title: UMass-Dekker_5C_GM12878

tag: lab

value: UMass-Dekker

tag: lab description

value: Dekker - University of Massachusettes

tag: datatype

tag: datatype description

value: 5C Chromatin Interactions

value: human

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

value: mesoderm

value: F

value: ENM

value: ENCODE pilot manually-selected regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/referenceSequences/encodePilotRegions.hg19.bed)


title: GCC_processed-gDNA-Glucose - Lane 2

status: Public on Jul 19 2012

type: SRA

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
The paired end sequences were used to generate inter and intra chromosomal interaction maps
Genome Conformation Capture (GCC)
No experimental enrichment

library_source: genomic

data_processing:
Sequences were mapped onto the S. cerevisiae S288c genome  (The reference genome used in this study consists of the sixteen S. cerevisiae nuclear chromosomes [NC_001133.7, NC_001134.7, NC_001135.4, NC_001136.8, NC_001137.2, NC_001138.4, NC_001139.8, NC_001140.5, NC_001141.1, NC_001142.7, NC_001143.7, NC_001144.4, NC_001145.2, NC_001146.6, NC_001147.5, NC_001148.3] as well as the mitochondrial genome [NC_001224.1] and the 2-micron plasmid [YSCPLASM]) using Topography v1.19 which is coupled to the SOAP algorithm (Li. R., et al 2008). The GCC protocol incorporates restriction digestion (MspI) and a ligation steps to capture inter- and intra- chromosomal interactions. The Topography software aligns each "paired" sequence tag end against the genome using the SOAP algorithm with no mismatches allowed. If each sequence tag end aligns to a different MspI fragment then the Topography software records an interaction between these two MspI restriction fragments. If the sequence tag aligns uniquely to the genome it is placed into the .dat file (this means that the .dat processed data file contains only interactions which are unique), a copy of the unique interactions are also placed in the .datcomb file. If the sequence tag aligns against the genome more than once it is considered repetitive and is placed in the .datcomb file only. Interactions derived from sequence tags which aligned to multiple sites in the genome can be isolated by subtracting all the interactions in the .dat file from the .datcomb files. For further information see Rodley et al. (2009) supplemental program information. Topography is avaliable upon request from the corresponding author. The .dat files
Alignment - Topography 1.19 Proprietary Software Output files glu_pe.dat.txt and glu_pe.datcomb.txt are linked as supplementary files on the Series record.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Exponentially growing Saccharomyces cerevisiae in synthetic complete media containing glucose

growth_protocol: S. cerevisiae strain BY4741 was grown (30oC, 160 rpm) to an OD600 = 0.6 in synthetic complete media containing amino acid supplements and glucose (2% w/v).

extract_protocol: Cells were cross-linked (2% v/v formaldehyde, 10 mins, room temperature, with stirring) and quenched (0.125M glycine). Samples (residuals of 108 cells in 52.6μl) were digested (37°C, 2hr) with MspI (100U, Fermentas) in a final volume of 100 ml.  MspI was inactivated by the addition of 1% SDS (final v/v) and incubation (65°C, 20mins). Reactions were diluted in 2ml T4 ligation buffer (NEB) containing 1% Triton X-100. T4 DNA Ligase (20U, Invitrogen) was added and the reaction incubated (16°C, 2hrs). Samples were reverse cross-linked (65°C, O/N) in the presence of Proteinase K (7-11ug, Roche), 20μl EDTA (0.5M), 12μl NaCl (5M), 1.2μl Tris-HCl (1M).  RNase (20μg) was added and incubated (37°C, 15mins) prior to three Phenol:Chloroform (1:1) extractions.  Samples were purified using Zymo Clean and Concentrator columns. The sequencing centre nebulized the samples to 200bp+/-20bp. Sequencing was performed (36 bp paired end) on an Illumina Genome Analyser (Massey University, New Zealand).

tag: strain

tag: growth media

value: Glucose

tag: lane


title: UW_5C_Caco-2_UW-5C-Myc-Region

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

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=wgEncodeUw5C
library_strategy: 5C (Chromatin Conformation Capture Carbon Copy)

value: UW

value: Stamatoyannopoulous - University of Washington

tag: cell

tag: cell organism

tag: cell description

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: region

tag: region description

value: Myc upstream gene desert region used in UW 5C experiments (hg19 chr8:126445818-130737929)

tag: replicate


title: UW_5C_MCF-7_UW-5C-Myc-Region

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

value: ectoderm


title: UMass-Dekker_5C_K562

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=wgEncodeUmassDekker5C
library_strategy: 5C (Chromatin Conformation Capture Carbon Copy)

value: UMass-Dekker

value: Dekker - University of Massachusettes

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


title: GCC_processed-gDNA-Glucose - Lane 1


title: UW_5C_K562_UW-5C-Myc-Region

value: 5C Chromatin Interactions

value: human


title: UW_5C_GM12878_UW-5C-Myc-Region

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

value: normal

value: mesoderm

value: F


title: UW_5C_HepG2_UW-5C-Gene-Regions

value: UW

value: hepatocellular carcinoma

value: Set of 25 regions interrogated in UW 5C gene-targeted experiments


title: UW_5C_SK-N-SH_RA_UW-5C-Gene-Regions

value: Stamatoyannopoulous - University of Washington

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

value: cancer


title: UW_5C_BJ_UW-5C-Gene-Regions

source_name: BJ

value: BJ

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

value: M


title: UW_5C_LNCaP_UW-5C-Myc-Region

source_name: LNCaP

value: LNCaP

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

value: endoderm

value: Myc upstream gene desert region used in UW 5C experiments (hg19 chr8:126445818-130737929)


title: USC_ChipSeq_MCF-7_H3K36me3B_UCDavis

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=wgEncodeSydhHistone

value: USC

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

value: human

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

value: ectoderm

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions

tag: antibody vendorname

value: Cell Signaling

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: labversion


title: GIS-Ruan_ChiaPet_K562_CTCF

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=wgEncodeGisChiaPet
library_strategy: ChIP-Seq followed by ligation

tag: datatype

value: ChiaPet

tag: datatype description

value: Chromatin Interaction Paired-End Tags

value: Rabbit polyclonal. Antibody Target:CTCF

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

value: Millipore

tag: labexpid

tag: cell karyotype

value: cancer

value: mesoderm

value: F

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF


title: GIS-Ruan_ChiaPet_NB4_Pol2

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

value: RNA Polymerase II

value: Covance

tag: cell lineage

tag: cell sex

value: U


title: GIS-Ruan_ChiaPet_MCF-7_CTCF

tag: replicate

value: ectoderm


title: UW_5C_GM06990_UW-5C-Gene-Regions

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: 5C Chromatin Interactions

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: region

tag: region description

value: Set of 25 regions interrogated in UW 5C gene-targeted experiments


title: MR1_lactate_RNASeq

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

description: mid-log-phase MR-1 in minimal lactate

library_source: transcriptomic

data_processing:
Reads mapped to genome with bowtie
Genome_build: NC_004347.1 (main chromosome) and NC_004349.1 (megaplasmid)

molecule: total RNA

organism: Shewanella oneidensis MR-1

source_name: S. oneidensis MR-1 grown in D,L-lactate

growth_protocol: Aerobic growth to mid-logphase at 30C with shaking at 200 rpm in 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7

extract_protocol: We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3' ends with sodium periodate and we added a sequencing adaptor onto the 5' end with Ambion T4 RNA ligase.  We used random hexamer primers with a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR amplified the library to enrich for products that contained both adaptors and to complete the 5' adaptor.  We purified the PCR products and removed unincorporated nucleotides, primers, and adaptor-only products with AMPure XP Beads (Agencourt).

