title: RIKEN_Cage_GM12878_cell_longPolyA

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt

value: IDR

tag: replicate

tag: cell sex

value: F

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: replicate description

value: tier 1


title: sc_ChIPSeq_1 and 2

status: Public on Dec 16 2011

type: SRA

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

library_source: genomic

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: strain

value: iso1 (y; bw cn sp)

tag: developmental stage

tag: antibody name

value: sc

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: RIKEN_Cage_HUVEC_cytosol_longNonPolyA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

library_source: transcriptomic

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: HUVEC

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=wgEncodeRikenCage

tag: datatype

value: Cage

tag: datatype description

value: CAGE 5' RNA Tags

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: bedtools v2.7.1

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: U

value: cytosol

value: The fluid between the cells outer membrane and the nucleus

value: Delve version 0.9


title: RIKEN_Cage_HepG2_cytosol_longNonPolyA

tag: cell description

value: hepatocellular carcinoma

value: endoderm

tag: cell sex

value: M

tag: localization

tag: localization description


title: Prd_ChIPSeq_1 and 2

tag: strain

value: iso1 (y; bw cn sp)

tag: developmental stage

tag: antibody name

value: Prd


title: E0-12_INPUT_1


title: RIKEN_Cage_NHEK_nucleus_longNonPolyA

molecule: nuclear RNA

source_name: NHEK

value: ectoderm

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: Ash2_ChIPSeq_1 and 2

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: CNC_ChIPSeq_1 and 2

source_name: AdultMale

value: AdultMale

value: CNC


title: RIKEN_Cage_HepG2_nucleus_longNonPolyA

tag: datatype

value: Cage

tag: datatype description

value: CAGE 5' RNA Tags

tag: rnaextract

value: longNonPolyA

value: Poly(A)- RNA longer than 200 nt

value: bedtools v2.7.1


title: RIKEN_Cage_K562_nucleoplasm_total

value: total

tag: rnaextract description

value: Total RNA extract (longer than 200 nt)

tag: biorep

tag: labexpid

value: cancer

value: mesoderm

value: F

value: nucleoplasm

value: That part of the nuclear content other than the chromosomes or the nucleolus

value: Delve version 0.9


title: AdultMale_CNC_INPUT_1

value: iso1 (y; bw cn sp)


title: RIKEN_Cage_K562_chromatin_total

tag: labversion

tag: cell karyotype

tag: cell lineage

value: chromatin

value: Nuclear DNA and associated proteins


title: RIKEN_Cage_K562_nucleolus_total

tag: cell description

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

tag: cell sex

tag: localization

value: nucleolus

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: Amur grapevine miRNA-seq

city: Nanjing

first: Chen

last: Wang

address: Weigang 1#

department: Horticulture College

country: China

institute: Nanjing Agriculture University

data_processing:
Summarize the length distribution of small RNA,
Explore small RNA distribution across selected genome
Identify known miRNAs by aligning to designated part of miRBase
Annotate small RNAs into several categories based on priority
Predict novel miRNAs and their secondary structures by Mireap from unannotated small RNAs
Family analysis of known miRNA
Identify novel miRNA target

genome build: NCBI Build Number: 1 (ftp://ftp.ncbi.nih.gov/genomes/Vitis_vinifera)

WGS123_sRNA_distribution.txt: Explore small RNA distribution across selected genome,then statistics how much reads alignment to plus strand or minus strand of each chromosome
mireap-WGS123-table.txt: Identified novel miRNA by exploring the secondary structure?the Dicer cleavage site and the minimum free energy of the unannotated small RNA tags which could be mapped to genome

molecule: total RNA

organism: Vitis amurensis

source_name: flower and berry

extract_protocol: Total RNA was extracted using the modified CTAB method, small RNA was seperated with 4M LiCl, and small RNA library was constructed.

tag: tissue-type

value: Inflorescences (20 days)

value: berry (15 days, 30 days and 45 days)


title: RIKEN_Cage_NHEK_cytosol_longNonPolyA

value: Cage

value: CAGE 5' RNA Tags

value: longNonPolyA

value: Poly(A)- RNA longer than 200 nt

value: bedtools v2.7.1

value: normal

value: ectoderm

value: U

value: cytosol

tag: localization description

value: The fluid between the cells outer membrane and the nucleus


title: Endogenous small RNAs from human senescent fibroblast WI-38

status: Public on Dec 17 2011

city: paris

first: Moussa

last: BENHAMED

address: Institut pasteur

country: France

institute: Institut Pasteur

description: total small RNA

data_processing: Small RNA samples were prepared from RIPs or unfractionated, cellular RNA of senescent cells using small RNA-Seq sample Prep kit (Illumina) followed by the standard Illumina RNA sequencing protocol using the Genome Analyzer. Bioinformatic analysis of RNA Seq results was performed by GenomeQuest Inc. France (www.genomequest.com). Beginning with raw reads obtained from ILLUMINA G1 sequencing adaptor sequence was removed. All reads smaller than 18 nucleotides after removing the adaptor sequence were discarded allowing one mismatch within the adaptor sequence. Small RNA sequences were mapped to the complete, unmasked, version of the NCBI version of the human genome (Build 36). The alignment algorithm used aligns the entire read allowing one mismatch, insertion or deletion. Each sequence read was classified as (a) hit or (b) no hit and was annotated with the number of hits found. All reads mapping to a single contiguous position in the genome were then clustered. For each genomic cluster the genomic sequence was extracted and put into a separate sequence database (the genomic cluster database). The cluster database was mapped to mirBase (mirBase v12, http://www.mirbase.org/) resulting in a microRNA (miR) annotated cluster database. miR reads were normalized to one million small RNAs (cpm). All mappings used the Genomequest Kerr proprietary implementation. The KERR algorithm belongs to a class of approximate string matching algorithms. Given two sequences S1 and S2, KERR computes the minimal number of differences between S1 and S2, by trying to optimally fit the shorter sequence into the longer one (Myers). Differences in sequence alignments arise from mismatches or gaps. This strategy assures to find all the local alignments allowing a given number of mismatch, insertion or deletion. For all comparisons one error was allowed. For more information about the Genomequest Kerr implementation, please refer to: http://wiki.genomequest.com/index.php/LSPMUL_HELP#KERR_.28aka_GenePAST.29

source_name: human fibroblast

growth_protocol:
Culturing of cells of primary human diploid fibroblasts strain WI38 were performed at physiological oxygen concentration of 3%
Culturing of cells of primary human diploid fibroblasts strain WI38 were performed at physiological oxygen concentration of 3%

extract_protocol: Senescent cells induced by oncogenic RAS were crosslinked by UV at 100-400mJ/cm2 and immediately collected afterwards on ice.  Cell pellets were lysed in RIPA lysis buffer on ice, adjusted to a protein concentration of 10mg/ml and digested extensively with DNAse I for 15 minutes at 37ºC followed by digestion with RNAse T1 (1000U/ml) for 15 minutes at 23ºC. Lysates were cleared and incubated with pan-anti-AGO, anti-H3K9me2 antibodies or IgG-antibodies (Upstate). Immunoprecipitates were collected with protein A/G beads, washed extensively and incubated again with 5,000U/ml RNAse T1 at 23ºC to rid the precipitates of any unspecifically attached RNA molecules. Immuncomplexes were proteinase-K digested and purified RNA molecules ethanol-precipitated.

treatment_protocol: transformed by Retroviral vector pBABE-RASV12

tag: cell line

tag: antibody


title: RIKEN_Cage_GM12878_nucleus_longNonPolyA

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

value: mesoderm

value: F

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: RIKEN_Cage_HepG2_nucleolus_total

value: hepatocellular carcinoma

value: total

value: Total RNA extract (longer than 200 nt)

value: cancer

value: endoderm

value: M

value: nucleolus

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: RIKEN_Cage_prostate_cell_longNonPolyA

source_name: prostate

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

value: Cage

value: CAGE 5' RNA Tags

value: longNonPolyA

value: Poly(A)- RNA longer than 200 nt

tag: softwareversion

value: bedtools v2.7.1

value: cell

value: Whole cell

value: Delve version 0.9


title: NP RNA a

status: Public on Dec 15 2011

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing: 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. The wiggle files are showing the read counts in log2 scale.

organism: Mus musculus

source_name: Neuronal progenitor (NP) cells derived from mouse embryonic stem cells

growth_protocol: Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)) and differentiated to Neuronal Progenitors and further to Terminally differentiated Neurons (TN). Mouse embryonic fibroblasts were isolated from wild-type embryos (C57Bl/6).

