title: UT-A_ChipSeq_A549_CTCF

value: ChipSeq

value: Chromatin IP Sequencing

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

value: Rabbit polyclonal. Antibody Target:CTCF

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

value: Millipore

value: fseq v 1.84, iff_A549,baseAlignCounts.pl v 1,p-value cutoff:0.05


title: UT-A_ChipSeq_GM12891_CTCF

status: Public on Oct 25 2011

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

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

tag: datatype

tag: datatype description

tag: cell description

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

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

tag: replicate

value: align_on_cluster_bwa.pl v 1

tag: replicate description

value: tier 1


title: wild-type_rep2

city: BETHESDA

first: HARSHA

middle: KARUR

last: RAJASIMHA

state: MD

address: 6 CENTER DR RM 303D

department: ITMB

institute: NEI

description: RNA-seq of wild type mouse retina

library_source: transcriptomic

data_processing: Illumina Casava1.7 software, BWA, Partek

molecule: total RNA

organism: Mus musculus

source_name: Retina

growth_protocol: Normal mouse growth protocol.

extract_protocol: Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.

tag: strain

tag: genotype

value: wild type

tag: age

value: post natal day 21

tag: tissue

value: Retina


title: Nrl-KO_rep1

description: RNA-seq of Nrl-/- mouse retina

value: Nrl-/-


title: wild-type_rep1

description: RNA-seq of wild type mouse retina


title: UT-A_ChipSeq_GM12878_CTCF

tag: datatype

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

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_GM12878,p-value cutoff:0.05,1% ENCODE array platform validation tests


title: UT-A_ChipSeq_MCF-7_estrogen_CTCF

treatment_protocol: estrogen

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

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

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

value: estrogen

value: 45 min with 100 nM Estradiol (Crawford)

tag: antibody

value: CTCF

value: rabbit polyclonal


title: UT-A_ChipSeq_HUVEC_Pol2

source_name: HUVEC

tag: treatment

value: No special treatment or protocol applies

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_HUVEC

value: mouse monoclonal, clone 8WG16

value: HUVEC/Input


title: UT-A_ChipSeq_MCF-7_estrogen_c-Myc

tag: cell description

value: Rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:MYC

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: Santa Cruz Biotechnology

tag: treatment description

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin

value: Santa Cruz Biotech

value: align_on_cluster_bwa.pl v 1

value: tier 1


title: UT-A_ChipSeq_K562_c-Myc

value: ChipSeq

value: Chromatin IP Sequencing

tag: antibody antibodydescription

tag: antibody targetdescription

value: baseAlignCounts.pl v 1,p-value cutoff:0.01,1% ENCODE array platform validation tests,fseq v 1.84, iff_K562


title: UT-A_ChipSeq_A549_Pol2

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

value: No special treatment or protocol applies

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody vendorname

tag: antibody vendorid

value: fseq v 1.84, iff_A549,baseAlignCounts.pl v 1,p-value cutoff:0.05


title: UT-A_ChipSeq_HeLa-S3_c-Myc

tag: cell lineage

value: ectoderm

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,p-value cutoff:0.01,fseq v 1.84, iff_HelaS3,1% ENCODE array platform validation tests


title: UT-A_ChipSeq_HepG2_CTCF

value: hepatocellular carcinoma

value: Rabbit polyclonal. Antibody Target:CTCF

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

value: Millipore

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HepG2,p-value cutoff:0.05,1% ENCODE array platform validation tests

tag: replicate

tag: replicate description


title: UT-A_ChipSeq_MCF-7_Input

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

value: fseq v 1.84

tag: cell karyotype

value: cancer

tag: cell sex

value: F

value: Input

tag: antibody description

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


title: UT-A_ChipSeq_HeLa-S3_CTCF

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HelaS3,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: align_on_cluster_bwa.pl v 1

value: tier 1


title: UT-A_ChipSeq_HUVEC_CTCF

tag: treatment

value: No special treatment or protocol applies

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff:0.05,fseq v 1.84, iff_HUVEC

value: rabbit polyclonal

value: HUVEC/Input


title: UT-A_ChipSeq_HepG2_Pol2

tag: cell description

value: hepatocellular carcinoma

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance


title: UT-A_ChipSeq_HUVEC_Input

tag: treatment description

value: fseq v 1.84

value: umbilical vein endothelial cells

value: normal

value: mesoderm

value: U

tag: antibody


title: UT-A_ChipSeq_GM19238_CTCF

value: ChipSeq

value: Chromatin IP Sequencing

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

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

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

value: Millipore

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female


title: Total_RNA_Seq_Female_2

city: Milan

first: Giulio

last: Pavesi

address: Via Celoria 26

department: Biosciences

country: Italy

institute: Università di Milano

description: total whole body RNA-Seq

data_processing: Reads were mapped on the genome using the seqmap tool allowing at most one substitution per read. Reads were assigned to genes according to genomic coordinates using the FlyBase 5.12 annotation. Sequences from replicate experiments were pooled together. Enrichment of the IP samples with respect to the IgG control was computed using a 2x2 Chi-Square table.

