChIP-Seq of E2f1 0 min post LPS stimulation


title: ChIP-Seq of E2f1 120 min post LPS stimulation


title: ChIP-Seq of Ctcf 120 min post LPS stimulation


title: ChIP-Seq of Ctcf 0 min post LPS stimulation


title: ChIP-Seq of Ahr 60 min post LPS stimulation

value: Ahr


title: beta-catenin ChIP-seq JP332_ChIPSeq

description: beta-catenin ChIP-seq

value: beta-catenin

value: mixed background

tag: developmental stage

value: 4uM BIO

value: nephron progenitor

value: transgenic Six2GFPcre-positive


title: ChIP-Seq of Ahr 30 min post LPS stimulation

value: bone marrow-derived dendritic cells

value: LPS


title: ChIP-Seq of Ahr 0 min post LPS stimulation

value: 0 min


title: ChIP-Seq of Ahr 120 min post LPS stimulation

value: 120 min


title: SCN heat-stressed

city: La Jolla

first: Felipe

last: Barreto

state: California

address: 8750 Biological Grade

department: Marine Biology Research Division

institute: Scripps Institution of Oceanography

data_processing:
Raw fastq reads were imported into CLC Genomics Workbench v 4.5, where adapters were trimmed and reads were trimmed based on base quality (Phred = 20).
Remaining high-quality reads were then mapped to shotgun assembled transcriptomes of the respective population (Accession: SRP003815, Barreto et al. 2011, PubMed ID: 21199025).  Mapping parameters in CLC Genomics Workbench were: length fraction = 0.5; similarity fraction = 0.9).
Expression levels were estimated within each sample by normalizing the number of uniquely mapped reads for each contig by contig length and total number of mapped reads in the sample (RPKM).
Supplementary_files_format_and_content: For each sample, the file contains a tab-delimited matrix listing contig ID (specific to the Burton Lab), GenBank Accession, BLAST gene product, and RPKM.

organism: Tigriopus californicus

source_name: pool of 300-400 individuals

extract_protocol: Total RNA from each sample was extracted with Tri-reagent (Sigma) following manufacturer's protocol. The Illumina mRNA sequencing kit (RS-100-0801) and multiplexing kit (PE-400-1001) were used to isolate mRNA and prepare sequencing libraries. Matching barcodes were assigned to the SD control and heat stress sample (TGACCA), as well as the SC control and heat stress samples (GCCAAT), to allow for multiplexing on two lanes of an Illumina GA-II genome analyzer flow cell

value: all pooled

tag: condition


title: SCN control


title: SD heat-stressed

value: San Diego


title: PR-binding T47D ChIP-Seq

city: Basel

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

data_processing:
Sequence reads were mapped to the NCBI GRCh37/hg19 assembly of the human genome using the Solexa GAPipeline and the ELAND standalone program (CASAVA)
Only reads that mapped uniquely and had no more than two mismatches were considered.
Peaks were called with the Model-based Analysis of ChIP-Seq Algorithm (MACS ver 1.3.6)
Genome_build: hg19
Supplementary_files_format_and_content: BED files with PR binding locations

source_name: T47D cells

growth_protocol: T47D cells were cultured in RPMI 1640 with 10 % FBS. Human uterine leiomyoma smooth muscle cells were cultured in DEME/F12 with 10% FBS. T47D cells were hormone starved 2 days in RPMI 1640 with 5% charcol stripped FBS before treated with vehicle (ethanol) or RU486 (10-6 M). Uterine leiomyoma smooth muscle cells were hormone starved for 1 day in DMEM/F12 containing 1% charcol stripped FBS before treated with vehicle (ethanol) or RU486 (10-6 M).

extract_protocol: An aliquot of chromatin (30 µg) was precleared with protein G agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 µg antibody against PR (sc-7208, Santa Cruz Biotechnology). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65° C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: T47D or leiomyoma cells treated with RU486 for 1 hour were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.