extract_protocol: RNA was isolated using Trizol (Invitrogen) following the manufacturer's instructions. Ribosomal RNA was removed using the Ribo-Zero  kit (Epicentre).  Libraries for sequencing were prepared with the Illumina small RNA-Seq Prep Kit (Cat#FC-102-1009) according to Illumina's Directional mRNA-Seq Library Prep. (Pre-Release Protocol Rev.A). The DNA was PCR amplified with Illumina primers for 12 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: cell type

tag: strain


title: ES RNA b

source_name: Embryonic Stem (ES) Cells

value: Embryonic Stem (ES) cells


title: NP RNA b

value: Neuronal progenitor (NP) cells derived from mouse embryonic stem cells


title: RIKEN_Cage_K562_nucleus_longNonPolyA

tag: datatype

tag: datatype description

tag: rnaextract

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

value: mesoderm

value: F

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: ES RNA a


title: BM-HPC_Cbp

city: Cambridge

first: Wai-In

last: Chan

address: Wellcome Trust/MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: Cambridge Institute for Medical Research

description: Chromatin IP against Cbp protein

data_processing: All sequencing reads for each sample were converted into density maps (bedgraph files). Eland files were then generated from the bed files for peak calling. The peak finding program MACS was used. All peaks were standardized to 400bp wide. Aligments were made to the mm9 mouse genome.

source_name: BM-HPC cell line

growth_protocol: BM-HPC cell line was maintained in Iscove’s modified Dulbecco’s media (IMDM), supplemented with 10%FBS, monothiolglycerol, 100 ng/ml of stem cell factor and 10ng/ml of human IL-6. Cells were maintained at the concentration between 5 x 105 to 2 x 106/ml

extract_protocol: BM-HPC cells were crossed linked with 1% formaldehyde, lysed, immunoprecipitated with indicated anitbody. Libraries were prepared according to Illumina's instructions.

treatment_protocol: No treatment

value: BM-HPC

value: Hematopoietic progenitor/stem cell line derived from Mouse bone marrow

value: rabbit polyclonal Cbp antibody


title: stage HH10 chicken embryos

city: Guangzhou

first: Peng

last: Shao

state: Guangdong

address: No. 135, Xingangxi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing: txt: The 3' linker, CTGTAGGCACCATCAAT, was identified and stripped out of the raw reads using a dynamic programming algorithm, which request at least 5nt overlap between 35nt reads and 3' adaptor sequence.

organism: Gallus gallus

source_name: whole embryo

growth_protocol: The stage X chicken embryos were isolated from freshly laid fertile unincubated chicken eggs; HH10 chicken embryos were obtained by incubating the fertile chicken eggs at 37.8°C under humid conditions for about 30 hr

extract_protocol: After removal of the amnion, embryos were rinsed in DEPC-treated 0.75% NaCl solution, and immediately processed for RNA isolation using Trizol reagent (Invitrogen) according to the manufacturer's manual. Small RNAs ranging from 18 to 33nt were gel-purified and ligated to the 3' adaptor (5'-pUCGUAUGCCGUCUUCUGCUUGUidT-3'; p, phosphate; idT, inverted deoxythymidine) and 5' adaptor (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3'). Ligation products were gel-purified, reverse transcribed, and amplified using Illumina's sRNA primer set (5'-CAAGCAGAAGACG GCATACGA-3'; 5'-AATGATACGGCGACCACCGA-3'). Samples were sequenced on an Illumina 1G Genome Analyzer.

treatment_protocol: Chicken eggs were wiped with 70% ethanol before manipulation of the embryos

tag: breed

value: Lingnan Yellow

tag: developmental stage

value: stage HH10

tag: tissue

value: embryo


title: BM-HPC_IgG control

description: Chromatin IP against IgG

value: rabbit IgG


title: stage X chicken embryos

value: stage X


title: Scyliorhinus canicula pooled Stage 24-30 embryos

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

description: Six pooled stage 24-30 Scyliorhinus canicula embryos

data_processing:
Reads from each species exported by Illumina's pipeline software were trimmed and assembled using CLCBio Genome Workbench version 4 (http://www.clcbio.com).
contig_read_counts.csv file: RNAseq data formatted as number of reads that map to a particular transcriptome assembly contig #.
contigs.fa file: The transcriptome assembly contigs.

organism: Scyliorhinus canicula

source_name: Stage 24-30 embryonic

extract_protocol: Total RNA was extracted using Tri Reagent (Ambion) from pooled tissue samples and converted into a library of template molecules using the mRNA-Seq Sample Prep Kit (Illumina) according to manufacturer's protocol.

value: Stage 24-30 embryos

tag: lineage

value: elasmobranch


title: UW_ChipSeq_GM12866_CTCF

status: Public on Dec 14 2011

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=wgEncodeUwTfbs

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: ChIP-seq

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell lineage

value: M

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion

value: Bowtie 0.12.7

tag: replicate

tag: replicate description

value: tier 1


title: UW_ChipSeq_GM12871_CTCF

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: mesoderm

tag: cell sex

tag: antibody


title: UW_ChipSeq_GM12869_CTCF

value: UW

tag: cell organism

tag: cell description

tag: cell lineage

value: F

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid


title: UW_ChipSeq_GM12867_CTCF

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

tag: treatment

tag: treatment description

tag: control

tag: control description

tag: controlid

tag: labexpid

tag: labversion


title: UW_ChipSeq_GM12868_CTCF

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: ChIP-seq

tag: cell

value: human

tag: replicate

tag: replicate description


title: UW_DnaseDgf_HRCEpiC

source_name: HRCEpiC

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=wgEncodeUwDgf

value: DnaseDgf

value: DNase Digital Footprinting

value: HRCEpiC

tag: cell organism

tag: cell description

value: renal cortical epithelial cells

tag: cell karyotype

value: normal

tag: cell lineage

tag: cell sex

value: U


title: UW_ChipSeq_GM12870_CTCF

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

value: M

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std


title: UW_DnaseDgf_HPF

source_name: HPF

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: HPF

value: pulmonary fibroblasts isolated from lung tissue

tag: labversion

value: Bowtie 0.12.7


title: UW_DnaseDgf_HPAF

source_name: HPAF

value: DnaseDgf

value: DNase Digital Footprinting

tag: cell

value: HPAF

tag: cell organism

value: human

tag: cell description

value: pulmonary artery fibroblasts

value: mesoderm


title: UW_DnaseDgf_AoAF

source_name: AoAF

value: AoAF

value: aortic adventitial fibroblast cells

tag: cell karyotype

value: normal

tag: cell lineage

tag: cell sex

value: F


title: Stage40_1

status: Public on Dec 12 2011

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

description: 3' adapter sequence: ATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Fastq data files were processed using custom Perl scripts. Reads with missing bases were excluded. 3' adapter sequences were identified and removed based on at least six matching nucleotides, allowing for up to two mismatches. Trimmed reads shorter than 16 nucleotides were discarded, along with reads without recognizable adapter sequences. The resulting 16-30 nt inserts were aligned to the X. tropicalis genome (xenTro2) downloaded from the UCSC Genome Browser website (http://genome.ucsc.edu/) using the ELAND module within the Illumina Genome Analyzer Pipeline Software, v0.3.0. Only perfect alignments were considered. In the case of reads aligning to multiple locations, the read-depth was scaled by the number of possible alignments. Read counts for mature miRNAs were obtained by assigning each miRNA the total number of reads (normalized for multiple alignments) overlapping the genomic locus of the mature miRNA (miRBase release 16).
FASTA (.fa) file contains unique sequences after trimming, the total count of each unique sequence is added to the end of the identifier line.
miRNA_mapped_counts.txt: Contains the counts of reads mapped to miRNA loci. Each sample is represented by one column. The first row contains the total read count that was used for mapping purposes, for each library.

organism: Xenopus laevis

source_name: Retinas from stage 40 embryos

growth_protocol: Xenopus laevis embyros were grown in 0.1X Modified Bath’s Saline at 14-22 oC until stage 24, 32 or 40

extract_protocol:
A tolal of 100 eyes were extracted from stage 24, 32 and 40 Xenopus laevis embryos, anesthesized in 1.5 mM MS222 (3-aminobenzoic acid ethyl ester methanesulphonate salt).  Developing lenses were dissected out, to obtain eyes composed of the neural retina and retinal pigmented epithelium and placed in RNA later. Total RNA was subsequently extracted using standard Trizol protocol for small sample size.
Small RNAs were extracted from denaturing PAGE and a 3' adapter was ligated to the end of each RNA molecule. 5' dependent libraries were generated using the Illumina/Solexa IG sequencing instrument.

tag: tissue

value: retinas

tag: Stage


title: Stage32_2

source_name: Retinas from stage 32 embryos


title: Stage24_2

source_name: Retinas from stage 24 embryos


title: Stage40_0

description: 3' adapter sequence: TCGTATGCCGTCTTCTGCTTG


title: UW_DnaseDgf_HPdLF

source_name: HPdLF

value: HPdLF

value: periodontal ligament fibroblasts

value: M


title: Stage40_2


title: UW_DnaseDgf_NH-A

source_name: NH-A

value: UW

value: Stamatoyannopoulous - University of Washington

value: NH-A

value: astrocytes (also called Astrocy)

value: ectoderm

value: U


title: UW_DnaseDgf_SAEC

source_name: SAEC

value: DnaseDgf

value: DNase Digital Footprinting

value: SAEC

value: human

value: small airway epithelial cells

value: endoderm

value: Bowtie 0.12.7


title: Acar_28S

city: Tempe

first: Kenro

last: Kusumi

email: kenro.kusumi@asu.edu, weckalba@asu.edu

address: 427 E Tyler Mall

institute: Arizona State University

description: Anolis carolinensis embryo with 28 somite pairs.