organism: Drosophila melanogaster

source_name: whole body RNA

extract_protocol:
RNA from UNR immunoprecipitates was extracted with Trizol (Invitrogen). Immunoprecipitation from total extracts was performed using protein A-magnetic beads (Invitrogen). After extensive washing with 1xNET (50 mM TRISxHCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% NP40), beads were resuspended in elution buffer (50 mM Tris-HCl, pH 7.4, 5 mM EDTA, 10 mM DTT, 1% SDS) and treated with 40 µg proteinase K. RNA was then extracted from the supernatant using Trizol, precipitated and treated with DNase (TURBODNA free kit, Ambion). The amount of RNA was assessed by Nanodrop measurement. The quality of the RNA was assessed in  Bioanalyzer (Agilent Technologies). The efficiency of immunoprecipitation and the integrity of UNR were monitored by Western blot.
The UNR antibody was generated as described in Abaza et al. 2006. Genes Dev 20: 380-389 (Pubmed PMID 16452509). Is a rabbit polyclonal antibody. Purified anti-UNR IgG was used. The non-specific rabbit IgG was from Sigma, catalog num: I5006.
Sequencing of the Drosophila transcriptome was performed from total RNA of adult male and female flies following the RNA-Seq protocols. RIP-Seq samples were produced with the Solexa NlaIII protocol.

treatment_protocol: Adult male and female flies of mixed ages were manually separated, snap-frozen and grinded in liquid nitrogen.

tag: tissue

value: female whole body

tag: library strategy

value: RNA-Seq

tag: ip antibody


title: Total_RNA_Seq_Male_2

description: total whole body RNA-Seq

value: male whole body


title: UT-A_ChipSeq_K562_Pol2

value: No special treatment or protocol applies

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

tag: antibody vendorname

tag: antibody vendorid

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff:0.05,fseq v 1.84, iff_K562

value: mouse monoclonal, clone 8WG16

value: align_on_cluster_bwa.pl v 1

value: tier 1


title: Total_RNA_Seq_Female_1

description: total whole body RNA-Seq


title: UT-A_ChipSeq_GM19239_CTCF

value: ChipSeq

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

tag: replicate

tag: replicate description


title: UT-A_ChipSeq_GM19240_CTCF

tag: datatype

value: Chromatin IP Sequencing

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


title: UT-A_ChipSeq_H1-hESC_c-Myc

growth_protocol: missing

tag: datatype description

value: Rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:MYC

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

value: Santa Cruz Biotechnology

value: baseAlignCounts.pl v 1,p-value cutoff:0.01,fseq v 1.84, iff_generic_male

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin

value: Santa Cruz Biotech


title: UT-A_ChipSeq_GM12878_Pol2

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

tag: treatment

value: No special treatment or protocol applies

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: Covance

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_GM12878,p-value cutoff:0.05,1% ENCODE array platform validation tests


title: Total_RNA_Seq_Male_1

description: total whole body RNA-Seq

value: male whole body

value: RNA-Seq


title: UT-A_ChipSeq_HeLa-S3_Pol2

value: ChipSeq

tag: cell lineage

value: ectoderm

value: RNA Polymerase II

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HelaS3,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: align_on_cluster_bwa.pl v 1

value: tier 1


title: UT-A_ChipSeq_Gliobla_Input

source_name: Gliobla

value: Chromatin IP Sequencing

tag: treatment description

value: fseq v 1.84

tag: cell description

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)

tag: cell karyotype

value: cancer

tag: cell sex

value: U

value: Input

tag: antibody description

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

value: Gliobla/Input


title: Clark standard

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing: The 75 bp reads were mapped to the 78,744 Glyma cDNA gene models using Bowtie with up to 3 mismatches allowed and up to 25 alignments.  A total of the 91.4 and 88.7 million reads were generated in each lane of Illumina sequencing for the CS and CG libraries, respectively. Of these, 65.4 (71%) and 70.3 (79%) million reads aligned to the 78,744 target Glyma models with the Bowtie criteria used. RNA-Seq data was normalized in reads per kilobase of gene model per million mapped reads (RPKM). RPKM values included in sample supplementary files. Glycine max (soybean) cDNA models (Glyma models) from soybean genome from Joint Genome Institute Phytozome v.6 at  [http://www.phytozome.net/soybean.php] were used.

organism: Glycine max

source_name: shoot tip

growth_protocol: Soybean plants (Clark standard and Clark glabrous) were grown in the green house and young shoot tips were harvested from 4-week-old-multiple plants to represent biological replications. All tissues were lyophillized and stored at -70C till further use.

extract_protocol: Total RNA was extracted using standard phenol chloroform method with lithium chloride precipitation, based on the procedure from McCarty DR from 1986. RNA samples were quantified by nanodrop and the integrity was confirmed using agarose gel electrophoresis. Library construction and high-throughput sequencing was carried out using RNA-Seq technology with Illumina Ga II instrument by the Keck center, University of Illinois.

treatment_protocol: optimal green house growth conditions

tag: tissue

value: shoot tip

tag: cultivar

value: Clark standard

tag: genotype

value: wild type


title: UT-A_ChipSeq_NHEK_CTCF

source_name: NHEK

value: ChipSeq

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: rabbit polyclonal


title: TTSS/TT_replicate_1

status: Public on Oct 24 2011

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2053
small RNA sequencing

data_processing:
The 3' small RNA adapters were removed using an exact match to the first 7 bases of the adapter sequence
Processed data file build: tair9
sRNA libraries were generated from grafted Arabidopsis and aligned at the first nucleotide to 500 base pairs of the T enhancer where it is targeted by the S transgene.