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

tag: media

tag: strain


title: PS1

status: Public on Jul 17 2012

city: ACTON

first: Bala

last: Thumma

state: ACT

address: Clunies Ross st

department: Plant Industry

country: Australia

institute: CSIRO

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for  low-quality sequence, then mapped to Eucalyptus grandis reference genome (v1.0) bowtie  and TopHat. TopHat was run with the default parameters except for a maximum intron length of 5000 bp.
The BAM files were used to generate transcript annotations (in gene transfer file, or GTF, format) with the Cufflinks software package. Cufflinks was run with the default parameters without supplying any annotation file. Bias detection and correction to improve the accuracy of transcript abundance was used by supplying a multi fasta file of E. grandis genome. Secondly, sequencing reads from the individual libraries were mapped against the reference genome sequence with TopHat to obtain alignment files (BAM) for each of the 12 libraries.  The BAM file from each library was analysed with the BEDTools [44] software package, which provided counts of reads mapping to different gene products (transcripts) that were represented in the annotation file (GTF). These read counts were used in edgeR package to test the differential expression of genes under control and stress conditions
Genome_build: Eucalyptus grandis version1.0
Supplementary_files_format_and_content: tab-delimited text files include read counts of predicted transcripts

organism: Eucalyptus camaldulensis

source_name: leaf_stress treatment

extract_protocol: RNA was isolated from frozen leaf tissue. Sequencing libraries were prepared with Illumina mRNA-seq library was used with 10 ug of total RNA.

treatment_protocol: Eucalyptus camaldulensis seeds were sourced from three provenances with contrasting climates: Petford (humid tropics), Katherine (dry tropics) and Mt.Isa (semi-arid tropics). Fifteen genotypes from each provenance were grown in pots (approximately 8 l) in a glass house in April 2009. Temperatures in the glasshouse were maintained at 15°C minimum and 30°C maximum. The soil surface in the pots was covered with plastic beads to reduce evaporation. After growing the plants for five months water stress was imposed on ten genotypes by maintaining the pots at 30% of field capacity for two months. The other five genotypes were watered to field capacity (controls). Stomatal conductance, photosynthetic assimilation rates and pre-dawn water potential were measured just before imposition of water stress (8th of August) and during the stress period at periodic intervals from both stressed and control plants. At the same time leaf samples were taken for RNA extraction from both stressed and control plants and immediately stored at -80°C. Water usage was monitored throughout the experiment by weighing the pots. Two pots containing soil but no plants were also weighed, to estimate water loss by evaporation. All plants were harvested two months after imposing the stress treatment (10th of October).

tag: source provenance/climate

value: Petford (humid tropics)

tag: tissue

value: seedling leaf

tag: sample group

value: stress treatment


title: PS0

source_name: leaf_before stress-treatment

value: pre-treatment


title: GIS-Ruan_ChiaPet_HCT-116_Pol2

tag: datatype

value: ChiaPet

tag: datatype description

value: Chromatin Interaction Paired-End Tags

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: labexpid

value: cancer

value: endoderm

value: M

tag: antibody


title: PC1

source_name: leaf_control post-treatment

value: control post-treatment


title: GIS-Ruan_ChiaPet_K562_Pol2

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

value: RNA Polymerase II

value: Covance

tag: replicate

tag: cell lineage

value: mesoderm

tag: cell sex

value: F


title: GIS-Ruan_ChiaPet_HeLa-S3_Pol2

tag: cell karyotype

value: ectoderm


title: PC0

source_name: leaf_control pre-treatment

value: control pre-treatment


title: GIS-Ruan_ChiaPet_MCF-7_Pol2


title: MC1

value: Mt.Isa (semi-arid tropics)


title: KS0

value: Katherine (dry tropics)

value: seedling leaf


title: MS0

value: pre-treatment


title: KS1

value: stress treatment


title: MC0


title: KC1


title: ms0712A

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Wild type control
G(ms10)

data_processing:
Samples are prepared using ligation dependent method with 5' linker containing 4nt barcode and 3' linker added to the RNA, and single-end 36nt sequence was obtained using illumina genome analyzer. A custom PERL script is used to de-barcode the sample and remove the 3' linker CTGTAG and beyond. If the read does not contain the complete 3' linker, as represented by CTGTAG, then CTGTA/CTGT/CTG/CT at the very 3' end is removed only once to account for the incomplete 3' linker. RNA at least 17 nt was used in the following analysis.
use bowtie 0.12.7 with parameter v 3 -a --best --strata -m 400 and allow 1 mutation if the RNA size is 19-21, 2 mutations if the size 22-24, 3 mutations if the size is 25 or bigger.
The sample is normalized to 5 million of non-structural reads and the reads of an individual RNA are distributed evenly to all the genomic loci matched
A custom PERL pipeline is used to perform the post-bowtie analysis, including summarizing, making gff, drawing scatter plot, grouping reads, etc
Genome browse 1.70 plus custom perl script are used to visualize the RNA matched
Genome_build: Wormbase WS215
Supplementary_files_format_and_content: Fasta format sequence with id containing the RNA number matched to the genome and transgene (The 'x' and the number following  are the RNA counts and the number before the x is the id)

organism: Caenorhabditis elegans

source_name: N2 Wild type control

growth_protocol: adult gonade from gravid adults

extract_protocol:
Small RNAs of 18-40nt were gel purified from a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 40-nt) in separate lanes. To make the RNA clonable at the 5' end, either CIP/PNK or TAP treatment is required during cloning, as indicated in the paper. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated with 20mg of glycogen as the carrier. The gel purified RNA and 1µM of each standard were incubated with 10µM of 3’-end linker, 1 Unit/µl of SuperRNaseIN, 10% DMSO and 3 Units/µl T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2,10mg/mL BSA, 10mM DTT).  The 3’ ligated products were gel purified, eluted, precipitated and then incubated with 10µM of 5’ adapter oligonucleotide with 4nt barcode at the 5' end, 1 Unit/µl SuperRNaseIN (Ambion) and 3 Units/µl of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% DMSO. The ligated products were gel purified and reverse transcribed in a standard 20µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 8% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.) and single-end 36 nt reads were obtained.
Synchronous adult flag::wago-9 worms were dounced in a stainless steel homogenizer. FLAG¡ËWAGO-9 was immunoprecipitated from 20 mg of lysate essentially as described (Gu et al., 2009). Small RNAs were extracted from WAGO-9 immune complexes as well as a portion of the input lysate, gel-purified, pre-treated with TAP, cloned and sequenced as described (Gu et al., 2009).
More details in: PMID 19800275
small RNA cloning, 5' and 3' ligation dependent.