tag: cell line

value: PR

tag: chip antibody catalog #


title: SD contol

tag: strain


title: ChIP-Seq of E2f4 30 min post LPS stimulation

tag: chip antibody

tag: treatment

value: 30 min

value: Santa Cruz


title: PR-binding Leiomyoma ChIP-Seq

source_name: Leiomyoma cells

value: Leiomyoma cells


title: ChIP-Seq of E2f4 120 min post LPS stimulation

tag: time


title: CSHL_RnaSeq_CNS_E11.5 (superseded by GSE90194)

status: Public on Sep 10 2012

description:
****************************
GSM1000573 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90194
****************************

molecule: polyA RNA

source_name: CNS

tag: lab

value: CSHL-m

tag: lab description

value: Gingeras - Cold Spring Harbor Laboratory

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

value: CNS

tag: cell organism

value: mouse

tag: cell description

value: Central Nervous System

tag: cell sex

value: U

tag: age

tag: age description

value: Embryonic day 11.5

tag: biorep

tag: labexpid

tag: readtype

tag: readtype description

value: Paired 101 nt directed reads

tag: spikeinpool

tag: strain description

value: A substrain of C57BL/6


title: CSHL_RnaSeq_Liver_E14 (superseded by GSE90195)

description:
****************************
GSM1000574 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90195
****************************

source_name: Liver

value: Liver

value: Embryonic day 14

tag: strain


title: CSHL_RnaSeq_WholeBrain_E14.5 (superseded by GSE90197)

description:
****************************
GSM1000572 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90197
****************************

source_name: WholeBrain

tag: lab

value: WholeBrain

value: Whole Brain

value: Embryonic day 14.5


title: CSHL_RnaSeq_Liver_E14.5 (superseded by GSE90196)

description:
****************************
GSM1000571 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90196
****************************

tag: lab description


title: CSHL_RnaSeq_CNS_E18 (superseded by GSE90199)

description:
****************************
GSM1000570 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90199
****************************

tag: datatype

value: Embryonic day 18


title: CSHL_RnaSeq_Liver_E18 (superseded by GSE90202)

description:
****************************
GSM1000566 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90202
****************************

value: CSHL-m

tag: datatype description


title: CSHL_RnaSeq_CNS_E14 (superseded by GSE90198)

description:
****************************
GSM1000569 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90198
****************************

value: Gingeras - Cold Spring Harbor Laboratory

tag: cell


title: CSHL_RnaSeq_Limb_E14.5 (superseded by GSE90201)

description:
****************************
GSM1000568 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90201
****************************

source_name: Limb

value: RnaSeq

value: Limb

tag: cell organism


title: LICR_ChipSeq_Heart_Input_E14.5

source_name: Heart

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

value: Heart

tag: cell description

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

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion

value: Bowtie

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_MEL_Input_immortalized

source_name: MEL

value: MEL

value: mouse

value: Leukemia (K562 analog)

tag: cell sex

value: M

tag: age

value: immortalized

tag: age description

value: Immortal cells

value: HCS

value: Unknown

tag: strain description

value: Unknown strain origin


title: LICR_ChipSeq_BMDM_Input_adult-8wks

source_name: BMDM

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: BMDM

value: Bone marrow derived macrophage

value: F

value: Adult 8 weeks

tag: strain


title: LICR_ChipSeq_OlfactBulb_Input_adult-8wks

source_name: OlfactBulb

tag: datatype description

tag: cell

value: OlfactBulb

tag: cell organism

tag: cell description

value: Olfactory Bulb

value: Input

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

value: std

value: Standard input signal for most experiments.

value: Bowtie

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_BAT_Input_adult-24wks

source_name: BAT

value: BAT

value: mouse

value: Brown adipocytes tissue

value: M

tag: antibody

tag: antibody description

value: Adult 24 weeks

tag: control

tag: control description

value: HCS


title: LICR_ChipSeq_Testis_Input_adult-8wks

source_name: Testis

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

value: Testis

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion


title: LICR_ChipSeq_Thymus_Input_adult-8wks

source_name: Thymus

value: Thymus

tag: cell sex

value: Input

tag: age

tag: age description

value: Adult 8 weeks

tag: strain description


title: LICR_ChipSeq_MEL_H3K79me2_immortalized

tag: lab

tag: lab description

tag: datatype

value: MEL

value: Leukemia (K562 analog)

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

tag: antibody vendorname

value: Active Motif

tag: antibody vendorid

value: immortalized

value: Immortal cells

value: std

value: Standard input signal for most experiments.

value: Pooled & filtered

value: MACS

tag: strain

value: Unknown

value: Unknown strain origin


title: LICR_ChipSeq_Liver_H3K79me2_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Liver

tag: cell organism

value: mouse

tag: cell description

value: M

tag: antibody

tag: control

tag: control description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Liver_H3K9ac_adult-8wks

tag: cell sex

value: rabbit polyclonal. Antibody Target:H3K9ac

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

value: Abcam

tag: age

tag: age description

value: Adult 8 weeks

tag: controlid

tag: labversion

tag: softwareversion


title: LICR_ChipSeq_MEL_H3K36me3_immortalized

tag: lab

tag: lab description

tag: datatype

tag: line

value: MEL

value: Leukemia (K562 analog)

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

value: immortalized

value: immortalized cell line

value: std

value: Standard input signal for most experiments.

tag: strain description


title: LICR_ChipSeq_Liver_H3K36me3_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

tag: antibody vendorname

tag: antibody vendorid

value: Pooled & filtered

value: MACS

tag: strain


title: LICR_ChipSeq_Spleen_H3K27me3_adult-8wks

source_name: Spleen

value: tissue

value: mouse

value: Spleen

tag: Sex

value: M

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27me3

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

value: Millipore

tag: age

tag: age description

tag: control

tag: control description

tag: controlid

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Heart_H3K9ac_adult-8wks

tag: lab

tag: lab description

tag: datatype

value: heart

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

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

value: Abcam

value: Adult 8 weeks

tag: labversion

tag: softwareversion


title: LICR_ChipSeq_Liver_H3K27me3_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: datatype description

tag: cell organism

value: liver

tag: antibody targetdescription

value: std

value: Standard input signal for most experiments.

tag: strain description


title: LICR_ChipSeq_B-cell_(CD43-)_H3K36me3_adult-8wks

value: Chromatin IP Sequencing

tag: cell

value: mouse

tag: cell description

value: mouse spleen B cells, CD43-,CD11b-

tag: cell sex

value: rabbit polyclonal. Antibody Target:H3K36me3

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

tag: antibody vendorname

tag: antibody vendorid

value: Pooled & filtered

value: MACS

tag: strain


title: LICR_ChipSeq_Placenta_Input_adult-8wks

source_name: Placenta

value: Placenta

value: F

tag: antibody

value: Input

tag: antibody description

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

tag: age

tag: age description

tag: control

tag: control description

tag: controlid

tag: replicate

value: Bowtie

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Thymus_H3K27me3_adult-8wks

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Thymus

tag: cell organism

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

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

value: Millipore

value: Adult 8 weeks

tag: labversion

tag: softwareversion


title: LICR_ChipSeq_Testis_H3K27me3_adult-8wks

value: Chromatin IP Sequencing

tag: cell

value: Testis

value: mouse

tag: cell description

tag: cell sex

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: std

value: Standard input signal for most experiments.

value: Pooled & filtered

tag: strain

tag: strain description


title: LICR_ChipSeq_WholeBrain_H3K27me3_E14.5

value: tissue

value: Whole Brain

tag: Sex

tag: antibody

tag: age

tag: age description

value: Embryonic day 14.5

tag: control

tag: control description

tag: controlid

value: MACS


title: LICR_ChipSeq_MEL_H3K27ac_immortalized

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

tag: line

value: MEL

tag: cell organism

value: Leukemia (K562 analog)

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

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

value: Abcam

value: immortalized

value: immortalized cell line

tag: labversion

value: Unknown

value: Unknown strain origin


title: LICR_ChipSeq_MEL_H3K9ac_immortalized

value: Chromatin IP Sequencing

value: mouse

tag: cell description

tag: cell sex

value: M

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

value: std

value: Standard input signal for most experiments.

value: Pooled & filtered

tag: softwareversion

tag: strain


title: LICR_ChipSeq_Liver_H3K27ac_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: tissue

value: liver

tag: Sex

tag: antibody

tag: age

tag: age description

value: Adult 8 weeks

tag: control

tag: control description

value: MACS

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Spleen_H3K27ac_adult-8wks

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: Spleen

tag: cell organism

value: rabbit polyclonal. Antibody Target:H3K27ac

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

value: Abcam

tag: controlid


title: LICR_ChipSeq_Heart_H3K27ac_E14.5

value: Chromatin IP Sequencing

value: Heart

value: mouse

tag: cell description

tag: cell sex

value: U

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: Embryonic day 14.5

tag: labversion


title: LICR_ChipSeq_Heart_H3K4me1_E14.5

value: LICR-m

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: age

tag: age description

tag: control

value: std

value: Standard input signal for most experiments.

value: Pooled & filtered

tag: softwareversion

tag: strain


title: LICR_ChipSeq_MEF_H3K27ac_adult-8wks

source_name: MEF

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: MEF

value: Mouse Embryonic Fibroblast

value: M

value: Adult 8 weeks

tag: control description

value: MACS

tag: strain description


title: LICR_ChipSeq_Heart_H3K4me3_E14.5

value: Chromatin IP Sequencing

tag: cell

value: Heart

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: controlid

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_MEL_H3K27me3_immortalized

value: LICR-m

tag: line

value: MEL

value: mouse

value: Leukemia (K562 analog)

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

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

tag: antibody vendorname

tag: antibody vendorid

tag: age

value: immortalized

value: immortalized cell line

tag: labversion

value: Unknown

value: Unknown strain origin


title: LICR_ChipSeq_Placenta_H3K4me1_adult-8wks

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

value: Placenta

value: F

value: rabbit polyclonal. Antibody Target:H3K4me1

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

value: Abcam

tag: age description

value: Adult 8 weeks

tag: control

value: std

value: Standard input signal for most experiments.

value: Pooled & filtered

tag: softwareversion

value: MACS

tag: strain


title: LICR_ChipSeq_Heart_H3K27me3_adult-8wks

value: LICR-m

tag: datatype description

value: Chromatin IP Sequencing

value: tissue

tag: cell organism

value: mouse

value: heart

tag: Sex

value: M

value: rabbit polyclonal. Antibody Target:H3K27me3

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

value: Millipore

tag: control description

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Placenta_H3K4me3_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: cell

value: Placenta

tag: cell description

tag: cell sex

value: F

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

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

tag: controlid


title: LICR_ChipSeq_Heart_H3K36me3_adult-8wks

tag: lab

tag: lab description

tag: datatype

value: rabbit polyclonal. Antibody Target:H3K36me3

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: age

value: Adult 8 weeks

value: std

value: Standard input signal for most experiments.

tag: labversion

value: Pooled & filtered

value: MACS


title: LICR_ChipSeq_Heart_H3K79me2_adult-8wks

value: LICR-m

tag: datatype description

value: Chromatin IP Sequencing

value: Heart

tag: cell organism

value: mouse

value: M

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

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

value: Active Motif

tag: age description

tag: control

tag: softwareversion

tag: strain


title: LICR_ChipSeq_Placenta_H3K27ac_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: cell

value: Placenta

tag: cell description

tag: cell sex

value: F

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27ac

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

tag: control description

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_ES-Bruce4_H3K9me3_E0

tag: lab

tag: lab description

tag: datatype

tag: line

value: mouse embryonic stem cells

tag: antibody antibodydescription

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

tag: antibody targetdescription

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

value: Abcam

value: Embryonic day 0 (stem cell)

value: std

value: Standard input signal for most experiments.

tag: controlid

value: Pooled & filtered


title: LICR_ChipSeq_OlfactBulb_H3K4me3_adult-8wks

value: LICR-m

tag: datatype description

value: Chromatin IP Sequencing

value: OlfactBulb

tag: cell organism

value: mouse

value: Olfactory Bulb

value: M

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age

tag: age description

value: Adult 8 weeks

tag: labversion

value: MACS


title: LICR_ChipSeq_ES-E14_H3K27ac_E0

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: mouse embryonic stem cells

tag: cell sex

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27ac

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

tag: control

tag: softwareversion

tag: strain

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


title: LICR_ChipSeq_ES-E14_H3K36me3_E0

tag: lab

value: LICR-m

tag: lab description

tag: datatype

value: rabbit polyclonal. Antibody Target:H3K36me3

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

value: Abcam

value: Embryonic day 0 (stem cell)

value: std

tag: control description

value: Standard input signal for most experiments.

value: Pooled & filtered

tag: strain description


title: LICR_ChipSeq_ES-E14_H3K4me3_E0

tag: datatype description

value: Chromatin IP Sequencing

tag: line

value: mouse

value: M

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: Millipore

tag: controlid


title: LICR_ChipSeq_CH12_Input_immortalized

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: cell organism

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: Input

tag: antibody description

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

tag: age

value: immortalized

value: immortalized cell line

tag: replicate

value: HCS

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_CH12_H3K79me2_immortalized

value: LICR-m

tag: cell

tag: cell sex

tag: antibody

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

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

tag: antibody vendorname

value: Active Motif

tag: antibody vendorid

tag: age description

value: Immortal cells

tag: control

value: std

value: Standard input signal for most experiments.

tag: labversion

value: Pooled & filtered

tag: softwareversion

value: MACS


title: LICR_ChipSeq_ES-E14_H3K4me1_E0

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: line

value: mouse

value: mouse embryonic stem cells

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me1

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

value: Abcam

value: Embryonic day 0 (stem cell)

tag: control description

tag: strain

tag: strain description

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


title: LICR_ChipSeq_CH12_H3K4me1_immortalized

value: LICR-m

tag: cell organism

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: antibody targetdescription

tag: age

value: immortalized

value: immortalized cell line

tag: controlid

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_CH12_H3K4me2_immortalized

value: Ren - Ludwig Institue for Cancer Research

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me2

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

tag: antibody vendorname

tag: antibody vendorid

tag: control

value: std

value: Standard input signal for most experiments.

tag: labversion

value: Pooled & filtered

value: MACS


title: LICR_ChipSeq_CH12_H3K9ac_immortalized

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mouse

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: softwareversion


title: LICR_ChipSeq_CH12_H3K4me3_immortalized

value: LICR-m

tag: line

value: B-cell lymphoma (GM12878 analog)

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: control description

tag: strain

tag: strain description


title: LICR_ChipSeq_ES-Bruce4_H3K9ac_E0

value: Ren - Ludwig Institue for Cancer Research

tag: cell organism

value: mouse embryonic stem cells

tag: cell sex

value: M

tag: antibody targetdescription

value: Abcam

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Liver_Input_E14.5

tag: cell

value: Liver

tag: cell description

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: Embryonic day 14.5

tag: control

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: replicate

value: Bowtie


title: LICR_ChipSeq_ES-E14_H3K9ac_E0

tag: lab

value: LICR-m

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: line

value: mouse

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 vendorname

tag: antibody vendorid

tag: labversion

value: Pooled & filtered

tag: softwareversion

value: MACS

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


title: LICR_ChipSeq_Liver_H3K4me1_E14.5

value: Ren - Ludwig Institue for Cancer Research

value: Liver

tag: cell organism

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me1

tag: antibody targetdescription

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

value: Abcam

tag: age

tag: age description

tag: control description

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Liver_H3K27ac_E14.5

tag: lab

tag: lab description

tag: cell

tag: cell description

value: U

tag: antibody

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: Embryonic day 14.5

tag: control

value: std

value: Standard input signal for most experiments.

tag: controlid


title: LICR_ChipSeq_Liver_H3K4me3_E14.5

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mouse

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: labversion

tag: softwareversion


title: LICR_ChipSeq_B-cell_(CD43-)_Input_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

tag: cell organism

value: mouse spleen B cells, CD43-,CD11b-

tag: cell sex

value: M

value: Input

tag: antibody description

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

tag: age

tag: age description

value: Adult 8 weeks

tag: replicate

value: HCS


title: LICR_ChipSeq_BoneMarrow_H3K27ac_adult-8wks

source_name: BoneMarrow

tag: lab

tag: lab description

tag: cell

value: BoneMarrow

value: Bone Marrow

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: control description

value: Pooled & filtered

value: MACS

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Limb_H3K27ac_E14.5

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Limb

value: mouse

tag: cell description

value: U

tag: antibody

tag: antibody vendorname

tag: antibody vendorid

value: Embryonic day 14.5

tag: control

value: std

value: Standard input signal for most experiments.

tag: controlid


title: LICR_ChipSeq_WholeBrain_H3K9me3_E14.5

value: Ren - Ludwig Institue for Cancer Research

value: WholeBrain

tag: cell organism

value: Whole Brain

tag: cell sex

value: M

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

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

tag: age

tag: age description

tag: labversion

tag: softwareversion


title: LICR_ChipSeq_OlfactBulb_H3K27ac_adult-8wks

tag: lab

tag: lab description

tag: cell

value: OlfactBulb

value: Olfactory Bulb

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

value: Adult 8 weeks

tag: control description

value: Pooled & filtered

value: Peaks

tag: softwareversion description

value: Regions of enriched signal in experiment


title: LICR_ChipSeq_Thymus_H3K4me1_adult-8wks

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Thymus

value: mouse

tag: cell description

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me1

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

tag: antibody vendorname

value: std

value: MACS

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Thymus_H3K27ac_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

value: tissue

tag: cell organism

value: thymus

tag: Sex

value: M

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody vendorid

tag: age

tag: age description

tag: control

value: Standard input signal for most experiments.

tag: controlid


title: LICR_ChipSeq_WholeBrain_H3K4me1_E14.5

tag: lab

tag: lab description

value: Whole Brain

value: not determined

tag: antibody antibodydescription

tag: antibody targetdescription

value: Abcam

value: Embryonic day 14.5

tag: labversion

value: Pooled & filtered

tag: softwareversion


title: LICR_ChipSeq_Cortex_H3K27ac_adult-8wks

source_name: Cortex

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Cortex

value: mouse

tag: cell description

tag: cell sex

tag: antibody

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

value: Adult 8 weeks

tag: control description


title: LICR_ChipSeq_Cerebellum_H3K27ac_adult-8wks

source_name: Cerebellum

value: Ren - Ludwig Institue for Cancer Research

value: Cerebellum

tag: cell organism

tag: antibody vendorname

tag: antibody vendorid

tag: age

value: std

value: MACS

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Heart_H3K27ac_adult-8wks

tag: lab

tag: lab description

value: tissue

value: heart

tag: Sex

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: age description

tag: control

value: Standard input signal for most experiments.

tag: controlid


title: LICR_ChipSeq_WholeBrain_H3K27ac_E14.5

value: LICR-m

tag: datatype

tag: datatype description

value: Whole Brain

value: not determined

tag: antibody targetdescription

value: Abcam

value: Embryonic day 14.5

tag: labversion

value: Pooled & filtered

tag: softwareversion


title: LICR_ChipSeq_CH12_H3K36me3_immortalized

value: ChipSeq

value: Chromatin IP Sequencing

tag: line

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K36me3

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

tag: antibody vendorname

value: immortalized

value: immortalized cell line

tag: control description


title: LICR_ChipSeq_Kidney_H3K27ac_adult-8wks

source_name: Kidney

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: cell

value: Kidney

value: M

value: rabbit polyclonal. Antibody Target:H3K27ac

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

tag: antibody vendorid

tag: age

value: Adult 8 weeks

value: std

value: MACS

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Cerebellum_H3K27me3_adult-8wks

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Cerebellum

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

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

value: Millipore

tag: age description

tag: control

value: Standard input signal for most experiments.

tag: controlid

value: Pooled & filtered


title: LICR_ChipSeq_B-cell_(CD43-)_H3K27me3_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

tag: cell organism

value: mouse

tag: cell description

value: mouse spleen B cells, CD43-,CD11b-

tag: cell sex

tag: antibody

tag: labversion

tag: softwareversion


title: LICR_ChipSeq_Limb_H3K4me3_E14.5

tag: lab

tag: lab description

tag: cell

value: Limb

value: U

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: antibody vendorname

tag: antibody vendorid

value: Embryonic day 14.5

tag: control description


title: LICR_ChipSeq_Limb_H3K4me1_E14.5

value: LICR-m

tag: datatype

tag: datatype description

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me1

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

value: Abcam

tag: age

value: std

value: MACS

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_OlfactBulb_H3K4me1_adult-8wks

value: ChipSeq

value: Chromatin IP Sequencing

value: OlfactBulb

tag: cell organism

tag: cell description

value: Olfactory Bulb

value: M

tag: antibody targetdescription

tag: age description

value: Adult 8 weeks

tag: control

value: Standard input signal for most experiments.

tag: controlid

value: Peaks

tag: softwareversion description

value: Regions of enriched signal in experiment


title: LICR_ChipSeq_SmIntestine_H3K4me3_adult-8wks

source_name: SmIntestine

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: tissue

value: mouse

value: Small Intestine

tag: Sex

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: labversion

value: Pooled & filtered

tag: softwareversion


title: LICR_ChipSeq_Testis_H3K27ac_adult-8wks

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

value: Testis

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: std

tag: control description

value: MACS

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_MEL_H3K4me3_immortalized

value: Ren - Ludwig Institue for Cancer Research

value: Chromatin IP Sequencing

tag: line

value: MEL

tag: cell organism

tag: cell description

value: Leukemia (K562 analog)

value: M

tag: antibody targetdescription

tag: age

value: immortalized

value: immortalized cell line

tag: control

value: Standard input signal for most experiments.

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: LICR_ChipSeq_Testis_H3K4me3_adult-8wks

tag: lab

value: LICR-m

tag: lab description

value: ChipSeq

value: Testis

value: mouse

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: age description

value: Adult 8 weeks

tag: controlid

tag: labversion

value: Pooled & filtered

tag: softwareversion


title: LICR_ChipSeq_Thymus_H3K4me3_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: tissue

value: thymus

tag: Sex

tag: antibody antibodydescription

tag: antibody vendorname

tag: antibody vendorid

value: std

value: MACS

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Kidney_H3K27me3_adult-8wks

tag: cell organism

value: kidney

value: M

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

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

tag: age

tag: control description

value: Standard input signal for most experiments.


title: LICR_ChipSeq_Testis_H3K4me1_adult-8wks

tag: lab

value: LICR-m

value: ChipSeq

value: mouse

value: Testis

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: strain

tag: strain description


title: LICR_ChipSeq_WholeBrain_H3K4me3_E14.5

source_name: WholeBrain

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: Chromatin IP Sequencing

value: tissue

value: Whole Brain

value: not determined

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: age description

value: Embryonic day 14.5

tag: controlid

value: Pooled & filtered


title: LICR_ChipSeq_SmIntestine_H3K4me1_adult-8wks

value: LICR-m

tag: datatype

tag: datatype description

tag: cell

value: SmIntestine

tag: cell description

value: Small Intestine

tag: cell sex

value: M

value: Adult 8 weeks

value: std

value: Standard input signal for most experiments.

tag: labversion

tag: softwareversion

value: MACS

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_BMDM_H3K27ac_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

value: BMDM

tag: cell organism

value: mouse

value: Bone marrow derived macrophage

value: F

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: age


title: LICR_ChipSeq_BAT_H3K4me3_adult-24wks

tag: lab

value: LICR-m

tag: lab description

value: BAT

value: Brown adipocytes tissue

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

value: Adult 24 weeks

tag: control

tag: control description

value: Pooled & filtered

tag: strain

tag: strain description


title: LICR_ChipSeq_WholeBrain_Input_E14.5

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

value: WholeBrain

value: Whole Brain

value: U

tag: antibody

value: Input

tag: antibody description

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

tag: age description

value: Embryonic day 14.5

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: replicate

value: Bowtie

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_WholeBrain_H3K36me3_E14.5

value: LICR-m

value: Chromatin IP Sequencing

value: tissue

tag: cell organism

value: mouse

tag: Sex

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: labversion

tag: softwareversion

value: MACS


title: LICR_ChipSeq_SmIntestine_H3K36me3_adult-8wks

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: SmIntestine

tag: cell description

value: Small Intestine

tag: cell sex

tag: antibody vendorid

tag: age

value: Adult 8 weeks

tag: control

tag: control description

value: Pooled & filtered

tag: strain


title: LICR_ChipSeq_MEL_H3K4me1_immortalized

tag: datatype

tag: datatype description

tag: line

value: MEL

value: Leukemia (K562 analog)

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me1

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

value: immortalized

value: immortalized cell line

value: std

value: Standard input signal for most experiments.

tag: controlid

value: Unknown

tag: strain description

value: Unknown strain origin


title: LICR_ChipSeq_BAT_H3K27ac_adult-24wks

value: LICR-m

value: Chromatin IP Sequencing

tag: cell

value: BAT

tag: cell organism

value: mouse

value: Brown adipocytes tissue

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

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

tag: antibody vendorname

value: Abcam

tag: age description

value: Adult 24 weeks

tag: labversion

value: MACS

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_BMDM_H3K4me3_adult-8wks

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: BMDM

tag: cell description

value: Bone marrow derived macrophage

tag: cell sex

value: F

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

tag: antibody vendorid

tag: age

value: Adult 8 weeks

value: Pooled & filtered

tag: softwareversion


title: LICR_ChipSeq_Testis_H3K36me3_adult-8wks

value: LICR-m

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: Testis

value: mouse

value: M

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K36me3

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

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: strain


title: LICR_ChipSeq_Kidney_H3K36me3_adult-8wks

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: cell

value: Kidney

tag: cell organism

tag: antibody antibodydescription

tag: antibody targetdescription

value: Abcam

tag: controlid

value: MACS

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Thymus_H3K36me3_adult-8wks

tag: lab

tag: lab description

value: tissue

value: thymus

tag: Sex

tag: antibody vendorname

tag: age description

value: Adult 8 weeks

tag: labversion