organism: Arabidopsis thaliana

source_name: root tissue

growth_protocol: standard growth conditions (10hr light, 20 C)

extract_protocol: total nucleic acid (TNA) extracts were prepared from pooled shoot and root samples derived from 3-4 individual grafts according to White and Kaper, 1989. sRNAs were cloned by the Illumina sRNA cloning kit v1.5.

tag: tissue age

value: five weeks after grafting seven day-old seedlings

tag: transgene genotype

value: T transgene, homozygous


title: TTSS/TTSS_replicate_2

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2056
small RNA sequencing

source_name: shoot tissue

value: T and S transgenes, homozygous


title: TTSS/TT_replicate_2

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2054
small RNA sequencing


title: TTSS/TTSS_replicate_1

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2055
small RNA sequencing


title: TTSSdcl3/TT_replicate_1

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2049
small RNA sequencing


title: Clark glabrous

value: Clark glabrous

value: hairless mutant


title: TTSSdcl3/TT_replicate_2

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2050
small RNA sequencing


title: TTSSdcl3/TTSSdcl3_replicate_2

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2046
small RNA sequencing

value: Col-0, dcl3-5


title: TTSSdcl3/TTSSdcl3_replicate_1

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2045
small RNA sequencing


title: TT/TT_replicate_2

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2044
small RNA sequencing


title: TT/TT_replicate_1

description:
Grafted plants are described using "shoot/root" notation.
Sample name: SL 2043
small RNA sequencing


title: Chlamydomonas reinhardtii 2137 - TAP supplemented with a revised trace element recipe - 2

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description:
Illumina's RNA-Seq whole transcriptome analysis
poly-A purification, random fragmentation

data_processing:
Processed sequence files from the Solexa pipeline output were aligned against the v.3.1 assembly of the Chlamydomonas genome. The SOAP alignment program (Li et al., 2008) was used to map the short reads in two steps. In a first alignment round, the raw sequences were aligned to the genomic sequence with a tolerance of up to two mismatches and no indels. For those sequences that did not align to the genome a second round alignment was performed in which we recursively trim one base at a time (up to 21-mers or half of the read length) at either the 5’ or 3’ end of the reads until we found a (perfect) match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment. For differential expression analysis, per-base unique hits from both strands were pooled and summed across the genome to obtain gene counts.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cells were cultured under continuous light of ~50-90 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium supplemented with a revised trace element recipe.

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina by whole transcriptome analysis.

treatment_protocol: Cells grown on TAP agar plates supplemented with Hutner's trace elements were grown to mid to late log phase (10e6-10e7 cells/ml) in TAP supplemented with a revised trace element recipe and diluted 1/100 into fresh medium.

tag: strain

tag: medium

value: TAP

tag: sequencing cycles / read length

tag: library type

value: single-end


title: Chlamydomonas reinhardtii 2137 - Copper deficient - Minimal media - 1

data_processing:
Processed sequence files from the Solexa pipeline output were aligned against the v.3.1 assembly of the Chlamydomonas genome. The SOAP alignment program (Li et al., 2008) was used to map the short reads in two steps. In a first alignment round, the raw sequences were aligned to the genomic sequence with a tolerance of up to two mismatches and no indels. For those sequences that did not align to the genome a second round alignment was performed in which we recursively trim one base at a time (up to 21-mers or half of the read length) at either the 5’ or 3’ end of the reads until we found a (perfect) match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment. For differential expression analysis, per-base unique hits from both strands were pooled and summed across the genome to obtain gene counts. Additional normalization was performed to estimate gene expression levels.

molecule: polyA RNA

growth_protocol: Cultures were grown in Tris-acetate-phosphate (TAP), or minimal medium (TP) at 24 C with shaking (180 rpm), and under continuous light (~90x10-6mol/m2/s)

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina by either the NlaIII tag protocol or by whole transcriptome analysis.

treatment_protocol: Inoculum cultures were maintained under copper-deficient conditions. The minimal medium cultures were under constant aeration. Cells were collected at a density of 3x106 cell ml-1 (steady-state).

tag: genetic background

value: Chlamydomonas reinhardtii 2137

value: wt

tag: treatment

value: copper deficient

value: Minimal media

tag: analysis

value: Illumina's RNA-Seq whole transcriptome analysis

value: paired-end

tag: mean/std insert size


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 1

value: copper sufficient

value: Illumina's Digital Gene Expression


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 10


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 2


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 9


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 1


title: Chlamydomonas reinhardtii 2137 - TAP supplemented with a revised trace element recipe - 1


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - Minimal media - 1


title: Chlamydomonas reinhardtii 2137 - Copper deficient - Minimal media - 3


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 10


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 7


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 9


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 8


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 7


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 2


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - Minimal media - 3


title: Chlamydomonas reinhardtii crr1:CRR1 - Copper deficient - TAP - 2


title: Chlamydomonas reinhardtii crr1-2 - Copper deficient - TAP - 2


title: Chlamydomonas reinhardtii crr1:CRR1 - Copper deficient - TAP - 1


title: Chlamydomonas reinhardtii crr1-2 - Copper deficient - TAP - 1


title: Chlamydomonas reinhardtii crr1-2 - Copper deficient - TAP - 4


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 8


title: Chlamydomonas reinhardtii crr1-2 - Copper deficient - TAP - 3


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 5


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 3


title: S2_roX2_input

status: Public on Oct 21 2011

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: ChIRP-seq of roX2 from S2 cells

data_processing: Briefly, raw reads from "even" and "odd" in each samples were aligned using "Bowtie," and merged so that only signals common in both "even" and "odd" are retained (merge.wig files). These files were then converted into SAM formats for peaking calling by MACS. For complete methods please refer to the paper.

growth_protocol: Drosophila cell line: 10% Heat-Inactivated FBS in Schneider medium (pen/strep). Human cell lines: 10% FBS in DMEM (pen/strep)

extract_protocol: Cells are crosslinked in 1% glutaraldehyde and lysates clarified by sonication. lincRNA:chromatin adducts are isolated using specific probes. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

tag: cell type

value: modENCODE isolate of Schneider's line 2

tag: lincrna probes


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 6

tag: genotype


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 6


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 3


title: S2_roX2_odd

description: ChIRP-seq of roX2 from S2 cells


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 5


title: S2_roX2_even

description: ChIRP-seq of roX2 from S2 cells


title: HeLa_odd

description: ChIRP-seq of TERC from HeLa cells

source_name: HeLa

value: HeLa

value: HeLa S3 cells

value: TERC


title: MDA-231-LacZ

description: ChIRP-seq of HOTAIR from MDA-231 cells

value: MDA-231 cell line overexpressing human HOTAIR using LacZ probe

value: LacZ


title: HeLa_even

description: ChIRP-seq of TERC from HeLa cells


title: MDA-231_shEZH2_HOTAIR_even

description: ChIRP-seq of HOTAIR from MDA-231 cells (shEZH2)

value: MDA-231 cell line overexpressing human HOTAIR with EZH2 knocked down

value: HOTAIR


title: MDA-231_HOTAIR_input

description: ChIRP-seq of HOTAIR from MDA-231 cells

value: MDA-231 cell line overexpressing human HOTAIR


title: MDA-231_HOTAIR_even

description: ChIRP-seq of HOTAIR from MDA-231 cells


title: MDA-231_HOTAIR_odd

description: ChIRP-seq of HOTAIR from MDA-231 cells


title: HeLa_Terc_odd

description: ChIRP-seq of TERC from HeLa cells

value: HeLa S3 cells overexpressing human telomerase and TERC


title: HeLa_Terc_even

description: ChIRP-seq of TERC from HeLa cells


title: HeLa_Terc_input

description: ChIRP-seq of TERC from HeLa cells


title: RWPE1 FLAG ETV1

status: Public on Oct 20 2011

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

data_processing: Software from the Useq package was used to identify peaks.  ElandParser mapped sorted.txt files and SamParser mapped fastq files.  FilterPointData was used to remove reads mapping to repeat regions included in the satellite repeat track from the UCSC genome browser. PeakShift finder was used to measure the shift in peak location between each DNA strand.  Peak shifts were JunD:250, ETV1:100, ETS1:270, ERG:270, ETV4:260, GABPA:250.  ScanSeqs used a sliding window of approximately twice the peak shift to score enrichment across the genome and adjusted reads by the peak shift to remove peak shift bias.  Windows were 500 bp for all samples except ETV1 which was 250 bp.  Enriched regions maker identified enriched regions.  Significance was determined by calculating a bionomial P value for each window and controlled for multiple testing by calculating an empirical false discovery rate.

growth_protocol: Growth according to ATCC

extract_protocol: Libraries were constructed using the Illumina ChIP-seq kit following the included protocol

tag: antibody

value: FLAG(Sigma, cat# F1804, lot# 080M6035)

tag: retroviral expression


title: Normal prostate fibroblasts (NPF)

status: Public on Oct 22 2011

city: Edinburgh

first: Axel

last: Thomson

address: 47 Little France Crescent

institute: MRC Human Reproductive Sciences Unit

data_processing: Tags were mapped to the human genome using HG201

source_name: Normal prostate fibroblasts (NPF)

growth_protocol: CAF and NPF were grown in vitro, and tested for pro-tumorigenic signalling via recombination with BPH1 epithelia in vivo.

extract_protocol: Solexa protocol

tag: tissue

value: Prostate

tag: developmental stage

value: Adult

value: Fibroblasts


title: RWPE1 Input


title: Richmond 2

status: Public on Oct 19 2011

city: Blacksburg

first: Zach

middle: N.

last: Adelman

state: VA

address: 305 Fralin Life Science Institute

department: Entomology

institute: Virginia Tech

data_processing:
Raw sequencing reads from the Harlan (both male and female) and Richmond (male) strain bed bugs were assembled using the NEWBLER assembler either individually or together. Assembled contigs were converted into a BLAST database (Altschul et al 1997) and queried with P450, carboxylesterase and GST sequences. RNA sequences that did not match tRNA or rRNA sequences were mapped to an assembled bed bug transcriptome, only unique hits with at least 75bp of matching sequence were accepted.
For Newbler contigs, reads counts indicate the number of sequences used to assemble each contig. For P50, CE, and GST contigs, read counts indicate the number of mapping sequences using NCBI-BLAST (blastn). Only best scoring hits (defined as the lowest e-value) that did not match tRNA, rRNA sequences and had at least 75bp of matching sequence were accepted.

organism: Cimex lectularius

source_name: Adult (male only)

growth_protocol: Adult bed bugs were frozen in liquid nitrogen at seven days after the last molt and stored at -80Â°C until use

extract_protocol: Bed bugs were homogenized and total RNA extracted using TRIzol (Invitrogen, Carlsbad, CA). Bed bug mRNA was enriched from the total RNA sample using the PolyATract mRNA Isolation System (Promega BioSciences, San Luis Obispo, CA). Libaries were constructed from total polyA RNA by the Virginia Bioinformatics Institute according to standard protocols

value: 7 days post eclosion

tag: pyrethroid-resistance status

value: Insecticide resistant


title: Harlan 2

source_name: Adult (male and female)

value: Insecticide susceptible


title: RWPE1 FLAG ERG

value: FLAG-ERG


title: Richmond 1


title: Cancer-associated fibroblasts (CAF)

source_name: Cancer-associated fibroblasts (CAF)


title: Harlan 1


title: RWPE1 GABPA

value: GABPA(Santa Cruz Biotechnology, cat# sc-22810, lot# B2009)


title: Fetal prostate (EMB)

source_name: Fetal prostate (EMB)

value: Fetal

value: Fibroblasts and Epithelia


title: RWPE1 ETS1

value: ETS1(Santa Cruz Biotechnology, cat# sc-350, lot# E1010)


title: Su(Hw) f - IP

city: Iowa City

first: Alexey

middle: A

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

description: chromatin IP against Su(Hw)

data_processing:
Alignment: Sequence reads were obtained and mapped to the Drosophila (dm3) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Partek Genomics Suite version 6.5 (Partek Inc., St. Louis, MO, USA, www.partek.com)

growth_protocol: Newly eclosed virgin female flies were collected in the morning and dissected within 6 hours of eclosion. Dissected ovaries were kept on ice during the dissection and frozen at -80C for storage.

extract_protocol: Ovaries were cross-linked with 1.8% formaldegyde and Su(Hw)-DNA complexes were isolated with anti-Su(Hw) guinea pig antibody (Baxley et al., 2011).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

value: su(Hw)fv

value: ovary

value: less than 6 hour old virgin

value: anti-Su(Hw)


title: Su(Hw) f - preimmune

description: chromatin IP with preimmune serum


title: Su(Hw) wild type - input

description: input chromatin

value: Canton S


title: Su(Hw) wild type - preimmune

description: chromatin IP with preimmune serum


title: PC3 JUND

value: JUND(Santa Cruz Biotechnology, cat# sc-74, lot# C0310)


title: PC3 ETV4

value: ETV4(Aviva Systems Biology, cat# ARP32263, lot# QC1723)


title: RWPE1 FLAG control

value: FLAG(Sigma, cat# F1804, lot# 080M6035)


title: Su(Hw) f - input

description: input chromatin


title: SuUR-/- larval salivary gland rep 2

status: Public on Oct 18 2011

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

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

source_name: third instar larval salivary gland

extract_protocol: Tissues were lysed by homogenization in TRIzol reagent and RNA was prepared as indicated in the manufactures protocol. PolyA-selected RNA from 10 ug of total RNA was used to generate a cDNA library for Illumina based mRNA-sequencing according to the manufactures protocol.

value: salivary gland

value: SuUR-/-


title: larval salivary gland rep 2

value: OregonR


title: Glycine max inoculated Root Hair

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
GMA06b
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

data_processing: Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances . Twenty-one small RNA libraries were made the materials described above, representing four legume species, including eight libraries from M. truncatula, seven from Glycine max (soybean), two from Arachis hypogaea (peanut), and four from Phaseolus vulgaris (common bean); one PARE library was made from Medicago flower.These libraries were sequenced on an Illumina GAII, generating ~62 million small RNA sequences after removing adapters and low-quality reads, with trimmed lengths between 18 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), 12.1 million and 12.6 million reads were mapped to the M. truncatula genome (Mt3.5) (http://www.medicago.org) and the Glycine max genome (Gmax101) (Schmutz et al., 2010), respectively.

source_name: Root Hair

extract_protocol: Medicago small RNA libraries (except MTR01) were constructed and sequenced at Illumina; all other legume libraries plus MTR01 were constructed as previously described (Lu et al. 2007) and sequenced on an Illumina Genome Analyzer II instrument at the Delaware Biotechnology Institute. PARE library was constructed as previously described (German et al. 2008)

tag: accession/ecotype

value: Williams 82

value: Root Hair


title: larval salivary gland rep 1


title: USC_ChipSeq_PANC-1_Input_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment description

value: No special treatment or protocol applies

value: Input

tag: antibody description

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

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate


title: Su(Hw) wild type - IP

description: chromatin IP against Su(Hw)

tag: strain

value: Canton S

tag: tissue

value: ovary

tag: developmental stage

value: less than 6 hour old virgin

tag: antibody

value: anti-Su(Hw)


title: SuUR_3SG_orc2_ChIP

data_processing:
Alignment: Images acquired were processed by the bundled Illumina image extraction pipeline v1.6 and mRNA-Seq reads were aligned to BDGP Release 5/DM3 using ELAND, using the first 25 bases of a read as a seed.  Each matched seed was then extended up to 36 bases and scored to break any ties between multi-matches.  For mRNA expression counts, unique reads in the genome that landed within any known exons were counted.  The counts were normalized by the mRNA length to get the final RPKM values (reads per KB per million reads).
Peaks: The ChIPâseq reads were mapped back to the Drosophila melanogaster genome (Flybase v.5.2) using MAQ (v.0.7.1) with a maximum of three mismatches per read. For the SG cells, we then used the SPP package to remove anomalous reads and detect peaks using the WTD method. We used maximum estimated enrichment cutoffs of 2.105 and 2.092 in the OrR and SuUR mutant samples respectively  as determined by the SPP packagesâs MSER function.

source_name: third instar salivary gland from SuUR

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

extract_protocol: DNA was prepared using Illumina ChIP sample prep kit  according to instructions.

treatment_protocol: Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium and frozen within less than 30 min in liquid nitrogen. When enough were collected, ChIP was performed with anti-orc2 from Steve Bell lab (MIT)

tag: genotype

value: SuUR

value: orc2 (steve bell lab, MIT)

value: third instar salivary gland


title: OrR_3SG_orc2_ChIP

source_name: third instar salivary gland from OrR

value: OrR


title: USC_ChipSeq_PANC-1_H3K4me1_(pAb-037-050)_UCDavis

value: immortalized cell line

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: line

value: human

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

tag: treatment

tag: antibody antibodydescription

value: Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide. Antibody Target:H3K4me1

tag: antibody targetdescription

value: Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution.Histone tails undergo numerous posttranslational modifications. This antibodies recognizes histone H3 monomethylated on lysine 4.

tag: antibody vendorname

value: Diagenode

tag: antibody vendorid


title: Phaseolus vulgaris Dev.Seed

description:
PVU04
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Phaseolus vulgaris


title: USC_ChipSeq_PANC-1_H3K27ac_UCDavis

tag: cell

tag: cell organism

tag: cell description

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment description

value: No special treatment or protocol applies

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: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid


title: H54_cMYC_REP2

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: Chromatin IP against c-Myc

data_processing: peaks were identified using a Parzen window based algorithm as described previously with minor modifications (Shivaswamy et al. 2008. PLoS Biol 6: e65. )

source_name: glioblastoma

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA, library fragments of ~230 bp (insert plus adaptor and PCR primer sequences) were selected from an agarose gel.  The final size-selected lib. was amplified by 15 cycle of PCR followed by column purification of amplified DNA. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution (Bhinge et al. 2007; Birney et al. 2007). Immunoprecipitated DNA were sequenced using Illumina sequencers, (ChIP-seq). Input sequencing data were generated for GM12878, K562, HeLa-S3, HepG2, and HUVEC by cross-linking chromatin, shearing and reversing cross-links without immunoprecipitating.

tag: cell type

value: glioblastoma

tag: cell line

tag: antibody

value: cMYC

tag: antibody (vender, cat#, lot#)

value: Santa Cruz, sc-764X, K1810


title: H54_CTCF_REP2

description: Chromatin IP against CTCF

value: CTCF


title: H54_Pol2_REP1

description: Chromatin IP against Pol2


title: H54_CTCF_REP1

description: Chromatin IP against CTCF


title: SuUR-/- larval salivary gland rep1

tag: tissue

value: salivary gland

tag: strain

value: SuUR-/-


title: H54_cMYC_REP1

description: Chromatin IP against c-Myc


title: FB0167P_Pol2_REP2

description: Chromatin IP against Pol2

source_name: Progeria fibroblast

value: Progeria fibroblast


title: PC3 Input

tag: retroviral expression


title: FB0167P_cMYC_REP1

description: Chromatin IP against c-Myc

value: Santa Cruz, sc-764X, C1309


title: FB0167P_CTCF_REP1

description: Chromatin IP against CTCF


title: FB0167P_Pol2_REP1

description: Chromatin IP against Pol2


title: Glycine max Williams 82 uninoculated Root Hair

description:
GMA05b
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: uninoculated Root Hair

tag: accession/ecotype

value: Williams 82

value: uninoculated Root Hair


title: FB8470_INPUT

description: Chromatin Input

source_name: Normal child fibroblasts

value: Normal child fibroblasts

value: INPUT


title: FB8470_cMYC_REP1

description: Chromatin IP against c-Myc


title: FB8470_cMYC_REP2

description: Chromatin IP against c-Myc


title: MCF7_INPUT

description: Chromatin Input

source_name: breast adenocarcinoma cells

value: breast adenocarcinoma cells


title: FB0167P_CTCF_REP2

description: Chromatin IP against CTCF


title: FB8470_CTCF_REP1

description: Chromatin IP against CTCF


title: H54_Pol2_REP2

description: Chromatin IP against Pol2


title: MCF7_Pol2_REP2

description: Chromatin IP against Pol2


title: FB8470_CTCF_REP2

description: Chromatin IP against CTCF


title: MCF7_cMYC_REP2

description: Chromatin IP against c-Myc


title: MCF7_cMYC_REP1

description: Chromatin IP against c-Myc


title: MCF7_CTCF_REP1

description: Chromatin IP against CTCF


title: MCF7_Pol2_REP1

description: Chromatin IP against Pol2


title: Glycine max Williams 82 inoculated Stripped Root

description:
GMA07b
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: inoculated Stripped Root

value: inoculated Stripped Root


title: H54_INPUT

description: Chromatin Input


title: MCF7_CTCF_REP2

description: Chromatin IP against CTCF


title: FB0167P_INPUT

description: Chromatin Input


title: HY_RNA-Seq

first: Jae-Hyung

last: Lee

address: 611 Charles E. Young Drive

department: Department of Integrative Biology and Physiology

institute: University of California, Los Angeles

description: Reversetranscribed from mRNA of TAC mice at HY stage, Paired-end RNAseq

data_processing: processed_data not provided

source_name: TAC mice at hypertrophy stage

extract_protocol: We used the standard Illumina protocol to prepare libraries for RNA-Seq (http://www.illumina.com/support/documentation.ilmn). Briefly, 10Î¼g total RNA was first processed via poly-A selection and fragmentation. We generated first-strand cDNA using random hexamer-primed reverse transcription and subsequently used it to generate second-strand cDNA using RNase H and DNA polymerase. Sequencing adapters were ligated using the Illumina Paired-End sample prep kit. Fragments of ~200 bp were isolated by gel electrophoresis, amplified by 15 cycles of PCR and sequenced.

treatment_protocol: mRNA was prepared from left ventricle tissue of mice at hypertrophy (HY, 1week post-TAC) and heart failure (HF, 8weeks post-TAC) stages following transverse aortic constriction (TAC)

value: left ventricle tissue

tag: operation

value: transverse aortic constriction


title: SHAM-HF_RNA-Seq

description: Reversetranscribed from mRNA of SHAM mice at HF stage, Paired-end RNAseq

source_name: SHAM mice at heart failure stage

value: sham operation


title: HF_RNA-Seq

description: Reversetranscribed from mRNA of TAC mice at HF stage, Paired-end RNAseq

source_name: TAC mice at heart failure stage


title: fertile_donor3

status: Public on Oct 16 2011

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock, CS Mott Center

department: Obstetrics and Gynecology

institute: Wayne State University

data_processing: Alignment: Sequence reads obtained from Bustard (Illumina Genome Analyzer II) were mapped to the human (February, 2009) genome using Novoalign (2.05.33MT). Aligned sequence reads for each of the three samples were separated into two classes.  Those reads mapping to a unique region on the genome were classified as Uniquely Mapped (UM).  Sequence reads mapping to 2–10 locations were classified as Multiple Mapped (MM).

source_name: spermatozoa

extract_protocol: samples were thawed and the sperm cells were separated from contaminants through a 50% Percoll cushion.  The sperm cells were then processed for separate extraction of small (<200 b) and large (> 200b) RNA using Qiagen Rneasy kit

treatment_protocol: semen samples were frozen upon reception.

value: Spermatozoa


title: SHAM-HY_RNA-Seq

description: Reversetranscribed from mRNA of SHAM mice at HY stage, Paired-end RNAseq

source_name: SHAM mice at hypertrophy stage


title: Arachis hypogaea Flower

description:
AHY02
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Arachis hypogaea

source_name: Flower

value: Flower


title: fertile_donor2


title: Glycine max Dev.Seed

description:
GMA04
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences


title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; methylC-seq_h1_mesendoderm_r2b

status: Public on Oct 15 2011

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 and Activin A
Library name: methylC-seq_h1_mesendoderm_r2b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10257
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: GSM818006_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1_mesendoderm_r2b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_mesendoderm_r2b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library methylC-seq_h1_mesendoderm_r2b 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.12972
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 7
BROWSER_TRACK_NAME: HBDM BS 2b
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2b EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 206,428,327
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.5
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM818006_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1a-methylC-seq_h1-mesendoderm_r1b-methylC-seq_h1_mesendoderm_r2a-methylC-seq_h1_mesendoderm_r2b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells combined libraries 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.12976
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 7
BROWSER_TRACK_NAME: HBDM BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Combined Libraries EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 898,944,318
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.44

SPECIAL NOTE: generated from combined data in GSM818003, GSM818004, GSM818005, GSM818006 (thus .wig files on these records are identical)

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

source_name: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); methylC-seq_h1_mesendoderm_r2b

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 100-150 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16ËšC for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl final). The thermocycling parameters were: 95ËšC 2 min, 98ËšC 30 sec, then 4-8 cycles of 98ËšC 15 sec, 60ËšC 30 sec and 72ËšC 4 min, ending with one 72ËšC 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to three independent libraries from the same biological sample.

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium

tag: passage

tag: medium

value: TeSR

tag: Sex

value: Male

tag: batch

value: Replicate 2

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; methylC-seq_h1_mesendoderm_r2a

description:
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 and Activin A
Library name: methylC-seq_h1_mesendoderm_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10256
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10253
****************
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: GSM818005_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1_mesendoderm_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_mesendoderm_r2a.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library methylC-seq_h1_mesendoderm_r2a 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.12970
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 7
BROWSER_TRACK_NAME: HBDM BS 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2a EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 228,740,921
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.49
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM818005_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1a-methylC-seq_h1-mesendoderm_r1b-methylC-seq_h1_mesendoderm_r2a-methylC-seq_h1_mesendoderm_r2b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells combined libraries 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.12976
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 7
BROWSER_TRACK_NAME: HBDM BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Combined Libraries EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 898,944,318
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.44

SPECIAL NOTE: generated from combined data in GSM818003, GSM818004, GSM818005, GSM818006 (thus .wig files on these records are identical)

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

source_name: H1 cell line treated with BMP4 and Activin A biological replicate 2 (r2); methylC-seq_h1_mesendoderm_r2a

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 100-150 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl final). The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 4-8 cycles of 98C 15 sec, 60C 30 sec and 72C 4 min, ending with one 72C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to three independent libraries from the same biological sample.

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium

value: TeSR

value: 16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)


title: Medicago truncatula Flower_PARE

description:
MEDFL3all-PARE
Processed data contain distinct PARE tags with their raw abundance after removing the adapter sequences

organism: Medicago truncatula

value: Flower


title: Medicago truncatula Myc

description:
MRG1
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: Myc

value: Myc


title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; methylC-seq_h1-mesendoderm_r1b

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 and Activin A
Library name: methylC-seq_h1_mesendoderm_r1b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10255
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1_mesendoderm_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library methylC-seq_h1_mesendoderm_r1b 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.12975
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 7
BROWSER_TRACK_NAME: HBDM BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 231,518,888
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.42
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM818004_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1a-methylC-seq_h1-mesendoderm_r1b-methylC-seq_h1_mesendoderm_r2a-methylC-seq_h1_mesendoderm_r2b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells combined libraries 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.12976
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 7
BROWSER_TRACK_NAME: HBDM BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Combined Libraries EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 898,944,318
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.44

SPECIAL NOTE: generated from combined data in GSM818003, GSM818004, GSM818005, GSM818006 (thus .wig files on these records are identical)

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

source_name: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); methylC-seq_h1-mesendoderm_r1b

value: Male

value: Replicate 1

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)


title: Medicago truncatula Seeding

description:
MSDL1
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: Seeding

value: Seeding


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in Neural Progenitor Cells; renlab.H4K8ac.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK265
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10186
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM818060_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H4K8ac.AK265.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK265, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12422
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,453,485
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0463
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3279
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9412
IROC_PERCENTILE: 33
POISSON_SCORE: 0.428
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818060_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H4K8ac.AK265.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK265, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12495
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
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: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H4K8ac 65
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac Library AK265 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,453,485
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0463
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3279
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9412
IROC_PERCENTILE: 33
POISSON_SCORE: 0.428
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H4K8ac.NPC.01.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H4K8ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in Neural Progenitor Cells; renlab.H4K91ac.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK266
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10188
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM818062_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H4K91ac.AK266.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK266, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12424
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,205,506
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0359
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3067
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9416
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4045
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818062_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H4K91ac.AK266.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK266, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12497
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
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: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H4K91ac 66
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac Library AK266 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,205,506
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0359
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3067
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9416
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4045
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H4K91ac.NPC.01.01

value: Male

value: Histone H4K91ac

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in Mesenchymal Stem Cells; renlab.H4K91ac.MSC.01.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK277
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10232
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10198
****************
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: GSM818061_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H4K91ac.AK277.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.MSC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK277, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12415
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,842,488
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.1908
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2472
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9374
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4523
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818061_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H4K91ac.AK277.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.MSC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK277, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12488
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
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: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDMSC H4K91ac 77
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H4K91ac Library AK277 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,842,488
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.1908
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2472
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9374
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4523
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H4K91ac.MSC.01.01

value: H1 Derived Mesenchymal Stem Cells

value: Embryonic stem cell differentiated into mesenchymal stem cells


title: Medicago truncatula Leaf

description:
MLEF
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: Leaf

value: Leaf


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in hESC H1 Cells; renlab.H3K9me3.hESC.H1.06.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK54
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10091
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
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: GSM818057_UCSD.H1.H3K9me3.AK54.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H1.06.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on H1 Cell Line, Library AK54, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12381
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,778,009
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1788
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.172
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.8919
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2698
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

ANALYSIS FILE NAME: GSM818057_UCSD.H1.H3K9me3.AK54.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H1.06.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 Cell Line, Library AK54, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12454
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
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: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: H1 H3K9me3 54
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K9me3 Library AK54 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,778,009
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1788
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.172
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.8919
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2698
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K9me3.hESC.H1.06.01

value: H1 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: mTeSER

value: Histone H3K9me3


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in Mesenchymal Stem Cells; renlab.H4K8ac.MSC.01.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK276
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10224
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10198
****************
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: GSM818058_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H4K8ac.AK276.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.MSC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK276, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12434
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,790,108
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1987
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3052
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9573
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4831
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM818058_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H4K8ac.AK276.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.MSC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK276, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12507
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
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: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDMSC H4K8ac 76
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK276 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,790,108
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1987
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3052
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9573
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4831
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H4K8ac.MSC.01.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Publication in progress

value: Histone H4K8ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in Mesenchymal Stem Cells; renlab.H3K9ac.MSC.02.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK519
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10192
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
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: GSM818051_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K9ac.SK519.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.MSC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK519, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12391
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 88,246,833
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0984
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4151
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9062
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3473
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM818051_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K9ac.SK519.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.MSC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK519, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12464
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
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: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDMSC H3K9ac 19
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK519 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 88,246,833
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0984
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4151
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9062
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3473
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K9ac.MSC.02.01

value: Histone H3K9ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif