title: 482N1 shHmga2 ATG m7 2

status: Public on Sep 18 2013

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

description: Sample 17

data_processing:
Base calls were generated using Illumina’s Casava 1.8.2 pipeline
Paired-end reads were aligned to mm9 using tophat 2.0. Non-default parameters include –mate-inner-dist -40 –mate-std.dev 50 –read-mismatches 5 – read-edit-dist 5
RefSeq genes were quantified using the summarizeOverlaps fucntion within the GenomeRanges Bioconductor package.
Differential genes were identified using edgeR from Biocoductor fdr 0.0005
Genome_build: mm9
Supplementary_files_format_and_content:
'raw.gene.counts.txt': non-normalized fragment counts per gene, which was used as input into edgeR for differential analysis
'normalized.pergene.counts.txt': normalized fragment counts per-gene, log2 fold changes and p-values

extract_protocol:
1. Homogenization: Cells grown in monolayer were lysed directly in the culture dish by the addition of RNA-Bee with 1 ml of the reagent for a 6-well plate well. Pass the lysate through a pipette several times to ensure lysis.
2. Phase Separation: Add 0.2 ml chloroform per 1 ml of RNA-Bee, cap the tube and vortex for 15-30 seconds. Store the sample on ice for 5 minutes. Centrifuge the homogenate at 12,000g for 15 minutes at 4 degrees C. Following centrifugation, the sample forms the lower blue phenol-chloroform phase, interphase, and the upper colorless aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interphase and organic phase. The volume of the aqueous phase is about 50% of the initial volume of RNA-Bee plus sample volume. Chloroform should not contain isoamyl alcohol or any other additives.
3. RNA Precipitation: Transfer the aqueous phase to a clean tube, add 0.5 ml of isopropanol, and store the sample for 5-10 minutes at room temperature. Centrifuge at 12,000g for 5 minutes at 4 degrees C. RNA precipitate (often not visible before centrifugation) forms a white-yellow pellet at the bottom of the tube.
4. RNA Wash: Remove the supernatant and washs the RNA pellet with 70% ethanol, shaking or vortexing to dislodge the pellet from the side of the tube. Centrifuge for 5 minutes at 12000g at 4 degrees C. Use at least 1 ml of ethanol solution per 1 ml of RNA-Bee used for the initial homogenisation.
5. RNA Solubilization: At the end of the procedure, briefly air-dry the RNA pellet (5-10 minutes). It is important not to let the RNA pellet dry completely, as this greatly decreases its solubility. Dissolve the RNA in water and incubate for 10-15 minutes at 55 degrees C.
TruSeq Stranded mRNA protocol from Illumina

tag: cell line

value: mouse lung cancer cells

value: expressing shRNA targeting Hmga2 (shHmga2) plus full-length let-7 site/start codon mutated Hmga2 cDNA (ATG m7)


title: 482N1 shHmga2 ATG m7 3

type: SRA

city: London

country: United Kingdom

institute: The Francis Crick Institute

description: Sample 18

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: genotype/variation


title: 482N1 shHmga2 ATG m7 1

description: Sample 16


title: 482N1 shHmga2 ATG wt 3

description: Sample 15

value: expressing shRNA targeting Hmga2 (shHmga2) plus full-length start codon mutated Hmga2 cDNA (ATG wt)


title: 482N1 shHmga2 ATG wt 1

description: Sample 13


title: 482N1 shHmga2 ATG wt 2

description: Sample 14


title: 482N1 shHmga2 m7 2

description: Sample 11

value: expressing shRNA targeting Hmga2 (shHmga2) plus full-length let-7 site mutated Hmga2 cDNA (m7)


title: 482N1 shHmga2 m7 1

description: Sample 10


title: 482N1 shHmga2 empty 3

description: Sample 6

value: expressing shRNA targeting Hmga2 (shHmga2) plus empty expression vector (empty)


title: 482N1 shHmga2 wt 2

description: Sample 8

value: expressing shRNA targeting Hmga2 (shHmga2) plus full-length Hmga2 cDNA (wt)


title: 482N1 shHmga2 empty 2

description: Sample 5


title: 482N1 shHmga2 wt 1

description: Sample 7


title: Fli NICD 3df

status: Public on Sep 19 2013

city: Eggesteing Leopolshafen

first: marina

last: mione

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics

country: Germany

institute: Karlsruhe Institute of Technology

data_processing:
Base-calls and demultiplexing using Illumina Casava 1.8.
Low-quality base-calls were removed using the 'quality_trim' application in the CLC bio Assembly Cell 3.2 software package. Settings: minimum remaining read length 30, minimum quality 20, at least 50% of the read must be good quality.
Reads were aligned to Ensembl predicted cDNAs (Danio_rerio.Zv9.63.cdna.all.fa) using the 'clc_ref_assemble_short' application in the CLC bio Assembly Cell 3.2 software package. Settings: mismatch cost 2, gap cost 3, deletion cost 3, score limit 8; random placement of repeats, up to 50 alignments per read.
Alignment files were translated into counts per transcript using the 'assembly_table' application, and summarized into genes based on Ensembl transcript/gene annotations using a custom script. Non-unique alignments were divided amongst target genes by ratio of unique reads, yielding a corrected total reads count per gene. This count was divided by the total length of constituent transcripts and by the total number of aligned read, and multiplied by a billion, to arrive at a RPKM-like expression value.
Genome_build: Zv9 (Ensembl release 63)
Supplementary_files_format_and_content: Tab-delimited text files with read counts and RPKM-normalized values for every gene.

organism: Danio rerio

source_name: Whole zebrafish larvae

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Larvae for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.

tag: Stage

value: 3 days post fertilization

tag: tissue

value: whole larvae

tag: genetic background

value: AB

tag: genotype


title: 482N1 shluc empty 2

description: Sample 2

value: expressing control shRNA (shluc) plus empty expression vector (empty)


title: 482N1 shHmga2 empty 1

description: Sample 4


title: 482N1 shluc empty 3

description: Sample 3


title: 482N1 shluc empty 1

description: Sample 1


title: WT rep3

city: Umeå

first: Christer

last: Larsson

address: Bldng. 6K

country: Sweden

institute: Umeå universitet

data_processing:
Libraries were run on DNA1000 chip using the Agilent Bioanalyzer to assess size distribution and quality of the amplified library. Quantification of each library was performed by qPCR and equimolar concentrations of each library were pooled together to proceed with emulsion PCR and sequenced on the AB 5500xl SOLiD sequencer (Applied Biosystems, Carlsbad, CA).
Reads were aligned to CDC1551 using the Bioscope 1.3 Whole Transcriptome Analysis Pipeline using default settings (Applied Biosystems, Carlsbad, CA). CDC1551 transcript annotations were downloaded from TBDB.org (Reddy, Riley et al. 2009). The number of reads mapped to each transcript was calculated using HTSeq-count v0.5.3. The overlap resolution mode was set to “intersection-nonempty” and feature type was set to “exon”. (http://www.huber.embl.de/users/anders/HTSeq/doc/install.html#download)  Differential expression between the WT and whiB6Tn sample groups was determined using DESeq v1.4.1 (http://genomebiology.com/2010/11/10/R106), using a test based on the negative binomial distribution, modeling both biological and technical variation. p-values are adjusted for multiple comparisons using the Benjamini - Hochberg method. Transcripts with adjusted p values less than 0.05 were considered significant. Gene Ontology (GO) terms were downloaded from BioMart (Ensembl Bacteria release 13, http://bacteria.ensembl.org/) and enrichment of GO terms in differentially expressed genes was tested with topGO v2.6 (http://bioinformatics.oxfordjournals.org/content/22/13/1600.long). The list of p values generated from DESeq was loaded into topGO along with the list of gene ontology (GO) terms associated with each transcript. The Kolmogorov-Smirnov (KS) test was used to identify GO term enrichment and the weight01 algorithm was used to handle GO graph structure. GO terms with fewer than five genes have low confidence and high variability and thus were not used in the analysis.  Reads were aligned to CDC1551 using the Bioscope 1.3 Whole Transcriptome Analysis Pipeline using default settings (Applied Biosystems, Carlsbad, CA). CDC1551 transcript annotations were downloaded from TBDB.org (Reddy, Riley et al. 2009). The number of reads mapped to each transcript was calculated using HTSeq-count v0.5.3. The overlap resolution mode was set to “intersection-nonempty” and feature type was set to “exon”. (http://www.huber.embl.de/users/anders/HTSeq/doc/install.html#download)  Differential expression between the WT and whiB6Tn sample groups was determined using DESeq v1.4.1 (http://genomebiology.com/2010/11/10/R106), using a test based on the negative binomial distribution, modeling both biological and technical variation. p-values are adjusted for multiple comparisons using the Benjamini - Hochberg method. Transcripts with adjusted p values less than 0.05 were considered significant. Gene Ontology (GO) terms were downloaded from BioMart (Ensembl Bacteria release 13, http://bacteria.ensembl.org/) and enrichment of GO terms in differentially expressed genes was tested with topGO v2.6 (http://bioinformatics.oxfordjournals.org/content/22/13/1600.long). The list of p values generated from DESeq was loaded into topGO along with the list of gene ontology (GO) terms associated with each transcript. The Kolmogorov-Smirnov (KS) test was used to identify GO term enrichment and the weight01 algorithm was used to handle GO graph structure. GO terms with fewer than five genes have low confidence and high variability and thus were not used in the analysis.  Reads were aligned to CDC1551 using the Bioscope 1.3 Whole Transcriptome Analysis Pipeline using default settings (Applied Biosystems, Carlsbad, CA). CDC1551 transcript annotations were downloaded from TBDB.org (Reddy, Riley et al. 2009). The number of reads mapped to each transcript was calculated using HTSeq-count v0.5.3. The overlap resolution mode was set to “intersection-nonempty” and feature type was set to “exon”. (http://www.huber.embl.de/users/anders/HTSeq/doc/install.html#download)  Differential expression between the WT and whiB6Tn sample groups was determined using DESeq v1.4.1 (http://genomebiology.com/2010/11/10/R106), using a test based on the negative binomial distribution, modeling both biological and technical variation. p-values are adjusted for multiple comparisons using the Benjamini - Hochberg method. Transcripts with adjusted p values less than 0.05 were considered significant. Gene Ontology (GO) terms were downloaded from BioMart (Ensembl Bacteria release 13, http://bacteria.ensembl.org/) and enrichment of GO terms in differentially expressed genes was tested with topGO v2.6 (http://bioinformatics.oxfordjournals.org/content/22/13/1600.long). The list of p values generated from DESeq was loaded into topGO along with the list of gene ontology (GO) terms associated with each transcript. The Kolmogorov-Smirnov (KS) test was used to identify GO term enrichment and the weight01 algorithm was used to handle GO graph structure. GO terms with fewer than five genes have low confidence and high variability and thus were not used in the analysis.
The number of reads mapped to each transcript was calculated using HTSeq-count v0.5.3.
Genome_build: M. tuberculosis CDC1551
Supplementary_files_format_and_content: tab-delimited text file with one column for each sample

organism: Mycobacterium tuberculosis CDC1551

source_name: WT

growth_protocol: Bacteria were grown in 7H9 broth (Becton Dickinson, Sparks, MD) supplemented with 10% OADC (oleic acid, albumin, dextrose, and catalase) (Becton Dickinson, Sparks, MD), 0.5% v/v glycerol and 0.05% v/v Tween 80 (Sigma Aldrich, St. Louis, MO) at 37°C with agitation.

extract_protocol:
RNA from synchronized cultures in triplicate was extracted using a Trizol - spin column hybrid protocol followed by DNase treatment. RNA integrity was tested using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), and mRNA was enriched using the MICROBExpress kit according to the manufacturer's instructions (Life technologies, Grand Island, NY). Successful removal of rRNA was verified by another Bioanalyzer assay.
Starting with 200-500ng of rRNA-depleted total RNA, fragmentation of the whole transcriptome RNA was performed by chemically induced method as described in Applied Biosystems SOLiD™ Total RNA-Seq Kit protocol (Applied Biosystems, Carlsbad, CA). Fragmented RNA was purified using the Invitrogen RiboMinus Concentration Module (Life technologies, Grand Island, NY) and the size distribution and yield were assessed by Bioanalyzer using the RNA 6000 pico Chip Kit (Agilent technologies, Santa Clara, CA) and Qubit Fluorometer (Life technologies, Grand Island, NY) respectively. Once concentration was confirmed, construction of the amplified whole transcriptome library was performed as directed in the Applied Biosystems SOLiD™ Total RNA-Seq Kit protocol, which is intrinsically strand-specific.
After reverse transcription was complete, each sample was barcoded with a unique 3’primer during the library amplification step.

treatment_protocol: The two strains were synchronized by adjusting the OD600 to 0.1 in antibiotic-free 7H9 and grown for three days. This was repeated two more times to make sure the two strains were in the same growth phase. WT and whiB6Tn were grown shaking in E-flasks in biological triplicates and harvested three days later at an OD of 1 in the WT cultures and 0.9 in the whiB6Tn cultures.

value: WT

tag: strain


title: whiB6Tn rep3

value: whiB6 disrupted by transposon


title: WT rep1


title: WT rep2


title: whiB6Tn rep2


title: 5a-288

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

country: USA

institute: JCVI

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to GRCh3 using tophat v2.0.8
FPKM values were obtained from the tophat output
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for genes and transcript isoforms, and read counts per gene.

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood, and depleted of rRNA (Ribo-zero; Epicentre) and globin RNA (Globinclear; Life Technologies) before amplification (Ovation; Nugen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: pre- or post-challenge

value: Pre

value: whole blood


title: 4b-396

value: Post


title: 7-407

value: Unchallenged control


title: whiB6Tn rep1


title: 6-305


title: 4a-280


title: 482N1 shHmga2 wt 3

description: Sample 9


title: 5b-404


title: 482N1 shHmga2 m7 3

description: Sample 12


title: 2b-387


title: 1b-386


title: 2a-271


title: 3a-277


title: 1a-270


title: Digital Genomic Footprinting assay of Fibroblasts, Fetal Skin, Quadriceps, Right; DGF.DS19943

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19943
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18700
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11331
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing: Various levels of processed data files will be made available as this project proceeds.

molecule: genomic DNA

source_name: Fibroblasts, Fetal Skin, Quadriceps, Right, day 97 donor; DGF.DS19943

extract_protocol: Library construction protocol: Single read - Illumina

tag: sra sample accession

tag: disease

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Cell Culture

tag: markers

value: day 97

value: Male

value: short term

value: Digital Genomic Footprinting

value: Qiagen minElut


title: Digital Genomic Footprinting assay of Fibroblasts, Fetal Skin, Biceps, Right; DGF.DS19745

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19745
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18705
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fibroblasts, Fetal Skin, Biceps, Right, day 97 donor; DGF.DS19745

value: Fibroblasts, Fetal Skin, Biceps, Right


title: Digital Genomic Footprinting assay of Fibroblasts, Fetal Skin, Upper Back; DGF.DS19706

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19706
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18684
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11317
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fibroblasts, Fetal Skin, Upper Back, day 97 donor; DGF.DS19706

value: Fibroblasts, Fetal Skin, Upper Back


title: Chromatin accessibility assay of Fetal Kidney; DS20988

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20988
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18640
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14146
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney primary tissue, day 113; DS20988

value: Primary Tissue

value: Fetal Kidney

value: UW

value: fetal

value: day 113

value: Female

value: Chromatin Accessibility


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS19419

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS19419
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18652
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9806
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Stomach primary tissue, day 101; RNA.RS19419

extract_protocol: Library construction protocol: Illumina TruSeq RNA PART# 15008136 REVISION A

value: Fetal Stomach

value: day 101

value: Unknown

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: Digital Genomic Footprinting assay of Fibroblasts, Fetal Skin, Back; DGF.DS19174

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19174
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18713
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11359
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fibroblasts, Fetal Skin, Back, day 96 donor; DGF.DS19174

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Cell Culture

value: Fibroblasts, Fetal Skin, Back

value: day 96

value: Male

value: short term

value: Digital Genomic Footprinting

value: Qiagen minElut


title: Digital Genomic Footprinting assay of Fibroblasts, Fetal Skin, Abdomen; DGF.DS19561

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19561
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18720
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11370
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fibroblasts, Fetal Skin, Abdomen, day 97 donor; DGF.DS19561

value: Fibroblasts, Fetal Skin, Abdomen

value: day 97


title: Digital Genomic Footprinting assay of CD19 Primary Cells; DGF.DS17186

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17186
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18725
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6965
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD19+ Cells, year 21; DGF.DS17186

value: FHCRC HEIMFELD

value: Primary Cell

value: CD19 Primary Cells

value: year 21

value: Caucasian


title: Digital Genomic Footprinting assay of Fibroblasts, Fetal Skin, Scalp; DGF.DS19449

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19449
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18690
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11325
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fibroblasts, Fetal Skin, Scalp, day 97 donor; DGF.DS19449

value: Fibroblasts, Fetal Skin, Scalp


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS18776

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Back
Library name: lib-RNA.RS18776
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18673
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8377
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Muscle, Back primary tissue, day 91; RNA.RS18776

value: Primary Tissue

value: Fetal Muscle, Back

value: UW

value: fetal

value: day 91

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS18772

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Arm
Library name: lib-RNA.RS18772
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18671
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8512
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Muscle, Arm primary tissue, day 91; RNA.RS18772

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Fetal Muscle, Arm

value: Male


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS18778

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS18778
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18661
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8483
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Stomach primary tissue, day 105; RNA.RS18778

value: Fetal Stomach

value: day 105

value: Female


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS18244

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS18244
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18658
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7168
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal  primary tissue, day 98; RNA.RS18244

value: Primary Tissue

value: UW

value: day 98


title: 3b-393

value: Post

value: whole blood


title: RNA-Seq (Total RNA) Fetal Thymus; RNA.RS18816

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Thymus
Library name: lib-RNA.RS18816
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18679
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9801
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Thymus primary tissue, day 127; RNA.RS18816

value: Fetal Thymus

value: fetal

value: day 127

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) Fetal Spleen; RNA.RS18161

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Spleen
Library name: lib-RNA.RS18161
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18675
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7258
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal  primary tissue, day 112; RNA.RS18161

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Fetal Spleen

value: day 112

value: Unknown

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Thymus; RNA.RS18164

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Thymus
Library name: lib-RNA.RS18164
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18650
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7171
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal  primary tissue, day 108; RNA.RS18164

value: Primary Tissue

value: UW

value: day 108

value: Male


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS18162

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS18162
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18666
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18665
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Stomach primary tissue, day 110; RNA.RS18162

tag: sample alias

tag: sample common name

value: Fetal Stomach

value: fetal

value: day 110

value: Female


title: RNA-Seq (Total RNA) Fetal Thymus; RNA.RS18243

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Thymus
Library name: lib-RNA.RS18243
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18677
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7180
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal  primary tissue, day 98; RNA.RS18243

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Fetal Thymus

value: day 98

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS20237

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS20237
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18654
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7126
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal  primary tissue, day 108; RNA.RS20237

value: Ambion mirVana miRNA isolation kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA


title: RNA-Seq (Total RNA) Fetal Testes; RNA.RS19458

description:
sample_term_id: UBERON_0000473
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Testes
Library name: lib-RNA.RS19458
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18648
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11289
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Testes primary tissue, pool; RNA.RS19458

value: Primary Tissue

value: Fetal Testes

value: UW

value: pool

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Spleen; RNA.RS19457

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Spleen
Library name: lib-RNA.RS19457
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18669
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18668
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spleen primary tissue, day 120; RNA.RS19457

value: Fetal Spleen

value: fetal

value: day 120

value: Male


title: RNA-Seq (Total RNA) Fetal Adrenal Gland; RNA.RS23756

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Adrenal Gland
Library name: lib-RNA.RS23756
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18570
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2443
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Adrenal Gland primary tissue, day 96; RNA.RS23756

value: University of Washington, Congenital Defects Lab. Ian Glass

value: fetal adrenal

value: 96 days

value: Unknown

value: mRNA-Seq


title: RNA-Seq (Total RNA) Fetal Muscle, Trunk; RNA.RS23757

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Trunk
Library name: lib-RNA.RS23757
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18642
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11446
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Muscle, Trunk primary tissue, day 113; RNA.RS23757

value: Fetal Muscle, Trunk

value: day 113

value: Female

value: Ambion mirVana miRNA isolation kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA


title: RNA-Seq (Total RNA) Fetal Thymus; RNA.RS20016

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Thymus
Library name: lib-RNA.RS20016
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18681
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11281
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Thymus primary tissue, day 97; RNA.RS20016

value: Primary Tissue

value: Fetal Thymus

value: UW

value: day 97

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Placenta; RNA.RS23754

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Placenta
Library name: lib-RNA.RS23754
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18567
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11433
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Placenta primary tissue, day 113; RNA.RS23754

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Fetal Placenta

value: fetal


title: RNA-Seq (Total RNA) Fetal Spinal Cord; RNA.RS23753

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Spinal Cord
Library name: lib-RNA.RS23753
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18563
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11311
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 113; RNA.RS23753

value: Fetal Spinal Cord

value: day 113

value: mRNA-Seq


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS23752

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS23752
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18631
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Muscle, Leg primary tissue, day 113; RNA.RS23752

value: Fetal Muscle, Leg

value: Female

value: Ambion mirVana miRNA isolation kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) CD56 Primary Cells; RNA.RS23750

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD56 Primary Cells
Library name: lib-RNA.RS23750
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18629
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7027
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD56+ Cells, year 37; RNA.RS23750

value: FHCRC HEIMFELD

value: Primary Cell

value: CD56 Primary Cells

value: year 37

value: Male

value: Hispanic

value: Random Primers(hexamers)

value: TruSeq RNA


title: RNA-Seq (Total RNA) CD3 Primary Cells; RNA.RS23747

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD3 Primary Cells
Library name: lib-RNA.RS23747
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18572
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6984
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD3+ Cells, year 37; RNA.RS23747

value: CD3 Primary Cells

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: ChIP-Seq Input of Fetal Spinal Cord; Histone.DS23069

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS23069
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18600
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18575
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 108; Histone.DS23069

value: Fetal Spinal Cord

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 108

value: ChIP-Seq Input

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Input


title: RNA-Seq (Total RNA) Fetal Thymus; RNA.RS23751

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Thymus
Library name: lib-RNA.RS23751
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18560
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11269
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Thymus primary tissue, day 113; RNA.RS23751

value: Fetal Thymus

value: day 113

value: Female

value: mRNA-Seq

value: Ambion mirVana miRNA isolation kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: Histone H3K9me3 ChIP-Seq of CD4 Primary Cells; Histone.DS23725

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS23725
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18612
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7018
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD4+ Cells, year 37; Histone.DS23725

value: FHCRC HEIMFELD

value: Primary Cell

value: CD4 Primary Cells

value: year 37

value: Male

value: Hispanic

value: Histone H3K9me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS18815

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS18815
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18656
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9810
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Stomach primary tissue, day 127; RNA.RS18815

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Stomach

value: UW

value: fetal

value: day 127

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) CD19 Primary Cells; RNA.RS23749

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD19 Primary Cells
Library name: lib-RNA.RS23749
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18627
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6973
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD19+ Cells, year 37; RNA.RS23749

value: FHCRC HEIMFELD

value: Primary Cell

value: CD19 Primary Cells

value: year 37

value: Male

value: Hispanic

value: mRNA-Seq

value: Ambion mirVana miRNA isolation kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) CD14 Primary Cells; RNA.RS23748

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD14 Primary Cells
Library name: lib-RNA.RS23748
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18625
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6962
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD14+ Cells, year 37; RNA.RS23748

value: CD14 Primary Cells


title: Histone H3K4me3 ChIP-Seq of Fetal Spinal Cord; Histone.DS23457

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS23457
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18581
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18580
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 113; Histone.DS23457

value: Fetal Spinal Cord

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 113

value: Female

value: Histone H3K4me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2


title: Histone H3K9me3 ChIP-Seq of Fetal Spinal Cord; Histone.DS23073

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS23073
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18597
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18575
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 108; Histone.DS23073

value: day 108

value: Histone H3K9me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K4me1 ChIP-Seq of CD8 Primary Cells; Histone.DS23313

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS23313
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18603
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7035
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD8+ Cells, year 37; Histone.DS23313

value: FHCRC HEIMFELD

value: Primary Cell

value: CD8 Primary Cells

value: year 37

value: Male

value: Hispanic

value: Histone H3K4me1


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS18163

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS18163
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18663
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8487
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Stomach primary tissue, day 107; RNA.RS18163

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Stomach

value: UW

value: fetal

value: day 107

value: Female

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: Histone H3K4me1 ChIP-Seq of CD4 Primary Cells; Histone.DS22905

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22905
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18618
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7018
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD4+ Cells, year 37; Histone.DS22905

value: FHCRC HEIMFELD

value: Primary Cell

value: CD4 Primary Cells

value: year 37

value: Male

value: Hispanic

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K4me1 ChIP-Seq of Fetal Spinal Cord; Histone.DS23072

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS23072
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18576
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18575
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 108; Histone.DS23072

value: Fetal Spinal Cord

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 108

value: Female

value: Histone H3K4me1


title: Histone H3K36me3 ChIP-Seq of Fetal Spinal Cord; Histone.DS23075

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS23075
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18594
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18580
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 113; Histone.DS23075

value: day 113

value: Histone H3K36me3


title: RNA-Seq (Total RNA) Fetal Thymus; RNA.RS18165

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Thymus
Library name: lib-RNA.RS18165
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18646
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18645
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Thymus primary tissue, day 115; RNA.RS18165

value: Fetal Thymus

value: day 115

value: Male

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: Histone H3K27me3 ChIP-Seq of CD4 Primary Cells; Histone.DS23723

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23723
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18615
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD4+ Cells,year 21; Histone.DS23723

value: FHCRC HEIMFELD

value: Primary Cell

value: CD4 Primary Cells

value: year 21

value: Caucasian

value: Histone H3K27me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Millipore


title: Histone H3K27me3 ChIP-Seq of Fetal Thymus; Histone.DS23461

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23461
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18584
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Thymus primary tissue, day 110; Histone.DS23461

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Thymus

value: UW

value: fetal

value: day 110

value: Female


title: Histone H3K27me3 ChIP-Seq of Fetal Spinal Cord; Histone.DS23460

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23460
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18588
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18575
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 108; Histone.DS23460

value: Fetal Spinal Cord

value: day 108


title: Histone H3K27ac ChIP-Seq of Fetal Spinal Cord; Histone.DS23458

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS23458
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18591
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.18575
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 108; Histone.DS23458

value: Histone H3K27ac

value: Invitrogen Dynabeads

value: Active Motif


title: RNA-Seq (Total RNA) Fetal Stomach; RNA.RS23755

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Stomach
Library name: lib-RNA.RS23755
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18634
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7168
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal  primary tissue, day 98; RNA.RS23755

value: Fetal Stomach

value: day 98

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: optimized ligation for hela cell miRNAs

city: Boulder

first: Zhaojie

last: Zhang

state: CO

address: 2300 Arapahoe Ave

institute: University of Colorado at Boulder

description: no barcode

data_processing:
adaptor removal with self-written python scripts
miRNA mapping with BLAST, parameters: -m 8
BLAST results parsing and miRNA counts with self-written python scripts
Genome_build: Mouse miRNA sequences from Mirbase.org
Supplementary_files_format_and_content: .xls file containing counts assigned to each miRNA

source_name: hela cells

growth_protocol: Mice were housed in the Mouse Facility under standard conditions.

extract_protocol:
RNA was extracted from cells with the use of Trizol according to the Trizol manufacturer's instructions. Synthetic miRNAs were chemically synthesized by ThermoFisher according to published mouse miRNA sequences.
An improved Ligation-based small RNA cloning protocol based on the Illumina protocol for small RNA cloning. Two adaptors (3' adaptor and 5' adaptor) were ligated to small RNAs followed by RT-PCR and gel-purification. Then purified PCR products were sent out for sequencing.

value: HeLa


title: Histone H3K27ac ChIP-Seq of CD4 Primary Cells; Histone.DS21777

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21777
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18621
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD4+ Cells,year 21; Histone.DS21777

value: FHCRC HEIMFELD

value: Primary Cell

value: CD4 Primary Cells

value: year 21

value: Male

value: Caucasian

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: Bisulfite-Seq analysis of foreskin fibroblast from skin03 (A20919) using Illumina HiSeq 2000
library name: A20919
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris-E210
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.92 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 1.00 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 200-400 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 215-370 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.64
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127120_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Bisulfite-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A20919-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Penis Foreskin Fibroblast Primary Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18773
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFF BS 03 19
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Bisulfite-Seq Donor skin03 Library A20919 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 328,604,139
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.77
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Fibroblast

tag: is tumor

value: No

value: primary cell culture

value: foreskin fibroblast


description:
design description: Bisulfite-Seq analysis of UCSF-4 embryonic stem cell line (A21772) using Illumina HiSeq 2000
library name: A21772
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 177-385 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 95.29
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 8
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127123_UCSF-UBC.UCSF-4star.Bisulfite-Seq.A21772.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21772-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of UCSF-4* Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the UCSF-4* Cell Line, Library A21772 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18766
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: UCSF4* BS 72
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Bisulfite-Seq Library A21772 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 543,245,204
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.02
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: cell line

tag: line

value: female

value: Embryo ICM

value: Embryonic stem cell


description:
design description: Bisulfite-Seq analysis of breast luminal epithelial cell from RM066 (A22478) using Illumina HiSeq 2000
library name: A22478
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 200-400 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.1
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 8
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127125_UCSF-UBC.Breast_Luminal_Epithelial_Cells.Bisulfite-Seq.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22478-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Breast Luminal Epithelial Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM066 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18774
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BLEC BS 66 78
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Luminal Epithelial Cells Bisulfite-Seq Donor RM066 Library A22478 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 480,904,445
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.61
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Breast

value: Luminal epithelial cell

value: primary cell

value: breast luminal epithelial cell


description:
design description: Bisulfite-Seq analysis of cortex neural stem and progenitor cells from HuFNSC04 (A22477) using Illumina HiSeq 2000
library name: A22477
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 200-450 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.19
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 8
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127124_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.Bisulfite-Seq.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22477-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Neurosphere Cultured Cells Cortex Derived Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC04 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18768
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: NCD BS 04 77
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Bisulfite-Seq Donor HuFNSC04 Library A22477 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 455,130,678
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.59
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: Brain

value: Cortex neurosphere culture

tag: cell type

value: cortex neural stem and progenitor cells


description:
design description: Bisulfite-Seq analysis of UCSF-4 embryonic stem cell line (A21771) using Illumina HiSeq 2000
library name: A21771
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 157-500 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 94.99
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 8
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127122_UCSF-UBC.UCSF-4star.Bisulfite-Seq.A21771.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21771-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of UCSF-4* Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the UCSF-4* Cell Line, Library A21771 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18765
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: UCSF4* BS 71
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Bisulfite-Seq Library A21771 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 548,953,928
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.19
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.99

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


description:
design description: Bisulfite-Seq analysis of testis sperm cell from 390ATA (A22288) using Illumina HiSeq 2000
library name: A22288
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 160-400 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.28
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 6
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127119_UCSF-UBC.Testis_Spermatozoa_Primary_Cells.Bisulfite-Seq.390ATA.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22288-1-A22287-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Testis Spermatozoa Primary Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Testis Spermatozoa Primary Cells, Donor 390ATA were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18775
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: TS BS TA 88
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Testis Spermatozoa Primary Cells Bisulfite-Seq Donor 390ATA EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,063,455,878
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.51
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1127119, GSM1127117 (thus .wig files on these records are identical)

value: male

value: Testis

value: Spermatozoa

value: testis sperm cell


description:
design description: Bisulfite-Seq analysis of testis sperm cell from 390ATA (A22287) using Illumina HiSeq 2000
library name: A22287
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 154-383 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.33
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 6
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127117_UCSF-UBC.Testis_Spermatozoa_Primary_Cells.Bisulfite-Seq.390ATA.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22288-1-A22287-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Testis Spermatozoa Primary Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Testis Spermatozoa Primary Cells, Donor 390ATA were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18775
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: TS BS TA 88
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Testis Spermatozoa Primary Cells Bisulfite-Seq Donor 390ATA EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,063,455,878
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.51
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1127119, GSM1127117 (thus .wig files on these records are identical)

value: No


description:
design description: Bisulfite-Seq analysis of breast myoepithelial cell from RM066 (A12230) using Illumina HiSeq 2000
library name: A12230
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 22 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 3.5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 150-300 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 200-500 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 99.02
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 18
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127057_UCSF-UBC.Breast_Myoepithelial_Cells.Bisulfite-Seq.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17783-1-A12230-1-A12231-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Breast Myoepithelial Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Breast Myoepithelial Cells, Donor RM066 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18769
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BMC BS 66 83
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Myoepithelial Cells Bisulfite-Seq Donor RM066 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 475,603,248
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.0
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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SPECIAL NOTE: generated from combined data in GSM1127059, GSM1127057, GSM1127054 (thus .wig files on these records are identical)

value: Myoepithelial cell

value: breast myoepithelial cell