data_processing:
genes_28S.expr.txt; genome build: Anocarol2.0.61
transcripts_28S.expr.txt; genome build: Anocarol2.0.61
Raw reads from Illumina Hi-Seq 2000 were aligned to the Anolis carolinensis genome build (Anocar2.0.61) using tophat under default conditions. Cufflinks was run using the .bam files from tophat under default conditions and giving it the Anocarol2.0.61 gtf file for gene annotations. The Cufflinks output files (genes_*.expr, transcripts_*.expr) contain the RNA-seq data aligned to the Anolis carolinesis genome build 2.0.61.

organism: Anolis carolinensis

source_name: Anolis carolinensis whole embryo, 28 somite pairs

extract_protocol: Total RNA was extracted using the total RNA component of the mirVana (Ambion) kit. RNA-Seq library prep was carried out using the NuGEN Ovation RNA-Seq kit.

value: whole embryo

tag: developmental stage

value: 28 somite stage embryo


title: Acar_38S

description: Anolis carolinensis embryo with 38 somite pairs.

data_processing:
genes_38S.expr.txt; genome build: Anocarol2.0.61
transcripts_38S.expr.txt; genome build: Anocarol2.0.61
Raw reads from Illumina Hi-Seq 2000 were aligned to the Anolis carolinensis genome build (Anocar2.0.61) using tophat under default conditions. Cufflinks was run using the .bam files from tophat under default conditions and giving it the Anocarol2.0.61 gtf file for gene annotations. The Cufflinks output files (genes_*.expr, transcripts_*.expr) contain the RNA-seq data aligned to the Anolis carolinesis genome build 2.0.61.

source_name: Anolis carolinensis whole embryo, 38 somite pairs

value: 38 somite stage embryo


title: Callorhinchus milii pooled Stage 32 embryos

description: Six pooled stage 32 Callorhinchus milii embryos

organism: Callorhinchus milii

source_name: Stage 32 embryonic

value: Stage 32 embryos

tag: lineage

value: non-elasmobranch


title: WPP_CG8478_ChIPSeq_1 and 2

source_name: WPP

tag: strain

value: iso1 (y; bw cn sp)

value: WPP

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: Leucoraja erinacea pooled Stage 20-29 embryos

description: Six pooled stage 20-29 Leucoraja erinacea embryos

organism: Leucoraja erinaceus

source_name: Stage 20-29 embryonic

value: Stage 20-29 embryos

value: elasmobranch


title: Stage24_1

value: retinas


title: Stage24_0


title: RNA-seq Induced and PS1145-treated Replicate 1

city: PASADENA

first: Jevgenij

middle: A.

last: Raskatov

state: California

address: 1200 EAST CALIFORNIA BOULEVARD

department: CCE

institute: CalTech

description: A549 nonsmall lung cancer cell line

data_processing:
Bowtie mapping to hg19; Erange
Tophat for mapping; Cufflinks module cuffdiff to compare transcript levels
processed_RNAseq_N_way_cuffdiff_combined_replicates_NIvIvPAvPS1145.diff: transcript level comparison (fpkm)

source_name: Lung cancer cell line

growth_protocol: F12-k medium supplemented with 10%FBS and Pen-Strep

extract_protocol:
Two-step crosslinking of chromatin; coupling of antibody to beads (16-20h); incubation with sonicated lysates (16-20h); libraries prepared using standard Illumina reagents and protocols
Trizol isolation protocol, DNAase digest, double poly-A select; libraries prepared using standard Illumina reagents and protocols

treatment_protocol: Polyamide 1 (72 hours) or PS1145 (2 hours), where applicable; TNFa induction (12 hours), where applicable

tag: protocol

value: Induced and PS1145-treated

tag: cell line

tag: experiment type

value: RNA-seq


title: RNA-seq Induced and PS1145-treated Replicate 2

description: A549 nonsmall lung cancer cell line


title: RNA-seq Induced and PA-treated Replicate 2

description: A549 nonsmall lung cancer cell line

value: Induced and PA-treated


title: RNA-seq Induced and PA-treated Replicate 1

description: A549 nonsmall lung cancer cell line


title: Stage32_0


title: RNA-seq Induced Replicate 1

description: A549 nonsmall lung cancer cell line

value: Induced


title: RNA-seq Induced Replicate 2

description: A549 nonsmall lung cancer cell line


title: Stage32_1


title: RNA-seq Non-induced Replicate 2

description: A549 nonsmall lung cancer cell line

value: Non-induced


title: RNA-seq Non-induced Replicate 1

description: A549 nonsmall lung cancer cell line


title: ChIP-seq TNFa induced Replicate 2

description: A549 nonsmall lung cancer cell line

data_processing:
processed_ChIPseq_30minTNFa_v_input_replicate2.out; genome build: hg19
Bowtie mapping to hg19; Erange
Tophat for mapping; Cufflinks module cuffdiff to compare transcript levels
processed_RNAseq_N_way_cuffdiff_combined_replicates_NIvIvPAvPS1145.diff: transcript level comparison (fpkm)

value: TNFa induced

tag: chip antibody

value: f-6 (Santa-Cruz)

value: ChIP-seq


title: ChIP-seq TNFa induced Replicate 1

description: A549 nonsmall lung cancer cell line

data_processing:
processed_ChIPseq_30minTNFa_v_input_replicate1.out; genome build: hg19
Bowtie mapping to hg19; Erange
Tophat for mapping; Cufflinks module cuffdiff to compare transcript levels


title: K562 cells with shRNA targeting ATF3 gene cultured with no doxycycline (uninduced - UI), rep1.

city: Huntsville

first: Anita

last: Bansal

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Uninduced K562-shATF3 cells used as control to measure the change in mRNA expression profile after ATF3 knock down
K562-shATF3_UI_rep1

data_processing:
SL2585.bam; genome build: hg19
SL2585.bw; genome build: hg19
SL2585.gtf; genome build: hg19
Bowtie, Cufflinks

growth_protocol: Refer to http://hudsonalpha.org/sites/default/files/pdf/shRNA%20K562%20protocol.pdf for growing conditions for these cell lines

extract_protocol: Standard Illumina RNA-seq library construction

treatment_protocol: Refer to http://hudsonalpha.org/sites/default/files/pdf/shRNA%20K562%20protocol.pdf for culturing conditions for these cell lines

tag: shRNA expression

value: no shRNA expression

tag: treatment

value: Puromycin


title: K562 cells with shRNA targeting ATF3 gene cultured with doxycycline for 24 hours (24 hr), rep1.

description:
K562-shATF3 cells showing decreased expression of ATF3 gene after induction of shRNA targeting ATF3 with doxycycline.
K562-shATF3_3ugDox_24hrs_rep1

data_processing:
SL2592.bam; genome build: hg19
SL2592.bw; genome build: hg19
SL2592.gtf; genome build: hg19
Bowtie, Cufflinks

value: expressing shRNA targeting ATF3

value: Puromycin, doxycycline


title: K562 cells with shRNA targeting EGR1 gene cultured with doxycycline for 72 hours (72 hr), rep2.

description:
K562-shEGR1 cells showing decreased expression of EGR1 gene after induction of shRNA targeting EGR1 with doxycycline.
K562-shEGR1_3ugDox_72hrs_rep2

data_processing:
SL4486.bam; genome build: hg19
SL4486.bw; genome build: hg19
SL4486.gtf; genome build: hg19
Bowtie, Cufflinks

value: expressing shRNA targeting EGR1


title: K562 cells with shRNA targeting ATF3 gene cultured with no doxycycline (uninduced - UI), rep2.

description:
Uninduced K562-shATF3 cells used as control to measure the change in mRNA expression profile after ATF3 knock down
K562-shATF3_UI_rep2

data_processing:
SL4337.bam; genome build: hg19
SL4337.bw; genome build: hg19
SL4337.gtf; genome build: hg19
Bowtie, Cufflinks


title: K562 cells with shRNA targeting EGR1 gene cultured with doxycycline for 72 hours (72 hr), rep1.

description:
K562-shEGR1 cells showing decreased expression of EGR1 gene after induction of shRNA targeting EGR1 with doxycycline.
K562-shEGR1_3ugDox_72hrs_rep1

data_processing:
SL1583.bam; genome build: hg19
SL1583.bw; genome build: hg19
SL1583.gtf; genome build: hg19
Bowtie, Cufflinks


title: Cell line RNA-Seq (I)

city: Shanghai

first: Tieliu

last: Shi

address: Dongchuan Road 500

department: The Institute of Biomedical Sciences

institute: East China Normal University

data_processing: We  aligned all the reads onto human reference genome hg19 (download from UCSC http://genome.ucsc.edu/) using the software Tophat (http://tophat.cbcb.umd.edu/) with default parameters.

source_name: Stratagene Universal Human Reference RNA  sample A (UHRR, Catalog #740000), 10 mixed cell lines

extract_protocol: Standard Illumina mRNA-Seq protocol and reagents

tag: sample composition

value: 10 human cell lines of various origins (B lymphocyte, brain, breast, cervix, liposarcoma, liver, macrophage, skin, testis, and T lymphocyte)

tag: vendor

tag: read length

value: 35 bp


title: Cell line RNA-Seq (II)

description: Stratagene Universal Human Reference RNA


title: Human brain RNA-Seq (I)

description: Ambion Human Brain Reference RNA

source_name: Ambion Human Brain Reference RNA sample B (HBRR, Catalog #6050), Brain tissues

value: Several brain regions from 23 adult donors


title: K562 cells with shRNA targeting EGR1 gene cultured with no doxycycline (uninduced - UI), rep2.

description:
Uninduced K562-shEGR1 cells used as control to measure the change in mRNA expression profile after EGR1 knock down
K562-shEGR1_UI_rep2

data_processing:
SL6485.bam; genome build: hg19
SL6485.bw; genome build: hg19
SL6485.gtf; genome build: hg19
Bowtie, Cufflinks


title: Human brain RNA-Seq (II)

description: Ambion Human Brain Reference RNA


title: ChIP-seq Input

description: A549 nonsmall lung cancer cell line

data_processing:
Bowtie mapping to hg19; Erange
Tophat for mapping; Cufflinks module cuffdiff to compare transcript levels

value: Input


title: nrg1Δ at 37°C + CO2 replicate 2

status: Public on Dec 10 2011

city: St. Louis

first: Brian

middle: Clifton

last: Haynes

state: MO

address: 4444 Forest Park Ave

department: Computer Science

institute: Washington University

description: nrg1Δ at 37°C + CO2 biological replicate 2 of 2

data_processing:
bed: To produce bed alignments, sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using Tophat v1.2.0.  Only unique alignments were retained for further analysis. The resulting bam files were converted using bamToBed (v2.13.0)
cuff: Gene expression was quantified processing tophat produced bam alignments with Cufflinks v0.9.3 with the current H99 annotation (v2) provided by the Broad institute's Fungal Genome initiative.  Expression was normalized by applying the Cufflinks supplied quartile normalization routine.
wig: bam files were converted to wig files representing coverage using samtools 0.1.12a.

organism: Cryptococcus neoformans

source_name: cultured cells

growth_protocol: Cells were cultured overnight in YPD to a density of 1-2 OD600

extract_protocol: PolyA+ RNA was purified from total RNA using the Dynabeads mRNA Purification Kit according to the manufacturer's instructions (from Invitrogen). Each sample was resuspended in 2 µl of 100 mM zinc acetate and heated at 60°C for 3 minutes to fragment the RNA by hydrolysis. The reaction was quenched by the addition of 2 µl volumes of 200 mM EDTA and purified with an Illustra Microspin G25 column (from GE Healthcare). First strand cDNA was made using hexameric random primers and SuperScript III Reverse Transcriptase (from Invitrogen) according to the manufacturer recommendations, and the product was treated with E. coli DNA ligase, DNA polymerase I, and RNase H to prepare double stranded cDNA using standard methods. The cDNA libraries were end-repaired with a Quick Blunting kit (from New England BioLabs) and A-tailed using Klenow exo- and dATP. Illumina adapters with four base barcodes were ligated to the cDNA and fragments ranging from 150-250 bp in size were selected using gel electrophoresis as recommended by the manufacturer. The libraries were enriched in a 10-cycle PCR with Phusion Hot Start II High-Fidelity DNA Polymerase (from Finnzymes Reagents) and pooled in equimolar ratios for multiplex sequencing. Single read, 36-cycle runs were completed on the Illumina Genome Analyzer IIx.

treatment_protocol: Cells were transfered to grow for 90 minutes in either capsule-inducing (DMEM, 37 °C, 5% CO2) or capsule non-inducing (DMEM, 30 °C, room air) conditions prior to isolation of total RNA. Two biological replicates were performed for each mutant (ada2delta, nrg1delta and cir1delta) and four for wild type.

tag: genotype/variation

tag: condition

value: capsule-inducing


title: Liver-scAAV9-Mock-4weeks

city: Boston

first: Jui-Hung

last: Hung

address: 24 cummington st

institute: Boston University

description: 18-30 nt small RNAs

data_processing: supplementary files contain sequences of 18-30 nt small RNAs and frequencies

source_name: Liver

growth_protocol: C57BL/6 mouse was injected with scAAV9 expressing anti miR-122 or anti let-7 TuD or no TuD (Mock). 4 weeks after injection small RNAs were prepared from liver.

extract_protocol: Total RNA was extracted from liver of mice 4 weeks after injection of scAAV9 vectors using miRvana (Ambion), then short (18-30 nt) RNAs were gel-purified. Library was constructed as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)

tag: tissue

value: Liver

tag: time

value: 4 wks post-injection


title: Liver-scAAV9-TuD-let-7-4weeks

description: 18-30 nt small RNAs

tag: strain


title: wildtype  at 37°C + CO2 replicate 4

description: wildtype  at 37°C + CO2 biological replicate 4 of 4

value: wildtype


title: ada2Δ at 37°C + CO2 replicate 2

description: ada2Δ at 37°C + CO2 biological replicate 2 of 2


title: K562 cells with shRNA targeting ATF3 gene cultured with doxycycline for 24 hours (24 hr), rep2.

description:
K562-shATF3 cells showing decreased expression of ATF3 gene after induction of shRNA targeting ATF3 with doxycycline.
K562-shATF3_3ugDox_24hrs_rep2

data_processing:
SL4326.bam; genome build: hg19
SL4326.bw; genome build: hg19
SL4326.gtf; genome build: hg19
Bowtie, Cufflinks


title: cir1Δ at 37°C + CO2 replicate 1

description: cir1Δ at 37°C + CO2 biological replicate 1 of 2


title: nrg1Δ at 37°C + CO2 replicate 1

description: nrg1Δ at 37°C + CO2 biological replicate 1 of 2


title: wildtype  at 37°C + CO2 replicate 1

description: wildtype  at 37°C + CO2 biological replicate 1 of 4


title: cir1Δ at 30°C replicate 2

description: cir1Δ at 30°C biological replicate 2 of 2

value: capsule non-inducing


title: K562 cells with shRNA targeting EGR1 gene cultured with no doxycycline (uninduced - UI), rep1.

description:
Uninduced K562-shEGR1 cells used as control to measure the change in mRNA expression profile after EGR1 knock down
K562-shEGR1_UI_rep1

data_processing:
SL1584.bam; genome build: hg19
SL1584.bw; genome build: hg19
SL1584.gtf; genome build: hg19
Bowtie, Cufflinks


title: ada2Δ at 37°C + CO2 replicate 1

description: ada2Δ at 37°C + CO2 biological replicate 1 of 2


title: nrg1Δ at 30°C replicate 1

description: nrg1Δ at 30°C biological replicate 1 of 2


title: ada2Δ at 30°C replicate 2

description: ada2Δ at 30°C biological replicate 2 of 2


title: cir1Δ at 37°C + CO2 replicate 2

description: cir1Δ at 37°C + CO2 biological replicate 2 of 2


title: Liver-scAAV9-TuD-miR-122-4weeks

description: 18-30 nt small RNAs


title: nrg1Δ at 30°C replicate 2

description: nrg1Δ at 30°C biological replicate 2 of 2


title: wildtype  at 30°C replicate 2

description: wildtype  at 30°C biological replicate 2 of 4


title: wildtype  at 30°C replicate 4

description: wildtype  at 30°C biological replicate 4 of 4


title: wildtype  at 30°C replicate 3

description: wildtype  at 30°C biological replicate 3 of 4


title: wildtype  at 37°C + CO2 replicate 2

description: wildtype  at 37°C + CO2 biological replicate 2 of 4


title: ada2Δ at 30°C replicate 1

description: ada2Δ at 30°C biological replicate 1 of 2


title: wildtype  at 37°C + CO2 replicate 3

description: wildtype  at 37°C + CO2 biological replicate 3 of 4


title: wildtype  at 30°C replicate 1

description: wildtype  at 30°C  biological replicate 1 of 4


title: Saccharomyces_bayanus-nucleosome-reads

status: Public on Dec 09 2011

city: Toronto

first: Kyle

last: Tsui

address: 160 College Street

country: Canada

institute: University of Toronto

data_processing: The genome sequences were retrieved using SGD or Genolevures. Reads were mapped using Novocraft and only unique reads were further processed. As reads covered both ends of the ~150bp length DNA fragments that correspond to mono-nucleosomes, we converted the mapped positions into the estimated center position by adding or removing (depending on the strand) half the length of a typical DNA fragment. This typical length was evaluated in each sample by the distances between consecutive peaks of reads from the forward and backward strands, and was between 110bp to 130bp in all samples. For S. bayanus and C.glabrata, the reads from two biological repeats were combined into a single dataset. Data represents one-to-one orthologs which were defined based on Cliften et al. (Cliften, Sudarsanam et al. 2003) and Wapinski et al. (Wapinski, Pfeffer et al. 2007). Occupancy patterns were taken from -600 to +1000 (relative to the ATG) and for genes shorter than 1kb, we examined the pattern only until the end of the gene.

organism: Saccharomyces bayanus

source_name: Saccharomyces bayanus

growth_protocol: Cells were grown in YPD (2% peptone, 1% yeast extract, 2% dextrose) starting from a overnight culture until they reached mid-log phase (0.8 OD).

extract_protocol: Mono-nucleosomes were extracted by treating the cell spheroplast with Mnase.  Samples representing mono-nucleosomes were gel extracted, end repaired and adapter ligated.

treatment_protocol: Cells were then cross-linked with formaldehyde and mono-nucleosomes were isolated according to modified protocols from Lee, Tillo., et al. Nature Genetics (2007)


title: 4SU_GLD1_PARCLIP_1

city: Berlin

first: Dominic

last: Gruen

address: Robert-Roessle-Strasse 10

country: Germany

institute: Max-Delbrueck-Center

description:
PARCLIP RNA
RNAs bond to GLD-1 were purified and sequenced by in vivo PAR-CLIP

data_processing: adapter sequences were removed using the mirdeep2.0 package with default parameters (friedlaender et al NAR 2012) and collapsed to unique reads

organism: Caenorhabditis elegans

source_name: nematode whole worm

growth_protocol: Worms were cultivated at 24°C on NGM plates as previously described (Stiernagle, 2006)

extract_protocol:
Arrested L1 worms were grown in liquid culture supplemented with 2mM 4SU or 6SG. 250,000 worms were sufficient for one iPAR-CLIP experiment. Living adult worms were transferred to NGM plates and crosslinked on ice using a Stratalinker (Stratagene) with customized 365nm UV-lamps (energy setting: 2J/cm2). Worms were lysed on ice by douncing in NP40 lysis buffer (50 mM HEPES-K pH 7.5, 150 mM KCl, 2 mM EDTA, 0.5% (v/v) NP-40, 0.5 mM DTT, protease inhibitor cocktail (Roche)). Cleared lysates were treated with RNase T1 (Fermentas) (final concentration 1U/?l) for 15 min at 22ºC. GLD-1::GFP::FLAG fusion proteins were immunoprecipitated for 1h at 4ºC using anti-FLAG antibody (Sigma, F3165) coupled to Protein G magnetic beads (Invitrogen). For one iPAR-CLIP experiment (1ml cleared lysate obtained from 250,000 worms), 300µl beads and 150µg antibody were used. Immunoprecipitates were treated with RNase T1 (100U/?l) for exactly 12 min at 22 ºC. Subsequently, PAR-CLIP was carried out as described previously (Hafner et al, 2010).  cDNA libraries  were sequenced on a Genome Analyzer II (Illumina).

PARCLIP; GLD-1::FLAG IP + RNAse T1

value: BS1080 (GLD-1::GFP::FLAG)

tag: cultivation temperture

tag: developmetal stage

value: young adult


title: 6SG_GLD1_PARCLIP_1


title: 4SU_GLD1_PARCLIP_3


title: 4SU_GLD1_PARCLIP_2


title: EDC1_Total

city: San Francisco

first: Eugene

last: Oh

address: 1700 4th Street

department: CMP

institute: UCSF

description: Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized, rRNA subtracted, and PCR amplified.

data_processing: The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker.

organism: Escherichia coli

source_name: Harvested by rapid filtration; EDC treated ex vivo; Total footprints

growth_protocol: An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45.

extract_protocol:
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose gradient. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing.
library strategy: Ribosome profiling

treatment_protocol: Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 20 mM EDC, pH 5.8. The crosslinking reaction was quenched with 250 mM glycine, 100 mM Tris Cl 8.0, and 4 mM NaHCO3.

tag: growth stage

value: mid-log phase

value: MC4100 ∆tig::kan pTig-TEV-Avi


title: DSP3_Total

source_name: Harvested by rapid filtration; DSP treated ex vivo; Total footprints

treatment_protocol: Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3.


title: input

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing: The sequence tags were aligned to the mouse (mm9) genome with Bowtie 3.

source_name: input

growth_protocol: To generate the tamoxifen-inducible cre Lrh1 deletion, mice with floxed Lrh1 alleles (Lee et al. 2008) were crossed with a ROSA26 Tam-ERCre strain (no. 004847, Jackson Laboratories). This line was backcrossed to generate a mixed strain, homozygous Lrh1 floxed, and heterozygous ROSA26 Tam-ERCre line. From this line, adult male mice with or without ROSA26 Tam-ERCre (3–5 mo old) were treated with 0.25 mg/g tamoxifen (T5648, Sigma-Aldrich) in corn oil by oral gavage for two consecutive days followed by sacrifice after 5 d. Mice were kept on a 12-h light–dark cycle from 6:00 am to 6:00 pm with free access to water and standard chow diet (TD.2016, Harland-Teklad Laboratories).

extract_protocol: ChIP-seq was performed using antibodies against LRH-1 (R&D systems). An amplified library was prepared using manufacturer’s protocol (Illumina Inc). 0.7 femtomoles were analyzed with an Illumina/Solexa Genome analyzer.

value: pancreas

tag: gender

value: male

tag: background strain

value: ROSA26 Tam-ERCre

tag: antibody


title: Lrh1 ChIP

source_name: Lrh1 ChIP

tag: antibody vendor

value: R&D systems


title: EDC1_AP

source_name: Harvested by rapid filtration; EDC treated ex vivo; Affinity purified TF crosslinked RNC footprints

extract_protocol:
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose cushion, and affinity purified via TF. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing.
library strategy: Selective ribosome profiling


title: cir1Δ at 30°C replicate 1

description: cir1Δ at 30°C biological replicate 1 of 2


title: DSP2_Total

description: Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.

source_name: Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Total footprints

treatment_protocol: The culture was incubated with 100 µg/ml of chloramphenicol for 2 min, and harvested by centrifugation. The pellet with washed and resuspended in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris Cl, 0.4% Triton X100, 0.1% NP-40, and 100 µl/ml chloramphenicol, and flash frozen over liquid nitrogen. The frozen cell pellets were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3.


title: DSP3_AP

source_name: Harvested by rapid filtration; DSP treated ex vivo; Affinity purified TF crosslinked RNC footprints


title: DSP2_AP

source_name: Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Affinity purified TF crosslinked RNC footprints


title: DSP1_AP


title: MouseNP_BisSeq_GAIIx

description: bisulfite converted

data_processing: All C nucleotides in sequence reads from bisulfite converted samples were converted in silico to T nucleotides, and the converted reads were aligned to a similarly converted genome separately to each strand using the software bowtie (version 0.10.0.1)(Langmead et al., Genome Biol. 2009;10(3):212) with parameters --best --strata -v 3 --norc -a. Only reads with a unique alignment in this reduced alphabet base-space were retained, and C nucleotides from the original reads and genome were reintroduced. To eliminate effects caused by polymorphisms in our experimental system, C nucleotides that overlapped known SNPs between the reference C57BL/6J and the 129S5 strains were removed from further analysis based on the SNPs identified by the Mouse Genomes Project at Sanger Institute (downloaded from ftp://ftp-mouse.sanger.ac.uk/REL-1003/SNPs/20100301-all-snps.tab.gz). Total and methylated counts for all covered CpGs in the genome were calculated as the number of alignments with either C (methylated) or T (unmethylated) and the number of alignments with C (methylated), combining the counts from the two Cs in a CpG and its reverse complement (position i on plus strand and position i+1 on minus strand).

source_name: ES-derived neuronal progenitor cells

growth_protocol: Wild-type embryonic stem cells (129-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: The protocol was adapted from Illumina Genomic DNA Sample Preparation Guide and Paired-End Sample Preparation Guide. Briefly, One to five ug of input DNA were fragmented by sonication to 50-500 bp with a Bioruptor (Diagenode, Sparta, NJ). DNA fragments were end repaired by incubation at 20 degrees C. for 30 minutes with 400uM dNTP, 15 units of T4 DNA polymerase (NEB #M0203S), 5 units of DNA Polymerase I Lg. Frag. (Klenow) (NEB #M0210S), 50 units of T4 PNK (NEB #M0201S), 1x T4 DNA ligase buffer containing 10mM ATP (NEB). 3' ends of DNA fragments were adenylated by incubation at 37 degrees C. for 30 minutes with 200uM dATP, 1xNEB Buffer 2, 15 units Klenow Fragment (3'-> 5' exo-)(NEB # M0212L). Adapter sequences were reproduced based on Illumina adapter sequences (Oligonucleotide sequences 2006-2008 Illumina, Inc. All rights reserved). For single end sequencing: 5' P-GATXGGAAGAGXGGTTXAGXAGGAATGXXGAG and  5' AXAXTXTTTXXXTAXAXGAXGXTCTTXXGATXT, and for paired end sequencing:  5' P-GATXGGAAGAGXGGTTXAGXAGGAATGXXGAG and   5' AXAXTXTTTXXXTAXAXGAXGXTXTTXXGATXT where X is a methylated cytosine. Adapters were ordered as single stranded oligos (Microsynth AG), resupended in annealing buffer (10mM Tris pH7.5, 50mM NaCl, 1mM EDTA), annealed by heating at 95 degrees C. for 10 minutes and cooling down slowly. Annealed adapters were ligated to the DNA fragments as per manufacturer's instructions for genomic DNA library construction. Adapter-ligated DNA of 140-210 bp (for single end sequencing) or 340-410 (for paired end sequencing) was isolated by 2% agarose gel electrophoresis. Gel purified DNA was then converted with sodium bisulfite using the Imprint DNA Modification Kit (Sigma-Aldrich) as per manufacturer's instructions. One third of the bisulfite-converted, adapter-ligated DNA molecules were enriched by 7 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5ul 10X PfuTurbo reaction buffer, 25uM dNTPs, 0.5uM of Illumina PCR primers. The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 7 cycles of 98C 15 sec, 65C 30 sec and 72C 3 min, ending with one 72C 5 min step. The reaction products were purified using the MinElute PCR purification kit (Qiagen, Valencia, CA), separated by 2% agarose gel electrophoresis to separate the library from adapter-adapter ligation products, and purified from the gel using the MinElute gel purification kit (Qiagen, Valencia, CA). Quality of the libraries and template size distribution were assessed by running an aliquot of the library on an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell type

value: ES-derived neuronal progenitor cells


title: ES_PolII_ChIPseq_rep1

description: Chromatin IP against PolII

data_processing: 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.

extract_protocol: Chromatin immunoprecipitation (ChIP) assay for CTCF was performed according to the Upstate protocol. ChIP assay for REST was performed as previously described (Koch et al., 2007). ChIP experiments for Pax6, PolII and monomethylated H3K4 (H3K4me1) were performed as previously described (Weber et al., 2007). The antibodies used were: anti-monomethyl-H3K4(Abcam #ab8895), anti-CTCF(SantaCruz #15914), anti-PolII(), anti-REST (Santa Cruz #H-290)., anti-Pax6(Covance PRB-278P). ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/80 of ChIP or 20ng of input chromatin per PCR reaction. H3K4me1, CTCF, PolII and REST ChIP-seq libraries for Illumina sequencing were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illuminaâs instructions and sequenced on the Genome Analyzer 2 following the manufacturerâs protocols. Pax6 ChIP samples were amplified using the WGA2 kit (Sigma) and hybridized to a custom tiling microarray (NimbleGen Systems Inc.).

value: Embryonic stem cells

value: wild type

tag: chip antibody

value: anti-PolII(N20) (SantaCruz #sc-899)


title: ES_H3K4me2_ChIPseq_rep2

description: Chromatin IP against H3K4me2

value: anti-monomethyl-H3K4 (Abcam #ab8895)


title: ES_Input_ChIPseq_rep1

description: Input chromatin


title: ES_H3K4me1_ChIPseq

description: Chromatin IP against H3K4me1


title: ES_PolII_ChIPseq_rep2

description: Chromatin IP against PolII


title: ES_H3K4me2_ChIPseq_rep1

description: Chromatin IP against H3K4me2


title: ES_Input_ChIPseq_rep2

description: Input chromatin


title: MouseES_BisSeq_GAIIx

description: bisulfite converted

source_name: Embryonic stem cells


title: ES_H3K27me3_ChIPseq_rep2

description: Chromatin IP against H3K27me3

value: anti-H3K27me3 (Upstate 07-449)


title: ES_H3K27me3_ChIPseq_rep3

description: Chromatin IP against H3K27me3


title: WHOLE_WORM_WILDTYPE

description: wildtype young adult

data_processing: Deep sequencing read libraries of WT and glp-4 samples were mapped to the C. elegans genome sequence (ws190) by running TOPHAT v1.3.1 (with parameters –i 30 –I  10000  --mate-inner-dist 250 --mate-std-dev 125) and using gene models (see manuscript) to provide reference splice junctions. Subsequently, isoform expression was quantified by running CUFFLINKS v1.0.3 60 using the same gene models as reference annotation. Expression of gene loci was estimated by summing up FPKM values of all isoforms and confidence intervals were determined by summing up lower and upper boundaries for isoform expression as determined by CUFFLINKS.

molecule: polyA RNA

extract_protocol: Illumina paired end polyA standard protocol (polyadenylated transcripts), fragment length ~250nt, insert size ~50nt.


title: WHOLE_WORM_glp4

description: germline deficient young adult

value: glp-4(bn-2) TS


title: Candida_glabrata-nucleosome-reads

organism: Nakaseomyces glabratus

source_name: Candida glabrata


title: DSP1_Total


title: ES_H3K27me3_ChIPseq_rep1

description: Chromatin IP against H3K27me3


title: TKO_CTCF_ChIPseq_rep2

description: Chromatin IP against CTCF

value: Mixed (129SvJae-C57BL/6)

value: Dnmt1/3a/3b triple knock-out (TKO)

value: anti-CTCF (SantaCruz #15914)


title: TKO_CTCF_ChIPseq_rep1

description: Chromatin IP against CTCF


title: ES_CTCF_ChIPseq_rep3

description: Chromatin IP against CTCF


title: RV_Mu3 (Mutant sample 3)

first: Gladstone

last: Bioinformatics

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

description: Sample 2

data_processing: RNA expression levels: The raw data paired-end FASTQ files were first aligned to mm9 with TopHat 1.2.0 (with the specific command: tophat-1.2.0.Linux_x86_64/tophat --solexa1.3-quals -o <OUTPUT> --segment-mismatches 2 -m 2 --microexon-search -j dcc13/DSAGE/tables/mm9.juncs --butterfly-search -r 185 --mate-std-dev 75 mm9 <FIRST_FASTQ_FILE_IN_PAIR> <SECOND_FASTQ_FILE_IN_PAIR>). Mapped reads were aggregated into gene-level reads using Cufflinks. Differential expression P-values were calculated using the binomial test.

source_name: Ezh2-deficient_heart_right ventricle

extract_protocol: Library construction protocol is described in detail in the following paper: Christodoulou, D. C., Gorham, J. M., Herman, D. S. and Seidman, J. 2011. Construction of Normalized RNA-seq Libraries for Next-Generation Sequencing Using the Crab Duplex-Specific Nuclease. Current Protocols in Molecular Biology. 94:4.12.1–4.12.11.  Short summary excerpt from the paper: "This unit describes the generation of a normalized RNA-seq library for next-generation sequencing by utilizing the preference of the crab duplex nuclease (DSN) for digesting double-stranded, rather than single-stranded DNA (unit 5.12; also see Zhulidov et al., 2004). In this approach (Basic Protocol), polyadenylated RNA is used to generate a complex RNA-seq library. The library is denatured and incompletely renatured, and then digested with DSN. The kinetics of DNA annealing are such that at any given time abundant DNA molecules are more likely to have re-annealed and become double stranded, while rare molecules are more likely to remain single stranded. Thus, preferentially digesting double-stranded DNA with DSN yields a library markedly enriched for more rare DNA species.

value: Mixed background of C57BL/6

tag: genetic variation

value: Ezh2-deficient mutant

tag: development stage

value: Adult

value: Heart, Right ventricle


title: RV_Wt2 (Wildtype sample 2)

description: Sample 4

source_name: wt_heart_right ventricle

value: Wildtype


title: RV_Mu1 (Mutant sample 1)

description: Sample 1


title: NP_H3K4me1_ChIPseq

description: Chromatin IP against H3K4me1

source_name: Neural progenitor cells

value: ES-derived neural progenitor cells

value: Abcam

tag: antibody catalog#


title: ES_CTCF_ChIPseq_rep2

description: Chromatin IP against CTCF

tag: genotype/variation


title: MouseNP_BisSeq_HiSeq

description: bisulfite converted

value: ES-derived neuronal progenitor cells


title: MouseES_BisSeq_HiSeq

description: bisulfite converted

value: Embryonic stem cells


title: Saccharomyces_cerevisiae-nucleosome-reads

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae


title: p53_ChIP-seq

status: Public on Dec 08 2011

city: Berkeley

first: Krassimira

middle: I

last: Botcheva

address: One Cyclotron Rd MS977

department: Cell and Molecular Biology

institute: Lawrence Berkeley National Laboratory

description: Chromatin IP against p53

data_processing:
Alignment: Sequence reads were mapped to the human reference genome March, 2006 (hg18 / NCBI Build 36.1), using in-house developed software. All reads were mapped at 36 nt length (w/o truncation) allowing one mismatch. 3,741,438 ChIP-seq reads (69% from the total) and 8,001,237 Input-seq reads (80% from the total) were distinct reads mapped uniquely, and these were subjected to further analysis for peak detection.
Peak detection was performed using in-house developed software. Briefly, enriched locations were identified by adapting published methods whereby distinct uniquely mapped reads were used to construct a coverage map at each nucleotide at each genome position, yielding peaks at the enriched locations. These were then filtered by applying statistical confidence tests.
Fragment coverage was calculated by extending reads by 350nt in the appropriate direction. Coverage files are in bedGraph format.

source_name: normal human lung fibroblasts

growth_protocol: Normal human lung fibroblasts IMR90 were grown in EME Medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U penicillin and 100 µg streptomycin, at 37oC, in a humidified atmosphere containing 5% CO2.

extract_protocol: ChIP and Input DNA libraries for single end sequencing were prepared with the Illumina ChIP-Seq DNA Sample Prep kit (cat# IP-102-1001) according to the manufacturer's instructions (Illumina, cat# 11257047). Briefly, DNA was purified using QIAGEN PCR clean up kit, DNA fragments were 3' A-tailed and ligated to Illumina adapters. Adapter-ligated DNA was purified using magnetic beads (Agencourt AMPure kit, cat# A50850), and the entire amount of eluted DNA was used for PCR amplification (14-16 cycles) with Illumina PCR primers 1.1 and 1.2. The PCR amplified ChIP and Input libraries were subjected to electrophoresis and fragments with average size ~200-400 bp were recovered using the QIAGEN gel extraction kit. Each library was quantified on the Agilent Technologies 2100 Bioanalyzer using the High Sensitivity DNA kit (cat# 5067-4626, Agilent Technologies) and single end sequencing was performed on Illumina Genome Analyzer 2x instrument according to the manufacturer's protocol.

treatment_protocol: Cultures were treated with 375 Î¼M 5-fluorouracil (SIGMA) for 6 hrs.

tag: cell line

tag: pdl

value: p53-specific DO1

value: Santa Kruz Biotechnology Inc.

tag: catalog number


title: Sense control CHART

status: Public on Dec 07 2011

first: Mark

last: Borowsky

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: MGH

description: CHART-seq study

data_processing: DNA fragments were mapped to the Drosophila genome (dm3, Bowtie aligner, see: Langmead B, Trapnell C, Pop M, & Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25), recording positions of uniquely-mappable reads. The enrichment of biotin-CHART signal was determined relative to the sense-oligo controls and RNase H-eluted CHART signal was determined relative to input. Conservative enrichment profiles were determined using SPP package (Kharchenko PV, Tolstorukov MY, & Park PJ (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26(12):1351-1359), (lower bound of enrichment was determined based on a Poisson model, with a confidence interval of p = 0.001). Positions of top CHART sites were determined as peaks of the conservative enrichment profiles (with minimum separation of 3 kb).

source_name: S2 cells

growth_protocol: Drosophila S2 cells stably transfected with a plasmid expressing MSL3-TAP (Alekseyenko et al. High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes & Development (2006) vol. 20 (7) pp. 848-57) were grown in shaker flasks in serum-free CCM3 medium (Hyclone).

extract_protocol:
Libraries were constructed using a modified version of the Illumina PE ChIP-seq protocol.
Average insert size: 188 bp

treatment_protocol: Extract (250 µL, 8x107 cell equiv.) was adjusted to hybridization conditions (20mM HEPES pH7.5, 817mM NaCl, 1.9M Urea, 0.4% SDS, 5.7mM EDTA, 0.3mM EGTA, 0.03%NaDeoxycholate, 5XDenhardt’s) and pre-cleared with ultralink-streptavidin resin.  For biotin eluted CHART: Capture oligonucleotides (800 nM ea. R2.1-3) were added and hybridized (55°C 20min; 37°C 10min; 45°C 60min; 37°C for 30min). The bound material was captured using streptavidin beads rinsed and eluted with biotin. For RNase H eluted CHART: Capture oligonucleotides 1 µM nM ea. R2.1b-3b) were added and incubated overnight at room temperature. The biotin-bound material was captured using streptavidin beads, rinsed and eluted with RNase H.

tag: strain

value: S2 cells

tag: sample type

value: sense control


title: roX2 CHART RNase eluted rep 2

description: CHART-seq study

extract_protocol:
Libraries were constructed using a modified version of the Illumina PE ChIP-seq protocol.
Average insert size: 233 bp

value: roX2 CHART

tag: elution strategy

value: Rnase-eluted


title: roX2 CHART biotin eluted

description: CHART-seq study

extract_protocol: Libraries were constructed using a modified version of the Illumina PE ChIP-seq protocol.

value: biotin-eluted


title: Input DNA

description: Input


title: S2 input control

description: CHART-seq study

extract_protocol:
Libraries were constructed using a modified version of the Illumina PE ChIP-seq protocol.
Average insert size: 179 bp

value: input control


title: AdultFemale_CNC_INPUT_1

city: Chicago

first: Kevin

last: White

address: 900 E. 57th STR. 10th FL.

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

source_name: AdultFemale

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: developmental stage

value: AdultFemale

value: iso1 (y; bw cn sp)


title: ES_CTCF_ChIPseq_rep1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description: Chromatin IP against CTCF

value: wild type

value: anti-CTCF (SantaCruz #15914)


title: Rio-Zero total RNA fetal head

status: Public on Dec 06 2011

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

description: Ribo-Zero total RNA, Trizol isolated

data_processing: Alignment: Sequence reads were obtained using the Illumina HiSeq 2000 Pipeline and mapped to the mouse genome (mm9, July 2007) using Bowtie. All reads mapping with three or fewer mismatches were retained.

source_name: 14.5dpc fetal head

growth_protocol: CCE feeder-independent ES cells were grown under standard conditions, and differentiation was induced by withdrawal of LIF and addition of 0.266ÂµM retinoic acid (RA). Mouse fetal heads were dissected at 14.5 days postcoitum.

extract_protocol: DNase I treated 5Âµg of high quality total RNA from cells or tissues was subjected to ribosomal RNA depletion by using the Ribo-Zero rRNA removal Kit (Human/Mouse/Rat) according to the manufacturerâs  protocol. The quality of the purified RNA was checked on Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit according to the manufacturerâs protocol. The purified Ribo-Zero RNA fraction (100ng) was subsequently fragmented by addition of 5Ã fragmentation buffer (200mM Tris pH8.2, 500mM KAc and 150mM MgAc2) and heating at 94Â°C for 4min in a total volume of 100Âµl. The reaction was stopped by putting the sample on ice. The fragmented RNA was purified by RNeasy Mini Kit according to the manufacturer protocol, and subsequently ethanol precipitated and dissolved in 10Âµl nuclease-free ddH2O.The fragmented RNA was used as template for cDNA synthesis using 5Âµg random hexamers in a total volume of 20Âµl according to the Superscript II Reverse Transcriptase standard protocol. Second-strand synthesis was performed by adding 91.8Âµl water, 30Âµl 5Ã Second strand buffer, 3Âµl 10mM dNTP, 4Âµl DNA polymerase I, 1Âµl E. coli DNA ligase and 0.2Âµl RNase H, followed by incubation at 16Â°C for 2hour. T4 DNA Polymerase (1Âµl) was added followed by an additional 10 min at 16 Â°C. The ds-cDNA was purified by using the MinElute Reaction Cleanup Kit according to the manufacturerâs  protocol.

value: FVB/N

tag: tissue type

value: fetal head dissected from 14.5dpc mouse embryo

tag: fragmentation method

value: RNA hydrolysis

tag: rrna depletion

value: 1 round

tag: sequencing facility

value: CeMM, Vienna


title: CNC_ChIPSeq_1 and Seq_2

tag: antibody name

value: CNC

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: input DNA

city: Mississippi State

first: Feng

last: Tan

state: MS

address: Dorman Hall 402

department: Biochemistry and Molecular Biology

institute: Mississippi State University

description:
input DNA
input.1.fastq (lane 1)
input.2.fastq (lane 2)

data_processing:
Alignment: Sequence reads were obtained and mapped to the TIGR rice genome version 6 using the SeqMap program (http://www.stanford.edu/group/wonglab/jiangh/seqmap/). All reads mapping with two or fewer mismatches were retained.
Wiggle files: The FindPeaks program version 3.1.9 (http://vancouvershortr.sourceforge.net/) was used to convert the bed files into wiggle files using the parameters (-dist_type 1 200 -minimum 8 -hist_size 100 -eff_size 3.66E8 -trim .2 -subpeaks .5 -mcfdr 20).

organism: Oryza sativa

source_name: Rice Endosperm

growth_protocol: Rice immatured seed after 7-8 days pollitation were harvested and the embryo was removed.

extract_protocol: Input and ChIP samples were processed following Illumina’s protocol with ChIP DNA Sample Prep Kit. Briefly, input and ChIP enriched DNA (7.5 ng in 30 ul final volume) was subjected to end repair, addition of “A” bases to 3’ ends, ligation of adapters, agrose gel size selection for fragments with average size about 186 bp, and PCR amplication to produce a DNA library of adapter-modified fragments.  DNA sequencing was carried out using the Illumina/Solexa Genome Analyzer sequencing system at a concentration of 2 to 4 pM. Cluster amplification, linearization, blocking and sequencing primer reagents were provided in the Solexa Cluster Amplification kits and were used according to the manufacturer’s specifications.

value: Oryza sativa ssp japonica cv Nipponbare

tag: tissue

value: rice immatured seeds 7-8 days after pollination

tag: chip antibody


title: Saccharomyces_kudriavzevii-nucleosome-reads

organism: Saccharomyces kudriavzevii

source_name: Saccharomyces kudriavzevii

extract_protocol: Mono-nucleosomes were extracted by treating the cell spheroplast with Mnase.  Samples representing mono-nucleosomes were gel extracted, end repaired and adapter ligated.


title: Rio-Zero total RNA CCE

description: Ribo-Zero total RNA, Trizol isolated

source_name: Day5 differentiated CCE

tag: cell type

value: differentiated ES cells induced by retinoic acid for 5 days


title: Ribominus total RNA from fetal head 8

description: Ribominus total RNA, Trizol isolated

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the mouse genome (mm9, July 2007) using Bowtie. All reads mapping with two or fewer mismatches were retained.

growth_protocol: CCE feeder-independent ES cells were grown under standard conditions, and differentiation was induced by withdrawal of LIF and addition of 0.266µM retinoic acid (RA). Mouse fetal heads were dissected at 14.5 days postcoitum.

extract_protocol: DNase I treated 10µg of high quality total RNA from cells or tissues was subjected to ribosomal RNA depletion by using the RiboMinus Transcriptome Isolation Kit (Human/Mouse) according to the manufacturer’s  protocol. The quality of the purified RNA was checked on Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit according to the manufacturer’s protocol. The purified Ribominus RNA fraction (100ng) was subsequently fragmented by addition of 5× fragmentation buffer (200mM Tris pH8.2, 500mM KAc and 150mM MgAc2) and heating at 94°C for 3.5min in a total volume of 100µl. The reaction was stopped by putting the sample on ice. The fragmented RNA was purified by RNeasy Mini Kit according to the manufacturer protocol, and subsequently ethanol precipitated and dissolved in 10µl nuclease-free ddH2O.The fragmented RNA was used as template for cDNA synthesis using 5µg random hexamers in a total volume of 20µl according to the Superscript II Reverse Transcriptase standard protocol. Second-strand synthesis was performed by adding 91.8µl water, 30µl 5× Second strand buffer, 3µl 10mM dNTP, 4µl DNA polymerase I, 1µl E. coli DNA ligase and 0.2µl RNase H, followed by incubation at 16°C for 2hour. T4 DNA Polymerase (1µl) was added followed by an additional 10 min at 16 °C. The ds-cDNA was purified by using the MinElute Reaction Cleanup Kit according to the manufacturer’s  protocol.

value: NCMLS Solexa Sequencing facility, Nijmegen


title: Ribominus total RNA from fetal head 9

description: Ribominus total RNA, Trizol isolated


title: Ribominus total RNA from ES 11

description: Ribominus total RNA, Trizol isolated


title: Ribominus total RNA from fetal head 6

description: Ribominus total RNA, Trizol isolated

value: 2 rounds


title: H3K27me3_ChIPSeq

description:
Chromatin IP against H3K27me3
chip.3.fastq (lane 3)
chip.4.fastq(lane 4)

tag: chip antibody vendor

value: Millipore

tag: chip antibody lot#

tag: chip antibody catalog#


title: Ribominus total RNA from fetal head 7

description: Ribominus total RNA, Trizol isolated

tag: strain


title: Ribominus total RNA from ES 10

description: Ribominus total RNA, Trizol isolated


title: Ribominus total RNA from ES 9

description: Ribominus total RNA, Trizol isolated


title: Ribominus total RNA from fetal head 4

description: Ribominus total RNA, Trizol isolated

value: DNA shearing


title: wild type, 52 h, beta eliminated

first: Taiowa

last: Montgomery

address: 185 Cambridge Street, CPZN-7250

institute: Massachusetts General Hospital

description: Small RNA

data_processing: Raw datasets are fastq files generated using Illumina software. The sequence of the 3' adapter used during library preparation is 5'-TGGAATTCTCGGGTGCCAAGG. For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20. Sequences were not filtered for alignment to a genome. Tab-delimited files containing unique sequences and corresponding read counts were generated using custom Perl scripts.

source_name: Whole worms, larvae, beta eliminated

growth_protocol: Animals were grown at 20˚C on E. coli strain OP50.

extract_protocol: Total RNA was isolated from synchronized animals, and small RNAs were size selected, either treated with sodium periodate followed by beta elimination or untreated, tobacco acid pyrophosphatase (TAP)-treated to remove 5' di- and triphosphate groups, ligated to 3' and 5' adapters and subjected to RT-PCR.

tag: genotype

value: whole body

value: L4 larvae

tag: treatment

value: beta elimination


title: Ribominus total RNA from ES 8

description: Ribominus total RNA, Trizol isolated


title: Ribominus total RNA from ES 3

description: Ribominus total RNA, Trizol isolated

value: IMP Solexa Sequencing facility, Vienna


title: ChIP-Seq analysis of H3K4me3 in human fetal heart cells; DNA_Lib 465

status: Public on Dec 05 2011

city: Cambridge

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 465
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7528
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7547
****************
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: GSM772735_BI.Fetal_Heart.H3K4me3.UW_H23914.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 465.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Heart Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Heart, Donor UW H23914 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.8248
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,923,471
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.1286
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2217
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.937
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3076
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772735_BI.Fetal_Heart.H3K4me3.UW_H23914.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 465.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Heart, Donor UW H23914 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.8275
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 4
BROWSER_TRACK_NAME: FH H3K4me3 14 65
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart Histone H3K4me3 Donor UW H23914 Library DNA_Lib 465 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,923,471
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.1286
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2217
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.937
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3076
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

organism: Homo sapiens

source_name: Primary fetal heart tissue; DNA_Lib 465

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 201

tag: sample common name

value: Fetal Heart

value: Post-Mortem

value: presumed normal

tag: molecule

value: genomic DNA

tag: disease

value: Male

value: Primary Tissue

value: Heart

value: University of Washington

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K4me3

value: Bioruptor


title: Ribominus total RNA from fetal head 3

description: Ribominus total RNA, Trizol isolated

value: FVB/N

tag: tissue type

value: fetal head dissected from 14.5dpc mouse embryo

tag: fragmentation method

value: RNA hydrolysis

tag: rrna depletion

value: 2 rounds

tag: sequencing facility


title: Ribominus total RNA from ES 6

description: Ribominus total RNA, Trizol isolated

value: differentiated ES cells induced by retinoic acid for 5 days

value: 1 round

value: NCMLS Solexa Sequencing facility, Nijmegen


title: Ribominus total RNA from ES 5

description: Ribominus total RNA, Trizol isolated

value: DNA shearing


title: Ribominus total RNA from fetal head 5

description: Ribominus total RNA, Trizol isolated


title: roX2 CHART RNase eluted rep 1

description: CHART-seq study

organism: Drosophila melanogaster

extract_protocol:
Libraries were constructed using a modified version of the Illumina PE ChIP-seq protocol.
Average insert size: 237 bp

value: S2 cells

tag: sample type

value: roX2 CHART

tag: elution strategy

value: Rnase-eluted


title: ChIP-Seq analysis of WCE in human fetal kidney cells; DNA_Lib 464

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 464
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7526
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7548
****************
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: GSM772733_BI.Fetal_Kidney.Input.UW_H23435.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 464.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Kidney ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Kidney, Donor UW H23435 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.8250
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,518,935
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0625
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9551
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0929
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772733_BI.Fetal_Kidney.Input.UW_H23435.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 464.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Kidney, Donor UW H23435 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.8277
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 4
BROWSER_TRACK_NAME: FK Input 35 64
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney ChIP-Seq Input Donor UW H23435 Library DNA_Lib 464 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,518,935
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0625
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9551
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0929
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary fetal kidney tissue; DNA_Lib 464

value: BioSam 200

value: Fetal Kidney

value: Post-Mortem

value: presumed normal

value: genomic DNA

value: Female

value: Primary Tissue

value: Kidney

value: University of Washington

value: standard

value: ChIP-Seq Input

value: Input


title: Ribominus total RNA from ES 1

description: Ribominus total RNA, Trizol isolated

organism: Mus musculus

tag: cell type

value: differentiated ES cells induced by retinoic acid for 5 days

value: 1 round

value: IMP Solexa Sequencing facility, Vienna


title: Ribominus total RNA from fetal head 2

description: Ribominus total RNA, Trizol isolated

value: FVB/N

value: fetal head dissected from 14.5dpc mouse embryo

value: RNA hydrolysis


title: Ribominus total RNA from ES 4

description: Ribominus total RNA, Trizol isolated


title: Ribominus total RNA from fetal head 1

description: Ribominus total RNA, Trizol isolated

value: DNA shearing


title: ChIP-Seq analysis of WCE in human fetal lung cells; DNA_Lib 398

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 398
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7136
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7162
****************
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: GSM706855_BI.Fetal_Lung.Input.UW_H22772.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 398.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Lung, Donor UW H22772 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.8228
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,667,799
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.0417
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9725
IROC_PERCENTILE: 50
POISSON_SCORE: 0.0847
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM706855_BI.Fetal_Lung.Input.UW_H22772.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 398.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Lung, Donor UW H22772 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.8255
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 4
BROWSER_TRACK_NAME: FL Input 72 98
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung ChIP-Seq Input Donor UW H22772 Library DNA_Lib 398 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,667,799
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.0417
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9725
IROC_PERCENTILE: 50
POISSON_SCORE: 0.0847
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Primary fetal lung tissue; DNA_Lib 398

value: BioSAli 187

value: Fetal Lung

value: Post-Mortem

value: Lung

value: 82 Days

value: SDS lysis

value: Bioruptor


title: Ribominus total RNA from ES 7

description: Ribominus total RNA, Trizol isolated

value: NCMLS Solexa Sequencing facility, Nijmegen