treatment_protocol: normal growth condition

tag: strain background

tag: genotype/variation

value: wild type

tag: age

value: gravid adults

value: adult gonade

tag: 5' barcode

value: (A) TGAC


title: WAGO-9 Input

description:
WAGO-9 Input sample
Input(ms13)

source_name: WAGO-9 Input sample

tag: sample type

value: WAGO-9 Input

tag: tissue


title: WAGO-9 IP

description:
WAGO-9 IP sample
IP(ms13)

source_name: WAGO-9 IP sample

value: WAGO-9 IP

value: (D) ATCA

tag: ip antibody

value: M2 FLAG monoclonal antibody

tag: ip antibody vendor

value: Sigma

tag: ip antibody cat. #


title: KC0

tag: source provenance/climate

tag: sample group


title: ms1101B

description:
gfp::csr-1 silenced line
C(ms11)

source_name: gfp::csr-1 silenced line

value: neSi10 gfp::csr-1 RNAe

value: (B) CAGT


title: ms1101A

description:
gfp::csr-1 expressed line
B(ms11)

source_name: gfp::csr-1 expressed line

value: neSi10 gfp::csr-1


title: ms0425D

description:
cdk-1::gfp expressed line
K(ms14)

source_name: cdk-1::gfp expressed line

value: neSi12 cdk-1::gfp


title: ms0712C

description:
gfp::csr-1 expressed line
D(ms10)

value: neSi9 gfp::csr-1

value: (C) GCTG


title: ms0425B

description:
cdk-1::gfp silenced line
I(ms14)

source_name: cdk-1::gfp silenced line

value: neSi12 cdk-1::gfp RNAe


title: ms0425C

description:
gfp::cdk-1 silenced line
J(ms14)

source_name: gfp::cdk-1 silenced line

value: neSi11 gfp::cdk-1 RNAe


title: USC_ChipSeq_MCF-7_H3K27me3B_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

tag: cell organism

value: human

tag: cell description

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

value: cancer

value: ectoderm

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: rabbit monoclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27) marks repressed chromatin regions

tag: antibody vendorname

value: Cell Signaling

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: labversion


title: ms0425A

description:
Wild type cotrol
H(ms14)

tag: strain background

tag: genotype/variation

value: wild type

tag: age

value: gravid adults

tag: tissue

value: adult gonade

tag: 5' barcode

value: (A) TGAC


title: GIS-Ruan_ChiaPet_MCF-7_ERalpha_a

tag: datatype

value: ChiaPet

tag: datatype description

value: Chromatin Interaction Paired-End Tags

value: Rabbit affinity purified polyclonal antibody. Epitope is the C-terminus of human estrogen receptor alpha (ESR1). Recommended for detection of estrogen receptor of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:ESR1

value: This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq)

value: Santa Cruz Biotechnology

tag: labexpid

tag: replicate

tag: cell lineage

tag: cell sex

tag: antibody

value: Rabbit affinity purified polyclonal antibody. Epitope is the C-terminus of human estrogen receptor alpha (ESR1). Recommended for detection of estrogen receptor  of m, r and h origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target:ERalpha_a

value: Santa Cruz Biotech


title: ms0712B

description:
gfp::csr-1 silenced lne
A(ms10)

source_name: gfp::csr-1 silenced lne

value: neSi9 gfp::csr-1 RNAe

value: (B) CAGT


title: Environmental DNA from contaminated aquifer Sep. 08 6.7m rep.c

status: Public on Jul 16 2012

city: Neuherberg

first: Giovanni

last: Pilloni

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz-Centre Munich

description: small rRNA were amplified using specific PCR primers from total nucleic acids extracted from environmental samples

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
6708c.fas.txt: not applicable

organism: environmental samples

source_name: Aquifer Sediment

extract_protocol: Nucleic acids extracted with a bead beating-phenol/chloroform protocol from sediment samples were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. One of the samples (replicate c) from the quantitative assessment (via spiking of 16S rRNA-quantified A.fisheri sequences not originally present in the sample) was run as 2 steps PCR. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads from 2 runs were furhter trimmed for quality and lenght (>250 bp).

tag: sampling time

value: 26 September 2008

tag: depth

value: 6.7 m below ground

value: c

tag: sample type

value: Environmental sample

tag: rna subtype

value: small RNA

tag: file accn

tag: barcode

value: CGTCTAGTAC


title: Environmental DNA from contaminated aquifer Jun. 09 6.9m rep.c

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
6909c.fas.txt: not applicable

value: 6.9 m below ground

value: TGTACTACTC


title: Environmental DNA from contaminated aquifer Sep. 08 6.7m rep.b

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
6708b.fas.txt: not applicable

value: b

value: TCACGTACTA


title: Environmental DNA from contaminated aquifer Jun. 09 6.9m rep.b

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
6909b.fas.txt: not applicable

value: TCTACGTAGC


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.b

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
6906b.fas.txt: not applicable

value: 23 February 2006

value: CGAGAGATAC


title: small RNAs from Cyprinus carpio

city: Beijing

first: J

middle: T

last: Li

department: The Centre for Applied Aquatic Genomics

country: China

institute: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences,

description: The RNAs from the above tissues of 17 samples were mixed together, each with equivalent concentration.

data_processing: Raw data processing: Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequence were trimed by our Perl scripts. Small RNA fragments were compared with the sequences of non-coding RNAs (rRNA, tRNA, snRNA, snoRNA) available in Rfam and the GenBank database.

organism: Cyprinus carpio

source_name: 17 German mirror carps

growth_protocol: Fish were maintained in out-door tanks with running fresh water at 23℃ and fed a commercial diet twice daily.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s standard protocol.The isolated total RNA was treated with DNase I (Invitrogen) to remove genomic DNA contamination.The concentration and integrity of RNAs were assessed with NanoVue Plus (GE Healthcare Life Sciences, Piscataway, NJ, USA) and RNA electrophoresis. The A260/280 ratio of RNA samples were found to be approximately 1.9. Then, the 17 samples were prepared with Illumina's 'TruSeq small RNA Sample Prep kit'. They were sequenced on a HiSeq2000, using version 5 chemistry and analysis pipeline 1.8.

treatment_protocol: extract total RNA by Trizol reagent

tag: average weight

value: brain, skin, liver, muscle, spleen, head kidney, body kidney, intestine, gill and heart


title: Bbd - KD 2

city: Boston

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: H2A.Bbd knock-down, replicate 2

data_processing:
Paired-end RNA-seq tags were mapped using Tophat software package. Transcript annotations were taken from UCSC RefSeq track.
Tag pairs that had less than 50-bp separation between the mates were filtered out.
RNA-seq coverage was estimated as a number of paired-end fragments spanning over each interrogated genomic position. Coverage was normalized by total number of fragments.
Genome_build: hg18

source_name: H2A.Bbd KD

growth_protocol: HeLa cells were grown in DMEM with 10% calf serum

extract_protocol: For RNA-seq experiments, toRNA from nuclei were depleted of rRNA (Epizyme kit) and libraries were cloned using the truSeq RNAseq kit from Illumina.

treatment_protocol: RNA-seq experiments were done from trizol purified toRNA from nuclei isolated as described in Pandya-Jones & Black (RNA 15:1896, 2009).

tag: cell line

value: HeLa

tag: treatment

value: H2A.Bbd KD

tag: lentiviral construct


title: Z - KD 1

description: H2A.Z knock-down, replicate 1

source_name: H2A.Z KD

value: H2A.Z KD


title: OCI-Ly8-H3K4me3-ChIPseq

city: New York

first: Yanwen

last: Jiang

state: NY

institute: Weill Cornell Medical College

data_processing:
ly8_h3k4me3_GCCAAT_L004_R1.fastq.gz.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs; genome build: hg18
After sequencing, short reads were aligned to the human genome (hg18) using the BWA short read aligner.  We then detected single nucleotide variants (SNVs) by using an algorithm, SHMseeqer, developed in house.  After eliminating known dbSNPs and low confidence novel SNVs, SHMseeqer searches for SNVs that occur at dC or dG within the WRCY or the RGYW motif, which represent the features of somatic hypermutaiton.  SHMseeqers then calculates Z-scores to measure the over-representation of SHMs in SNVs at a 4-kb window centered at the transcription starting site (TSS) of each RefSeq gene.  Any promoters with 3 and more SHMs and a Z-score greater than 1 will be defined as SHM hotspots.

source_name: Diffuse Large B-cell Lymophoma

growth_protocol: The OCI-Ly1 cells were cultured in medium containing 90% Iscove medium (Cellgro, Manassas, VA), 10% fetal bovine serum (Gemini, Irvine, CA), and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA).  The OCI-Ly8 cells were grown in RPMI with 10% fetal calf serum, 1% penicillin/streptomycin, and N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid.

extract_protocol: Sequencing libraries were constructed from 10ng ChIP or Input DNA following Illumina protocol.  Fragments between 200bp to 300bp in size were selected.  7 pM of final library product was sequenced either on GAIIX or HiSeq2000.

treatment_protocol: Primary cells were purified from normal fresh human tonsillectomy specimens by magnetic cell separation based on the expression of phenotypic markers, such as IgD for Naïve B cells, and CD77 for germinal center B cells.  These human tissues were obtained with the approval of the Institutional Review Boards of the Weill Cornell Medical College in accordance with the Declaration of Helsinki.  Ficoll Histopaque gradient centrifugation was used to isolate tonsilar mononuclear cells.  Individual tonsilar B cell populations were collected by antibody-based microbead cell separation (Miltenyi Biotec, Auburn, CA).  The purity of the isolated cells is normally more than 90%.

tag: chip antibody


title: MS1

source_name: leaf_stress treatment

tag: source provenance/climate

value: Mt.Isa (semi-arid tropics)

tag: tissue

value: seedling leaf

tag: sample group

value: stress treatment


title: Bbd - KD 1

description: H2A.Bbd knock-down, replicate 1


title: neg C - KD 2

description: control, replicate 2

source_name: control

value: control


title: neg C - KD 1

description: control, replicate 1


title: bulk chromatin

description: bulk chromatin before immunoprecipitation

data_processing:
Sequenced reads were mapped to the human genome (hg18) using Bowtie aligner. Only uniquely mapped tags with no more than two mismatches in the first 28 base pairs of the read were retained.
Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous, potentially resulting from amplification bias, and the tags mapped to those positions were discarded.
The tag frequency at each genome position was calculated separately for DNA positive and negative strands.
Genome_build: hg18
Supplementary_files_format_and_content: Processed files list the 5'-end coordinates of Solexa reads retained for all replicates of the corresponding sample, after data filtering for possible library preparation artifacts. These are tab delimited text files.

source_name: HeLa

extract_protocol: Nuclei were digested with Mnase and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (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.

treatment_protocol: Nuclei were isolated and chromatin was prepared as described in Foltz et al. (Nature Cell Biology 8:458, 2006)

tag: shearing protocol

value: Mnase

tag: affinity tag


title: hsH2A.Bbd

value: FLAG


title: hsmacroH2A


title: hsH2A


title: hsH2A.Z


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 0.2% qPCR quantified DNA from A. fisheri (rep. c)

description: small rRNA were amplified as 2 steps PCR using specific primers from total nucleic acids extracted from environmental samples amended with increasing concentration of external DNA reference (A. fisheri)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af02%_c.fas.txt: not applicable

organism:
Aliivibrio fischeri
environmental samples

value: 6.9 m below ground

tag: replicate

value: Environmental sample + pure culture (A. fisheri) DNA

value: small RNA

value: ACGACTACAG


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 0% qPCR quantified DNA from A. fisheri (rep. b)

description: small rRNA were amplified using specific PCR primers from total nucleic acids extracted from environmental samples amended with increasing concentration of external DNA reference (A. fisheri)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af0%_b.fas.txt: not applicable

tag: sampling time

value: CTCGCGTGTC


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 0.2% qPCR quantified DNA from A. fisheri (rep. b)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af02%_b.fas.txt: not applicable

value: 23 February 2006

tag: depth

value: CGTGTCTCTA


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 2% qPCR quantified DNA from A. fisheri (rep. c)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af2%_c.fas.txt: not applicable

tag: sample type

value: TGTACTACTC


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 2% qPCR quantified DNA from A. fisheri (rep. b)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af2%_b.fas.txt: not applicable

tag: rna subtype

value: ATATCGCGAG


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 20% qPCR quantified DNA from A. fisheri (rep. c)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af20%_c.fas.txt: not applicable

tag: file accn

value: TCTACGTAGC


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 0% qPCR quantified DNA from A. fisheri (rep. a)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af0%_a.fas.txt: not applicable

tag: barcode

value: AGCACTGTAG


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 20% qPCR quantified DNA from A. fisheri (rep. b)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af20%_b.fas.txt: not applicable

value: ATCAGACACG


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
6906c.fas.txt: not applicable

value: c

value: Environmental sample

value: ATACGACGTA


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 0.2% qPCR quantified DNA from A. fisheri (rep. a)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af02%_a.fas.txt: not applicable

value: AGACGCACTC


title: Z - KD 2

description: H2A.Z knock-down, replicate 2

value: HeLa

value: H2A.Z KD


title: NBC-H3K4me3-ChIPseq

data_processing:
NB062510_H3K4me3_Run083010_s_5_sequence.txt.gz.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs; genome build: hg18
After sequencing, short reads were aligned to the human genome (hg18) using the BWA short read aligner.  We then detected single nucleotide variants (SNVs) by using an algorithm, SHMseeqer, developed in house.  After eliminating known dbSNPs and low confidence novel SNVs, SHMseeqer searches for SNVs that occur at dC or dG within the WRCY or the RGYW motif, which represent the features of somatic hypermutaiton.  SHMseeqers then calculates Z-scores to measure the over-representation of SHMs in SNVs at a 4-kb window centered at the transcription starting site (TSS) of each RefSeq gene.  Any promoters with 3 and more SHMs and a Z-score greater than 1 will be defined as SHM hotspots.

source_name: Human tonsilar naïve B cells

tag: cell type

value: Human tonsilar naïve B cells (IgD+)


title: OCI-Ly1-H3K4me3-ChIPseq

data_processing:
LY1_H3K4me3May09Feb10_BWA.SNVs.dbSNP.annot.1KG.kmut.TFBS.cons.flseq.qs; genome build: hg18
After sequencing, short reads were aligned to the human genome (hg18) using the BWA short read aligner.  We then detected single nucleotide variants (SNVs) by using an algorithm, SHMseeqer, developed in house.  After eliminating known dbSNPs and low confidence novel SNVs, SHMseeqer searches for SNVs that occur at dC or dG within the WRCY or the RGYW motif, which represent the features of somatic hypermutaiton.  SHMseeqers then calculates Z-scores to measure the over-representation of SHMs in SNVs at a 4-kb window centered at the transcription starting site (TSS) of each RefSeq gene.  Any promoters with 3 and more SHMs and a Z-score greater than 1 will be defined as SHM hotspots.

tag: cell line


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 20% qPCR quantified DNA from A. fisheri (rep. a)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af20%_a.fas.txt: not applicable

value: 6.9 m below ground

value: Environmental sample + pure culture (A. fisheri) DNA

value: small RNA

value: ACGAGTGCGT


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 2% qPCR quantified DNA from A. fisheri (rep. a)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af2%_a.fas.txt: not applicable

value: 23 February 2006

value: ACGCTCGACA


title: input_wildtype_KCl

status: Public on Jul 15 2012

city: Cambridge

first: Kristen

middle: E

last: Cook

address: 52 Oxford Street, NW Labs Rm 442

department: Molecular and Cellular Biology

institute: Harvard University

description:
processed data file: ORFcounts.txt
processed data file: promoter_counts.txt
processed data file: downstream_counts.txt

data_processing:
base calling with Illumina pipeline
alignment with Bowtie (Langmead et al, 2009) to June 2008 assembly of S. cerevisiae genome
count reads in Matlab, screen out spikes that occur in only one strand (where reads one strand are >10x the other strand)
Genome_build: SGD/sacCer2 assembly (June 2008) from UCSC browser
Supplementary_files_format_and_content: .txt tables with sequencing reads summed within each ORF, promoter region for RNA Pol II and Hog1, and lists of binding peaks for the transcription factors Sko1 and Hot1
The .txt tables are linked as supplementary files on the Series record.

source_name: S. cerevisiae liquid culture in logarhithmic growth

growth_protocol: Cells were diluted from an overnight culture to an OD600 of 0.1.  Cells were grown at 30° C in YEPD, with shaking, to OD600 0.6.  Cultures were split for stress treatment and mock treatment.

extract_protocol:
Samples were resuspended in 1 mL lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X 100, 0.1% Na Deoxycholate) in the presence of protease inhibitors (Roche; Complete) and mechanically lysed by bead beading.  Lysates were sonicated (9 cycles of 15 seconds each, power 2 on Misonix 3000) to solubilize chromatin and then clarified by centrifugation.  Ten percent of the clarified lysate was reserved to serve as an input control.  Clarified lysates (~10 mg for ChIP-seq, ~ 2.5 mg for ChIP qPCR) were incubated with 12CA5 anti-HA antibody or 1Y26 anti Rpb3 antibody, for 2 hours at 4° C before addition of Protein G Dynabeads (Invitrogen).  After incubation for 4 hours up to overnight, beads were washed twice with lysis buffer, once with high salt buffer (50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton-X 100, 0.1% Na Deoxycholate), once with lysis buffer and once with TE (10 mM Tris, 1 mM EDTA, pH 8).  All washes were performed at room temperature for five minutes each, on an end-over-end mixer.  Samples were eluted from beads in TE plus 0.67% SDS at 65° C for 30 minutes.  Supernatants were removed from beads and incubated overnight at 65° C to break crosslinks.  DNA was isolated by digestion of RNA with RNAse A for 2 hours at 37° C, protein digestion with Proteinase K for 2 hours at 55° C, and purified by phenol chloroform extraction and precipitation with ethanol and NaCl.  DNA pellets were stored in TE.
For ChIP-seq, ~ 10 ng IP material was used to generate each library, following the Illumina protocol for their paired end DNA sample prep kit (v1).  After addition of adaptors, DNA in a size range of 175-300 base pairs was isolated by gel electrophoresis for amplification.  Size ranges of prepared libraries were measured on an Agilent Biolanalyzer (average size 225 base pairs) before sequencing on an Illumina Genome Analyzer II (performed by Christian Daly at the FAS Center for Systems Biology Core Facility).  Thirty-six base reads were obtained and aligned to the Saccharomyces cerevisiae genome using ELAND (Jianwen Zhang performed the alignments).  For Hog1 and transcription factor ChIP-seq samples, five million to ten million reads were obtained.  Uniquely alignable sequence tags were mapped to the genome and extended by the average length of the library (minus the adaptor length) in MATLAB.

treatment_protocol: For stress treatment, YEPD supplemented with KCl was added to ~120 OD units of culture, bringing the final concentration of KCl to 0.4 M; for mock treated cells, the same volume of YEPD was added to cultures.  After five minutes in stress, samples were crosslinked with 1% formaldehyde at room temperature for 15 minutes.  Crosslinking was quenched with 125 mM glycine for five minutes, and then samples were harvested by centrifugation, washed twice in cold PBS (137 mM NaCl, 2.7 mM KCl, 10 mM sodium phosphate dibasic, 2 mM potassium phosphate monobasic, pH 7.4) and then snap-frozen in liquid nitrogen.

tag: target of ip

tag: stress treatment

value: YEPD + 0.4 M KCl for 5 minutes

tag: genetic background

value: wildtype


title: CLRDV_Infected_plant_rep2

city: Rio de Janeiro

first: Tatiane

middle: Franca

last: Silva

state: Rio de Janeiro

address: Professo Rodolpho Paulo Rocco

department: Virologia

country: Brazil

institute: Universidade Federal do Rio de Janeiro

data_processing: sRNA sequences ranging from 18-26 nt were parsed from FASTA formatted files.The adapter sequences (3' adapter: âATCTCGTATGCCGTCTTCTGCTTGT) were removed using Perl scripts locally developed.  Processed files: small RNA hit name _ n_number indicates how many times small RNA sequence was recovered.

organism: Gossypium hirsutum

source_name: Leaves from cotton infected plant with Cotton leafroll dwarf virus (CLRDV)

growth_protocol: Plants were grown under standard conditions

extract_protocol: Total RNA was extracted using Invisorb Spin Plant RNA Mini Kit (Invisorb) ~ 10 microgrames were used  for sequencing on the Illumina Genome Analyzer (Illumina, San Diego, USA). Small RNA libraries were prepared according to a modified Illumina protocol. Small RNAs of 15-30 nt were purified on acrylamide gel; the 3'IDT miRNA cloning linker (Integrated DNA Technologies, San Diego, USA) and then the 5' Illumina adapters were single-stranded ligated with T4 RNA ligase. The constructs were purified again on acrylamide gel to remove empty adapters and submitted to reverse transcription and PCR. The primers used for cDNA synthesis and PCR were designed to insert an index in the 3' adapter The libraries were quality controlled by cloning an aliquot into a TOPO plasmid and capillary sequencing 4-8 clones. High-throughput sequencing was performed on a Genome Analyzer GAIIx for 38 cycles plus 7 cycles to read the indexes. After demultiplexing and adapter removal, 10.5 millions pass filter reads were obtained in libraries. For more details see manufacturer's website of FASTERIS SA HiSeq Service (http://www.fasteris.com/ga/ga_descript.html)

treatment_protocol: Plant were infected by viruliferous aphid (Aphis gossypii), which removed through sprayed with Confidor Insecticide after 24 h

tag: cultivar

value: Cultivar Fibermax966

tag: age

value: 50  days

value: noninoculated systemic leaves 5 days post-infection:Virus CLRDV


title: Environmental DNA from contaminated aquifer Feb. 06 6.9m rep.c + 0% qPCR quantified DNA from A. fisheri (rep. c)

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
Genome Build:
Af0%_c.fas.txt: not applicable

value: CGTAGACTAG


title: Not-infected_plant

source_name: Leaves from cotton not-infected plant

treatment_protocol: sprayed with Confidor Insecticide

value: 50 days

tag: tissue

value: correspondent noinculated systemic leaves


title: Hot1IP_wildtype_KCl

description: processed data file: Hot1_peak_list.txt

value: Hot1-3HA (endogenous locus)

tag: chip antibody

value: 12CA5 anti-HA (not from a commercial source)


title: mockIP_wildtype_YEPD

value: (mock-treated by addition of YEPD)


title: mockIP_wildtype_KCl


title: input_wildtype_YEPD


title: Sko1IP_wildtype_KCl

description: processed data file: Sko1_peak_list.txt

value: 3HA-Sko1 (endogenous locus)


title: Hog1IP_Dsko1Dhot1_KCl

value: Hog1-3HA (endogenous locus)


title: Hog1IP_Dsko1Dhot1_YEPD


title: Hog1IP_wildtype_YEPD


title: Rpb3IP_Dsko1Dhot1_YEPD

description: processed data file: ORFcounts.txt

value: Rpb3 (untagged)

value: 1Y26 (neoclone, catalog# WP012, lot# A5081456)


title: Rpb3IP_Dhog1_KCl

description: processed data file: ORFcounts.txt


title: GCB-H3K4me3-ChIPseq

data_processing:
CB062510_H3K4me3_Run083010_s_6_sequence.txt.gz.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs; genome build: hg18
After sequencing, short reads were aligned to the human genome (hg18) using the BWA short read aligner.  We then detected single nucleotide variants (SNVs) by using an algorithm, SHMseeqer, developed in house.  After eliminating known dbSNPs and low confidence novel SNVs, SHMseeqer searches for SNVs that occur at dC or dG within the WRCY or the RGYW motif, which represent the features of somatic hypermutaiton.  SHMseeqers then calculates Z-scores to measure the over-representation of SHMs in SNVs at a 4-kb window centered at the transcription starting site (TSS) of each RefSeq gene.  Any promoters with 3 and more SHMs and a Z-score greater than 1 will be defined as SHM hotspots.

source_name: Human tonsilar germinal center B cells

value: Human tonsilar germinal center B cells (CD77+)


title: Rpb3IP_Dhog1_YEPD

description: processed data file: ORFcounts.txt


title: Rpb3IP_Dsko1Dhot1_KCl

description: processed data file: ORFcounts.txt


title: Rpb3IP_wildtype_KCl

description: processed data file: ORFcounts.txt


title: Rpb3IP_wildtype_YEPD

description: processed data file: ORFcounts.txt


title: CLRDV_Infected _plant_rep1


title: T7.1 (overexpressed DGCR8 IP)

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

institute: MDC-Berlin

data_processing:
Read were processed with MIRO (http://seq.crg.es/main/bin/view/Home/MiroPipeline) to remove reads containing Ns and with a sequence complexity below 0.5. We also removed PCR duplicates.
HITS-CLIP reads were aligned using bowtie v0.11.3 with parameters --best -v2 -a to an index file containg hg18 genome, Ensembl54 transcripts and lincRNA from Ensembl59 mapped to hg18. Initially, all reads are mapped to the index file. After the mapping, all those reads that could not be mapped are trimmed 1 base at the 3’ end of the read and mapped again to the index file. This procedure is repeated until the reads have a minimum length of 21nt. For further analyses, only uniquely mapped reads to the genome were used.
Reads mapped to the same strand were clustered according to their position in the reference sequence to generate clusters. To identify significant clusters we applied a modified false discovery rate (mFDR) using Pyicos. Only significant clusters (pval < 0.01) were kept.
Clusters overlapping Genomic and Centromeric Gaps (hg18 Gap Track from UCSC) and Satellites (hg18 repeat masked track from UCSC) were discarded.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph files. Each of the files contains all the significant clusters identified for a sample in a strand (+ or -). The score given represents the amount of reads in a position.

growth_protocol: HEK293T cells were grown in standard conditions

extract_protocol: RNAs (20-100nt long) associated to DGCR8 were phenol extracted and ethanol precipitated. Libraries were prepared from these RNAs using the Illumina Small RNA kit (v1.5)

tag: rna associated

value: overexpressed (T7) DGCR8


title: D8.1 (endogenous DGCR8 IP)

value: endogenous (D8) DGCR8


title: D8.2 (endogenous DGCR8 IP)


title: Hot1IP_wildtype_YEPD

description: processed data file: Hot1_peak_list.txt

value: wildtype


title: T7.2 (overexpressed DGCR8 IP)


title: Sko1IP_wildtype_YEPD

description: processed data file: Sko1_peak_list.txt


title: Hog1IP_wildtype_KCl

value: YEPD + 0.4 M KCl for 5 minutes


title: HighDL_Chow_8623

status: Public on Jul 14 2012

city: Winston-Salem

first: Genesio

last: Karere

state: NC

address: 1 medical center blvd

department: Internal Medicne

institute: Wake Forest Baptist Health Sciences

description: small RNA

data_processing:
Data processed using mirTools software and aligned to human genome and small RNA databases.
Supplementary_files_format_and_content: Fasta files contain trimmed small RNA sequences with read counts

organism: Papio hamadryas

growth_protocol: Baboon liver biospy collected and snap frozen in liquired nitrogen.

extract_protocol: Libraries were constructed with the Illumina small RNA kit version 1.5

treatment_protocol: Total RNA siolated using Trizol and miRNA enriched using miRVana miRNA Isolating Kit from Ambion.

value: liver


title: LowLDL_Chow_6910

description: small RNA


title: HighDL_Chow_1x 4154

description: small RNA


title: LowLDL_HCHF_8024

description: small RNA


title: HighDL_Chow_1x 3817

description: small RNA


title: LowLDL_Chow_8024

description: small RNA


title: HighLDL_HCHF_1x 4154

description: small RNA


title: LowLDL_HCHF_6265

description: small RNA


title: LowLDL_Chow_6265

description: small RNA


title: HighLDL_HCHF_8623

description: small RNA


title: KO K70A R2

status: Public on Jul 13 2012

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

description: KO + Helicase (K70A) Replicate 2

data_processing: Raw reads summarized by sequence identity (observations).  Custom software was used for processing, as described in the manuscript. The processed data files represent sequence counts (summarized by sequence identity) in the various libraries. The data processing steps have been described in the manuscript and associated supplementary material.

organism: Mus musculus

source_name: Dicer -/- murine mesenchymal stem cells (MSCs)

extract_protocol: Small RNA libraries were prepared for cloning and sequencing using total RNA extracted from murine mesenchymal stem cells (MSCs) with Trizol (Invitrogen) from the following: Dicer f/f (WT), Dicer -/- (KO), and Dicer -/- cells transfected with hsDicer point mutants. Small RNA were selected from total RNA using a 15-50nt range cut from 15% polyacrylamide TBE-urea gel. Libraries were cloned and sequenced using standard Illumina protocol (3' adapter sequence:  AGATCGGAAGAGCGGTTCAGCAGGAATGCCGA)

value: mesenchymal stem cells (MSCs)

tag: genotype

value: Dicer -/-

tag: strain

tag: transfection

value: Helicase (K70A)


title: KO Y971A/Y972A R2

description: KO + PAZ (Y971A/Y972A) Replicate 2


title: KO D1709A R2

description: KO + RNase IIIB (D1709A) Replicate 2

value: RNase IIIB (D1709A)


title: KO D1320A/D1709A R2

description: KO + IIIA/IIIB (D1320A/D1709A) Replicate 2

value: IIIA/IIIB (D1320A/D1709A)


title: WT R2

description: WT + mCherry Replicate 2

source_name: Dicer f/f murine mesenchymal stem cells (MSCs)

value: Dicer f/f

value: mCherry Fluorescent Protein


title: KO D1320A R2

description: KO + RNase IIIA (D1320A) Replicate 2

value: RNase IIIA (D1320A)


title: KO Dicer R2

description: KO + hsDicer Replicate 2

value: Human Dicer endoribonuclease


title: KO Y971A/Y972A R1

description: KO + PAZ (Y971A/Y972A) Replicate 1


title: KO R2

description: KO + mCherry Replicate 2


title: KO K70A R1

description: KO + Helicase (K70A) Replicate 1


title: LowLDL_HCHF_6910

description: small RNA


title: KO Dicer R1

description: KO + hsDicer Replicate 1


title: KO D1709A R1

description: KO + RNase IIIB (D1709A) Replicate 1


title: KO D1320A/D1709A R1

description: KO + IIIA/IIIB (D1320A/D1709A) Replicate 1


title: KO D1320A R1

description: KO + RNase IIIA (D1320A) Replicate 1


title: KO R1

description: KO + mCherry Replicate 1


title: HighLDL_HCHF_1x 3817

description: small RNA


title: 0dpp

city: East Lansing

first: Kevin

middle: M

last: Carr

state: MI

address: Plant Biology Lab, 612 Wilson Rd., Rm. S-20 A

department: Research Technology Support Facility

institute: Michigan State University

description:
SRP013979
SRX157287

data_processing:
Basecalls were performed with Roche/454 gsRunProcessor
Reads were screened and filtered using DFCI Gene Indices tools SeqClean pipeline (http://compbio.dfci.harvard.edu/tgi/software/)
Cleaned reads were assembled in to contigs using TGI Clustering Tools (TGICL, http://compbio.dfci.harvard.edu/tgi/software/) followed by CAP3
Number of reads from each sample contributing to each contig were counted.
Genome_build: n/a
Supplementary_files_format_and_content: tab delimited text with column headers: column 1 gb accession from transcriptome shotgun assembly TSA submission; column 2 internal contig name; column 3 total reads from all samples contributing to contig; column 4 length of contig in nt; columns 5-9 normalized representation of each sample for contig, TPT==Transcripts per Thousand.

organism: Cucumis sativus var. sativus

source_name: Fruit during early development

growth_protocol: Sets of 80 cucumber plants per experiment were grown in the greenhouse in 3.78 L plastic pots filled with BACCTO (Michigan Peat Co., Houston, TX) media and fertilized once per week.  Temperature was kept between 21 to 25 °C, supplemental lights were used to provide an 18 h light period.  Pest control was performed according to standard management practices.  All flowers for each experiment were hand pollinated on a single date (1-2 flowers per plant).  The experiment was repeated three times.

extract_protocol: RNA and cDNA sample preparation were based on the procedures of Schilmiller et al. (PNAS (2009) 106:10865-10870) and Ando and Grumet (J Am Soc Hort Sci (2010) 135:176-182).

value: Vlaspik

value: pericarp, placenta

tag: developmental stage

value: 0 days post polination


title: 12dpp

description:
SRP013979
SRX157289

value: 12 days post polination


title: 16dpp

description:
SRP013979
SRX157290

value: 16 days post polination


title: 8dpp reg2

description:
SRP001601
SRX015372

value: 8 days post polination


title: WT R1

description: WT + mCherry Replicate 1


title: 4dpp

description:
SRP013979
SRX157288

value: 4 days post polination


title: Caltech_RnaSeq_LHCN-M2_2x75_200_DIFF_7d

status: Public on Jul 12 2012

molecule: polyA RNA

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=wgEncodeCaltechRnaSeq

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: readtype

tag: readtype description

value: Paired 75 nt reads

tag: insertlength

tag: insertlength description

value: insert length of 200nt

tag: labexpid

tag: labversion

value: myocyte

tag: mapalgorithm

tag: mapalgorithm description

value: TopHat v1.0.14

tag: treatment

tag: treatment description

value: Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold)

tag: replicate


title: Caltech_RnaSeq_LHCN-M2_2x75_200

tag: cell sex

value: U

value: myoblast

value: No special treatment or protocol applies


title: Caltech_RnaSeq_HSMM_2x75_200

source_name: HSMM


title: Caltech_RnaSeq_GM12892_2x75_200


title: Caltech_RnaSeq_GM12891_2x75_200


title: Caltech_RnaSeq_HCT-116_2x75_200

value: immortalized cell line

tag: line


title: Caltech_RnaSeq_HeLa-S3_1x75D

value: Single 75 nt directed reads


title: Caltech_RnaSeq_GM12878_2x75_400

value: insert length of 400nt


title: Caltech_RnaSeq_HepG2_1x75D (superseded by GSE90322)

description:
****************************
GSM958740 record metadata submitted on Jul 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90322
****************************


title: Caltech_RnaSeq_NHLF_2x75_200

source_name: NHLF


title: Caltech_RnaSeq_HUVEC_1x75D

source_name: HUVEC


title: Caltech_RnaSeq_MCF-7_2x75_200


title: Caltech_RnaSeq_HeLa-S3_2x75_200


title: 8dpp reg1

description:
SRP001601
SRX015371

tag: cultivar

value: Vlaspik

tag: tissue

value: pericarp, placenta


title: Caltech_RnaSeq_K562_1x75D

tag: datatype


title: Caltech_RnaSeq_HUVEC_2x75_200

tag: datatype description


title: Caltech_RnaSeq_NHEK_2x75_200

source_name: NHEK

tag: readtype


title: Caltech_RnaSeq_HepG2_2x75_200

tag: readtype description


title: H3K4me1 hypoxia ChIP-seq

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

data_processing:
All unique mapped sequences were analyzed by QuEST 2.4 software.
QuEST software was conducted according to the QuEST recommendations and added with FDR analysis in QuEST procedure.
The following paramters were used : positive region size=1000, KDE bandwidth=100, ChIP seeding fold enrichment=10, ChIP extension fold enrichment=3, ChIP-to-background fold enrichment=3.
Genome_build: hg18

source_name: H3K4me1 hypoxia ChIP-seq

growth_protocol: HUVECs are cultured under normoxia(20% oxygen) and hypoxic (1% oxygen) condition for 24hrs.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment 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 16 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 type

value: HUVEC

tag: chip antibody

value: H3K4me1 [kindly provided by Dr Kimura CMA302 (Cell Struct Funct.2008;33(1):61-73)]

tag: passage

value: within 6 times


title: H3K4me3 normoxia ChIP-seq

source_name: H3K4me3 normoxia ChIP-seq

value: H3K4me3 [kindly provided by Dr Kimura CMA304 (Cell Struct Funct. 2008;33(1):61-73)]


title: H3K4me3 hypoxia ChIP-seq

source_name: H3K4me3 hypoxia ChIP-seq


title: Caltech_RnaSeq_GM12878_1x75D

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: insertlength

tag: insertlength description

tag: labexpid


title: INPUT under normoxia ChIP-seq

source_name: INPUT under normoxia ChIP-seq


title: INPUT under hypoxia ChIP-seq

source_name: INPUT under hypoxia ChIP-seq


title: H3K4me1 normoxia ChIP-seq

source_name: H3K4me1 normoxia ChIP-seq


title: Caltech_RnaSeq_H1-hESC_2x75_400

growth_protocol: missing

value: Paired 75 nt reads

tag: mapalgorithm

tag: mapalgorithm description

tag: treatment


title: Caltech_RnaSeq_GM12878_2x75_200

value: insert length of 200nt

value: TopHat v1.0.14

tag: replicate

tag: treatment description


title: HIF1 under hypoxia ChIP-seq

source_name: HIF1 under hypoxia ChIP-seq

value: HIF1α [Novus Biologicals NB100-134 lot.K2]


title: Caltech_RnaSeq_NHEK_1x75D


title: HIF1 under normoxia ChIP-seq

source_name: HIF1 under normoxia ChIP-seq


title: PTBP1+PTBP2 siRNAs

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: Sample 3

data_processing:
The RNA-seq data were analyzed using the ExpressionPlot pipeline (Friedman and Maniatis 2011).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file of read counts and RPKMS by gene/sample

source_name: CAD_PTBP1+PTBP2 siRNAs

extract_protocol: RNA-Seq 36 base reads paired-end; RNA-seq libraries were prepared in principle as described (Mortazavi et al. 2008). Total RNAs were extracted from siRNA-treated CAD cells with Trizol (Invitogen) and the poly(A)+ mRNA fractions were prepared using a Dynabeads® mRNA Direct™ Kit (Invitogen). The purified mRNA samples were partially hydrolyzed at 94°C for 2.5 min in the presence of Mg2+, which was followed by the first strand cDNA synthesis with the SuperScript III and random primers (Invitrogen). The second strand cDNA synthesis and adapter ligation steps were carried out as recommended by Illumina. DNA fragments of 350±50bp were then purified SizeSelect E-gels (Invitrogen) and amplified by 15 cycles of PCR usinf Phusion DNA polymerase (NEB) and Illumina primers. Sequencing was carried out using a Genome Analyzer IIx (Illumina)

treatment_protocol: Mouse neuroblastoma CAD cells (Li et al. 2007) were transfected with Ptbp1 or/and Ptbp2-specific or control ON-TARGETplus siRNAs (Dharmacon) using Lipofectamine 2000 (Invitrogen) and analyzed 72 hours post transfection

tag: cell line

value: CAD

value: neuroblastoma

tag: transfected with

value: Ptbp1 and Ptbp2-specific ON-TARGETplus siRNAs


title: Caltech_RnaSeq_K562_2x75_200

tag: datatype

value: No special treatment or protocol applies


title: Caltech_RnaSeq_H1-hESC_2x75_200

tag: datatype description


title: Caltech_RnaSeq_H1-hESC_1x75D

tag: cell sex

value: U

tag: readtype

value: Single 75 nt directed reads


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90.09.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK106
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11833
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10203
****************
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: GSM959044_UCSD.IMR90.Input.AK106.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90.09.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of IMR90 Cell Line Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on IMR90 Cell Line, Library AK106, 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.13532
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,912,241
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0042
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0059
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0516
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM959044_UCSD.IMR90.Input.AK106.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90.09.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the IMR90 Cell Line, Library AK106, 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.13652
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 8
BROWSER_TRACK_NAME: IMR90 Input 06
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library AK106 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,912,241
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0042
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0059
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0516
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: IMR90 Cell Line, additional biological replicate; renlab.Input.IMR90.09.01

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

value: IMR90 cells

tag: sample alias

tag: sample common name

value: IMR90 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

tag: medium

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

tag: Sex

value: Female

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Control siRNA

description: Sample 1

value: CAD

tag: cell type

value: neuroblastoma

value: control ON-TARGETplus siRNAs


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of UCSF-4 embryonic stem cell line (A14674) using Illumina HiSeq 2000
library name: A14674
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 55-299 bp
****************
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: GSM941753_UCSF-UBC.UCSF-4star.Input.A14674.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14674-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the UCSF-4* Cell Line, Library A14674 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.13426
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,494,277
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0028
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0742
HOTSPOT_PERCENTILE: 47
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.0832
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM941753_UCSF-UBC.UCSF-4star.Input.A14674.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14674-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4* Cell Line Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the UCSF-4* Cell Line, Library A14674 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.13435
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 8
BROWSER_TRACK_NAME: UCSF4* Input 74
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line ChIP-Seq Input Library A14674 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,494,277
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0028
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0742
HOTSPOT_PERCENTILE: 47
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.0832
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: cell line

value: female

tag: body site

value: Embryo ICM

tag: histological type

value: Embryonic stem cell

tag: is tumor

value: No


description:
design description: H3K27me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A14672) using Illumina HiSeq 2000
library name: A14672
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 103-362 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM941751_UCSF-UBC.UCSF-4star.H3K27me3.A14672.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14672-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the UCSF-4* Cell Line, Library A14672 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.13421
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,539,002
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0752
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.1555
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9029
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2758
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM941751_UCSF-UBC.UCSF-4star.H3K27me3.A14672.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14672-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4* Cell Line H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the UCSF-4* Cell Line, Library A14672 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.13430
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 8
BROWSER_TRACK_NAME: UCSF4* H3K27me3 72
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K27me3 Library A14672 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,539,002
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0752
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.1555
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9029
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2758
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K9me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A14671) using Illumina HiSeq 2000
library name: A14671
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 103-361 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
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: GSM941750_UCSF-UBC.UCSF-4star.H3K9me3.A14671.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14671-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the UCSF-4* Cell Line, Library A14671 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.13425
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,879,975
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.2682
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2596
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9711
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4607
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM941750_UCSF-UBC.UCSF-4star.H3K9me3.A14671.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14671-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4* Cell Line H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the UCSF-4* Cell Line, Library A14671 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.13434
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 8
BROWSER_TRACK_NAME: UCSF4* H3K9me3 71
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K9me3 Library A14671 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,879,975
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.2682
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2596
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9711
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4607
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K4me1 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A14669) using Illumina HiSeq 2000
library name: A14669
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 99-341 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM941748_UCSF-UBC.UCSF-4star.H3K4me1.A14669.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14669-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the UCSF-4* Cell Line, Library A14669 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.13428
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,972,072
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.0567
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1886
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8642
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3797
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM941748_UCSF-UBC.UCSF-4star.H3K4me1.A14669.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14669-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4* Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the UCSF-4* Cell Line, Library A14669 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.13437
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 8
BROWSER_TRACK_NAME: UCSF4* H3K4me1 69
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K4me1 Library A14669 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,972,072
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.0567
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1886
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8642
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3797
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K4me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A14670) using Illumina HiSeq 2000
library name: A14670
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 63-321 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM941749_UCSF-UBC.UCSF-4star.H3K4me3.A14670.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14670-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the UCSF-4* Cell Line, Library A14670 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.13427
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,736,444
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.4544
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4874
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4763
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM941749_UCSF-UBC.UCSF-4star.H3K4me3.A14670.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A14670-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4* Cell Line H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the UCSF-4* Cell Line, Library A14670 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.13436
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 8
BROWSER_TRACK_NAME: UCSF4* H3K4me3 70
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K4me3 Library A14670 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,736,444
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.4544
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4874
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4763
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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


title: Reference Epigenome: ChIP-Seq Input from Human Right Ventricle Tissue; renlab.Input.STL003RV.01.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK353
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12255
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
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: GSM915338_UCSD.Right_Ventricle.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003RV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Right Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Right Ventricle, Donor STL003, 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.13460
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,870,770
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0857
HOTSPOT_PERCENTILE: 53
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1362
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM915338_UCSD.Right_Ventricle.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003RV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Right Ventricle, Donor STL003, 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.13580
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 8
BROWSER_TRACK_NAME: RV Input 03 53
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle ChIP-Seq Input Donor STL003 Library AK353 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,870,770
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0857
HOTSPOT_PERCENTILE: 53
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1362
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Right Ventricle tissue; renlab.Input.STL003RV.01.01

value: Right Ventricle

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian