title: Yb mutant RNA-seq

status: Public on Feb 10 2011

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

institute: Yale University

description: total ovarian RNAs of Yb mutant

data_processing: Sequence reads were obtained and mapped to the Drosophila melanogaster genome release 5 by bowtie-0.10.0. All perfectly mapped reads were retained. Later cellular non-coding RNAs and miRNAs are removed before cluster analysis and transposon annotation analysis. Transposon annotation and cluster analysis are achieved by empolying in-house programs.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: All strains were grown at 25°C on standard Drosophila medium.w1118 served as the wildtype strain. Yb72 was previously described as a Yb null allele (23).

extract_protocol: Low molecular weight RNA was isolated from the adult ovaries of w1118 and the Yb72/Yb72 mutant using miRNA isolation kit (Ambion). Small RNAs ranging in size between 16-29 nt (below 2S rRNA) was gel purified, and small RNA libraries were prepared using small RNA sample prep kit (Illumina) according to the alternative v1.5 protocol. The clones were sequenced using Genome Analyzer II.

value: ovaries

value: germ line and somatic cells

value: Adult


title: WTTh17STAT5 (ChIP-Seq)

status: Public on Feb 09 2011

type: SRA

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

country: USA

institute: National Institutes of Health

description: Chromatin IP against STAT5

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Cisgenome was used for peak-calling.
CisGenome ( Nature Biotechnology, 26: 1293-1300)

molecule: genomic DNA

organism: Mus musculus

source_name: primary CD4+ T cells from spleen and lymph nodes

growth_protocol: Naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured for 72h with platebound anti-CD3, anti-CD28 (10 mg/ml each), IL-6 (20 ng/ml), TGF-beta (2 ng/ml), anti-IL-4 (10 mg/ml) and anti-IL-2 (100IU/ml) for 3 days.

extract_protocol: Cell lysates were made by sonication and protein-DNA complexes were isolated with anti-STAT5 (STAT5a (PA-ST5A: R&D) and STAT5b (PA-ST5B: R&D) antibodies, 2 ul each per IP) and anti-STAT3 (14-6727: eBioScience, 5 ug per IP.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: After 3 day culture in vitro, cells were restimulated for either IL-6 (40 ng/ml) or IL-2  (200 IU/ml) before chemically cross linked by 1% formaldehyde.

tag: strain

tag: genotype/variation

value: wild type

tag: cell type

value: in vitro polarized T helper17 cells

tag: passages

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th17 condition and restimulated with IL-2 for 30 minutes

tag: chip antibody

value: mixture of STAT5a (PA-ST5A:R&D) and STAT5b (PA-ST5B:R&D) antibodies, 2 ul each per IP


title: Wild type RNA-seq

description: total ovarian RNAs of WT

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: developmental stage


title: E0-12_Hr4_GFP_INPUT_1

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

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

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

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

treatment_protocol: No Treatment

tag: fly type

value: transgenic


title: E16-24h_anti-cbt_INPUT_1

value: iso1 (y; bw cn sp)


title: E0-4_Yki-91_ChIPSeq_1 and 2

tag: antibody name

tag: manufacturer

value: Irvine Lab

tag: lot/batch#

tag: catalog


title: E0-12_Hr4_GFP_ChIPSeq_1 and 2

value: White Lab


title: WPP_KW3-Trl-D2_ChIPSeq_1

source_name: WPP

value: WPP


title: wheat_leaf_insensitive_0H

status: Public on Feb 15 2011

city: BEIJING

first: mingming

last: xin

address: YUAN MING YUAN WEST ROAD 2, HAIDIAN DISTRICT

department: plant genetics and breeding

country: China

institute: China Agricultrual University

description: CK

data_processing:
Automated base calling of the raw sequence and vector removal were performed with PHRED and CROSS MATCH programs. Trimmed 3′ and 5′ adapters sequences, removed RNAs less than 17 nt and polyA , only sequences longer than 17 nt with a unique ID were used for further analysis.
Processed data represents clean tags, 18-30 nt, tab delimited, sequence | count | length.

organism: Triticum aestivum

source_name: wheat young leaf

growth_protocol: Hexaploid wheat (Triticum aestivum L.) line ‘8866’ (S)(susceptible to wheat powdery mildew), ‘Pm30’ (Resistant to wheat powdery mildew),‘TAM’ (tolerant to heat stress) were grown in a growth chamber at a relative humidity of 75% and 26/20℃ day and night temperature with light intensity of 3000 lx. 2 week-old plants were used for all experiments.

extract_protocol: Total RNA was isolated from the frozen leaves by using Trizol agent (TaKaRa, Inc., Dalian, China) according to the manufacturer’s instructions. Cloning of the small RNAs was performed as described by Sunkar and Zhu. Briefly, low molecular weight RNA was enriched by 0.5 M NaCl and 10% PEG8000 precipitation. About 100 μg low molecular weight RNA was separated on a denaturing 15% polyacrylamide gel. Labeled RNA oligonucleotides with 18 and 26 nt were used as size standards. The nucleotides from 18 to 26 nt were excised, and RNA was eluted overnight with 0.4M NaCl at 4˚C. The RNA was dephosphorylated by alkaline phosphatase (New England Biolabs Inc, Beijing China) and recovered by ethanol precipitated. The small RNAs were then ligated sequentially to RNA/DNA chimeric oligonucleotide adapters, and then reverse transcription was preformed, followed by PCR amplification. The resulting PCR products were sequenced using Solexa technology.

treatment_protocol: For powdery mildew infection, one isolate of Erysiphe graminis f. sp. tritici (Egt) (Isolate E09) was maintained on the wheat cultivar Fidel by weekly transfer to new plants. Inoculations were performed at a density of 100-150 conidia/mm2 by brushing plants. Leaves were collected at 12 hours after infection. For heat stress,the seedlings were subjected to 40°C (heat stress) for 0 hour and returned to normal conditions for 2 hours.

tag: line

value: CK (insensitive to heat stress)

tag: age

value: two week old

value: leaf

tag: stress

value: control

tag: time

value: 0 hours


title: WPP_K27me3_ChIPSeq_1 and 2

value: Upstate-Millipore


title: E0-4_Yki-91_INPUT_1


title: E16-24h_13T_exd-GFP_INPUT_1


title: WPP_K27me3_INPUT_1


title: BRC_core_INPUT_1

source_name: BRC

value: BRC


title: E16-24h_anti-cbt_ChIPSeq_1 and 2

value: anti-cbt

value: Paricio Lab


title: WPP_KW3-Trl-D2_INPUT_1


title: Miguel_CMC__rep26

status: Public on Feb 12 2011

city: Shenzhen

first: Yao

last: Qiong

state: Guangdong

address: Beishan Industrial Zone,Yantian District

institute: BGI-SZ

description:
sample for paired-end library with insert size of 150 bp
library selection: different insertion size

data_processing: Filter adaptors, detect possible contamination of samples, count data output(including read length, total read counts, data production), and on this basis, accomplish standardized analysis and personalized information analysis.  (1) Reads alignment with reference genome     Align all reads against ref.c2t and ref.g2a with SOAPaligner after converting C to T  on forward strand, G to A on backward strand. Each reads mapping to an unique location with minimum mismatches and clear information of positive and negative chain will be defined as uniquely matching reads and used to determine the methylated C.  (2) Combine original sequences and the soap results , according to the reads ID in soap results, find the corresponding sequences which have not converted C to T or G to A in raw data ,and then use the corresponding sequences to substitute the sequences in soap results.  (3) Align the sequences against the reference, record the information of base sites, and according to these sites information , select the reads with better aligning results: align the human.fa sequence with soap results according to certain patterns, and use symbols to record the results , on the basis of the results, extract local fragment of reads with best aligning results, getting align matching results.  (4) According to the align matching results, select the best results among repeat present sequences , the selection criteria being to select reads with larger sum of aligning length, and judge a chain is Watson chain or Click chain.  (5) Perform a detail statistic on mappable reads and remove redundancy.  (6) Methylation level of whole genome and/or different regions are deduced from the original sequence.

organism: Homo sapiens

source_name: iPSC clone (CMC28)

extract_protocol: a)  Mix up all genome DNA and randomly shear into fragments of 100~500bp.  b)  Repair the terminal of DNA fragments, 3'-dA and attach with methylation sequencing adaptors.  c)  Subject whole genome DNA to bisulfite processing.  d)  Subject to gel electrophoresis of 2% TAE, extract fragments of 320~380bp with IAquich Gel Extraction recycling, desalination and PCR amplification.  e)  Construct libraries with appropriate fragments for sequencing usin standard Illumina Genome Analyzer II protocol

value: iPSC clone


title: E16-24h_13T_exd-GFP_ChIPSeq_1 and 2

value: exd-GFP


title: BRC_core_ChIPSeq_1 and 2

value: core

value: Lepesant lab


title: E16-24h_KW4-Fer3-D1_INPUT_1

value: iso1 (y; bw cn sp)


title: wheat_leaf_insensitive_1H

description: TAM

growth_protocol: Hexaploid wheat (Triticum aestivum L.) line ‘8866’ (S)(susceptible to wheat powdery mildew), ‘Pm30’ (Resistant to wheat powdery mildew), and ‘TAM’ (tolerant to heat stress) were grown in a growth chamber at a relative humidity of 75% and 26/20℃ day and night temperature with light intensity of 3000 lx. 2 week-old plants were used for all experiments.

treatment_protocol: For powdery mildew infection, one isolate of Erysiphe graminis f. sp. tritici (Egt) (Isolate E09) was maintained on the wheat cultivar Fidel by weekly transfer to new plants. Inoculations were performed at a density of 100-150 conidia/mm2 by brushing plants. Leaves were collected at 12 hours after infection. For heat stress,the seedlings were subjected to 40°C (heat stress) for 1  hour and returned to normal conditions for 2 hours.

value: TAM (insensitive to heat stress)

value: 40°C (heat stress)

value: 1 hour


title: EcR_GFP_INPUT_2

value: transgenic


title: EcR_GFP_INPUT_1


title: E16-24h_KW4-Fer3-D1_ChIPSeq_1 and 2

value: White Lab


title: EcR_mF3d_GFP_ChIPSeq_1 and 2

value: GFP


title: E8-16h_KW3-h-D1_ChIPSeq_1 and 2


title: RNA-seq.null.rep2

status: Public on Feb 08 2011

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

description: mRNA enriched ds cDNA was sequenced paired end

data_processing: Reads are mapped to genome (mm9) using ELAND with up to 2 mismatches allowed.

extract_protocol: Total RNA was mRNA enriched using oligo(dT) capture and ds cDNA was prepared. The ds cDNA was fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors. Average insertion size 200bp, standard deviation 73bp.

tag: tissue type

value: 3 E18.5 rhombic lips (pooled)

tag: genotype

tag: sequencing protocol

value: paired-end, 37-mer sequencing


title: RNA-seq.null.rep1

extract_protocol: Total RNA was mRNA enriched using oligo(dT) capture and ds cDNA was prepared. The ds cDNA was fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors. Average insertion size 200bp, standard deviation 76bp.


title: RNA-seq.WT.rep1

extract_protocol: Total RNA was mRNA enriched using oligo(dT) capture and ds cDNA was prepared. The ds cDNA was fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors. Average insertion size 200bp, standard deviation 81bp.


title: RNA-seq.WT.rep2

extract_protocol: Total RNA was mRNA enriched using oligo(dT) capture and ds cDNA was prepared. The ds cDNA was fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors. Average insertion size 200bp, standard deviation 77bp.


title: H3K4me3.rep2.s_4

description: chromatin IP against Histone H3K4me3

extract_protocol: DNA was MNase digested and subject to ChIP using the indicated antibody. The recovered fragmented DNA was end polished and ligated with Illumina methylated PE adaptors. Sizes between 200 bp (including the adaptors) were selected and sequenced with the Illumina Genome Analyzer II.

value: 4 P5 cerebella (pooled)

value: single-end, 37-mer sequencing

value: Histone H3 (tri methyl K4)

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number


title: H3K4me3.rep1.s_3

description: chromatin IP against Histone H3K4me3

tag: chip antibody


title: Atoh1.rep2

description: chromatin IP against Atoh1

value: ANTI-FLAG BioM2

value: Sigma


title: IgG.s_5

description: chromatin IP against IgG (negative control)

value: Rabbit IgG, Millipore, 12-371


title: H3K4me1.rep2.s_2

description: chromatin IP against Histone H3K4me1

value: Histone H3 (mono methyl K4)


title: H3K4me1.rep1.s_1

description: chromatin IP against Histone H3K4me1


title: Atoh1.control

description: Atoh1 control


title: Atoh1.rep1

description: chromatin IP against Atoh1


title: wheat leaf_S_12H

growth_protocol: Hexaploid wheat (Triticum aestivum L.) line ‘8866’ (S)(susceptible to wheat powdery mildew), ‘Pm30’ (Resistant to wheat powdery mildew),‘CS’ (sensitive to heat stress) and ‘TAM’ (tolerant to heat stress) were grown in a growth chamber at a relative humidity of 75% and 26/20℃ day and night temperature with light intensity of 3000 lx. 2 week-old plants were used for all experiments.

value: 8866 (susceptible to wheat powdery mildew,also designed as ‘S’)

value: two week old

tag: tissue

value: leaf

tag: infection

value: powdery mildew

value: 12 hours


title: cycle 12 female

status: Public on Feb 07 2011

city: Berkeley

first: Michael

last: Eisen

state: CA

address: Stanley Hall 304B

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
mRNA isolated from single embryo
instrument model: Illumina Genome Analyzer IIx

data_processing:
alignment: TopHat v1.0.13 using default settings
expression levels: Cufflinks v0.8.2 and Cuffcompare using default settings

source_name: embryo

growth_protocol: embryos were collected from crosses of CantonS females and w1 males, imaged live under a fluorescent scope and harvested into Trizol at desired stage

extract_protocol: libraries were prepared according to a version of Illumina's mRNA-Seq protocol adapted for small sample inputs; sex was determined by genotyping genomic DNA from analyzed embryos

tag: paternal strain

value: Canton-S

tag: maternal strain

value: His2Av-mRFP III.1 (Bloomington 23650)

tag: mitotic cycle


title: cycle 13 unclear sex


title: cycle 14A female

value: 14 (0-25% membrane envagination)


title: cycle 14D female

value: 14 (75-100% membrane envagination)


title: cycle 14C female replicate 2

value: 14 (50-75% membrane envagination)


title: cycle 14B female

value: 14 (25-50% membrane envagination)


title: cycle 14D unclear sex


title: cycle 14A unclear sex


title: cycle 14C female


title: cycle 14D male


title: cycle 11 female


title: cycle 14D male replicate 2


title: cycle 10 female


title: cycle 14C male replicate 2


title: cycle 14C male


title: cycle 14B male replicate 2


title: cycle 14B male


title: cycle 14A male replicate 2


title: cycle 14B female replicate 2


title: cycle 14A male


title: cycle 10 male


title: cycle 12 male


title: cycle 11 male


title: [E-MTAB-189] A09-Input

status: Public on Feb 05 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

data_processing:
Flow cell and pre-filled reagants are placed in the Genome Analyzer according to manufacturer's protocol.  The Analyzer successively images nucleotides. Single-end reads of lengh 36.
ParameterValue Version 1.4.0
Automated base calls, alignment and polymorphism detection using the Genome Analyzer Software.
ParameterValue Version 1.4.0
ELAND alignment were performed against an UNMASKED version of human genome hg18. Using the ELAND alignments, we selected all reads that had a unique best alignment for further processing.
ParameterValue Version 1.4.0
In-House scripts: ELAND output was processe to select reads with a unique best match, i.e., where the match with the fewest mismatches was to a single location.  The position of the read is converted to UCSC-style coordinate where the start position is 0-based and the end position is 1-based.  The reads are given their unique ids from the Illumina run which includes the run, lane, tile and x,y coordinates in the tile.
IDOM Functional Genomics Core Pipeline: All reads from all of the replicates for each factor value, i.e., antibody or input, were pooled to create the set of reads for further analysis.
Normalization Name: Input pool
GLITR: Regions of enrichment were identifying using GLITR (Tuteja et al NAR 2008). The unique position/strand pairs for all reads were compared to in similarly-processed reads for the input pool.  Regions with an FDR less than or equal to a cutoff were selected. The columns in the GLITR files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - GLITR fold change which is median average fold change of peak to input* Name - position* PValue - left blank* FDR - GLITR FDR percent, should always be less than 1.5* ExtraContent - left blankThe columns in the merged GLITR region files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - total GLITR fold change for merged regions* Name - position* PValue - left blank* FDR - left blank* ExtraContent - left blank
ParameterValue version JS-1
ParameterValue FDR 1.5
processed data file:
kkrb_Input_normal_a_1p5_glitr.tla

source_name: Normal donor

extract_protocol:
nucleic_acid_extraction | Protocol after that of Tuteja et al. 2008 Nucleic Acid Research 36(12): 4149-4157.   Islets (10,000 IEQs) were centrifuged (13,000Xg /30 sec) at room temperature (RT) and resuspended in 500ml 2.22% formaldehyde/PBS while rotating them for 10-min/RT. 59 ml 2.5M glycine was added to a final conc of 0.14 M to stop cross linking, followed by rotation for 5min/RT. Cells were centrifuged (13,000Xg/ 1 min) and pellet was washed with 1 ml PBS followed by centrifugation (13,000Xg) and then resuspended in 200 ml cold CHIP Whole cell lysis buffer. Cells were homogenized with small plastic pestle by hand and incubated on ice for 10 min.  Cells were sonicated using Diagenode Bioruptor for 10 min on high at 30 s intervals, followed by centrifugation at 13,000Xg for 10 mins/40C. Sample was split and 10 ml of supernatant was used as input; remainder was frozen in liquid nitrogren. 2mg chromatin was added to 1mL CHIP dilution buffer  and proteinase inhibitor. 2mg anti-histone antibody was then added followed by rotation at 4C/overnight.  Protein G agarose beads were washed 3 times with 1 ml of CHIP dilution buffer, resuspended in BSA, protease inhibitor and CHIP dilution buffer for and rotated at 4C overnight. 100 ml of blocked agarose beads were added to each chromatin sample, incubate at 4C/1 hr followed by centrifugation at 13,000Xg to aspirate the supernatant.  1 ml of wash buffer was added (TSEI, TSEII, CHIP buffer 3 in consecutive order) to agarose pellet and rotate at RT/5min.  100ml elution buffer was added to the pellet and rotated for 15 min. This step was repeated and eluates were combined. 8 ml 5M NaCl/ 200 ml eluates were added and incubate at 65C overnight.  8 ml 1M Tris HCl (pH7.5), 0.5M EDTA and 1 ml 10mg/ml proteinase K, were added to the sample followed by incubation at 45C /1hr for reverse cross-linking. Un-crosslinked chromatin was purified using PCR purification kit and eluted in 50 ml EB.  Enrichment of CHIP samples was confirmed using qPCR using SYBR GreenER (Invitrogen) and Mx3000 PCR System (Stratagene, La Jolla, CA, USA). Enrichment of target region was calculated using control region (+60Kb of insulin gene) as a reference (lacking histone modifications) and by comparing input (sheared genomic DNA) to ChIP material.
labeling | The immunoprecipitated DNA was modified for sequencing following the Illumina sequencing following the manufacturer protocol (Preparing Sample for ChIP Sequencing of DNA (11257047 Rev A)).
sequencing | Flow cell and reagants placed into cluster station according to manufacturer protocol.  Samples applied to flow cell and bridge amplification performed.  Clusters generated and sequencing primer annealed.

tag: material type

tag: organismpart

value: pancreatic islet

tag: Sex

value: male

tag: phenotype

value: African American

tag: diseasestate

value: normal

tag: antibody

tag: antibody target


title: [E-MTAB-189] A07-H2K4me2-ChIP

data_processing:
Flow cell and pre-filled reagants are placed in the Genome Analyzer according to manufacturer's protocol.  The Analyzer successively images nucleotides. Single-end reads of lengh 36.
ParameterValue Version 1.3.2
Automated base calls, alignment and polymorphism detection using the Genome Analyzer Software.
ParameterValue Version 1.3.2
ELAND alignment were performed against an UNMASKED version of human genome hg18. Using the ELAND alignments, we selected all reads that had a unique best alignment for further processing.
ParameterValue Version 1.3.2
In-House scripts: ELAND output was processe to select reads with a unique best match, i.e., where the match with the fewest mismatches was to a single location.  The position of the read is converted to UCSC-style coordinate where the start position is 0-based and the end position is 1-based.  The reads are given their unique ids from the Illumina run which includes the run, lane, tile and x,y coordinates in the tile.
IDOM Functional Genomics Core Pipeline: All reads from all of the replicates for each factor value, i.e., antibody or input, were pooled to create the set of reads for further analysis.
Normalization Name: H3K4me2 pool
GLITR: Regions of enrichment were identifying using GLITR (Tuteja et al NAR 2008). The unique position/strand pairs for all reads were compared to in similarly-processed reads for the input pool.  Regions with an FDR less than or equal to a cutoff were selected. The columns in the GLITR files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - GLITR fold change which is median average fold change of peak to input* Name - position* PValue - left blank* FDR - GLITR FDR percent, should always be less than 1.5* ExtraContent - left blankThe columns in the merged GLITR region files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - total GLITR fold change for merged regions* Name - position* PValue - left blank* FDR - left blank* ExtraContent - left blank
ParameterValue version JS-1
ParameterValue FDR 1.5
processed data file:
kkrb_h3k4me2_normal_a_1p5_glitr.tla
TessLA tool MergeOverlappingSpans: Regions of enrichment identified by GLITR where merged if their adjacent end-points were close enough to each other.  The coordinates of the resulting region run from the start of the first region to the end of the last region.  Regions that are not close enough to any other regions are included as is.
ParameterValue MaxGapBp 2435
processed data file:
kkrb_h3k4me2_normal_a_1p5_glitrm.tla

value: female

tag: age

value: abcam cat no# ab11946


title: BrdU labelled DNA rep1

status: Public on Feb 06 2011

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing: Alignment: Sequence reads were obtained and mapped to the TAIR8 Arabidospis genome using SeqMap. Uniquely mapping with three or fewer mismatches were retained.

organism: Arabidopsis thaliana

source_name: MM2d cells

extract_protocol: The DNA libraries for both BrdU DNA and unlabelled DNA were generated and sequenced on Genome Analyzer II as per the manufacturer instructions.

tag: cell line

tag: label

value: BrdU


title: [E-MTAB-189] A12-Input

value: Caucasian


title: [E-MTAB-189] A06-H2K4me2-ChIP


title: [E-MTAB-189] A06-H2K4me1-ChIP

data_processing:
Flow cell and pre-filled reagants are placed in the Genome Analyzer according to manufacturer's protocol.  The Analyzer successively images nucleotides. Single-end reads of lengh 36.
ParameterValue Version 1.3.2
Automated base calls, alignment and polymorphism detection using the Genome Analyzer Software.
ParameterValue Version 1.3.2
ELAND alignment were performed against an UNMASKED version of human genome hg18. Using the ELAND alignments, we selected all reads that had a unique best alignment for further processing.
ParameterValue Version 1.3.2
In-House scripts: ELAND output was processe to select reads with a unique best match, i.e., where the match with the fewest mismatches was to a single location.  The position of the read is converted to UCSC-style coordinate where the start position is 0-based and the end position is 1-based.  The reads are given their unique ids from the Illumina run which includes the run, lane, tile and x,y coordinates in the tile.
IDOM Functional Genomics Core Pipeline: All reads from all of the replicates for each factor value, i.e., antibody or input, were pooled to create the set of reads for further analysis.
Normalization Name: H3K4me1 pool
GLITR: Regions of enrichment were identifying using GLITR (Tuteja et al NAR 2008). The unique position/strand pairs for all reads were compared to in similarly-processed reads for the input pool.  Regions with an FDR less than or equal to a cutoff were selected. The columns in the GLITR files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - GLITR fold change which is median average fold change of peak to input* Name - position* PValue - left blank* FDR - GLITR FDR percent, should always be less than 1.5* ExtraContent - left blankThe columns in the merged GLITR region files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - total GLITR fold change for merged regions* Name - position* PValue - left blank* FDR - left blank* ExtraContent - left blank
ParameterValue version JS-1
ParameterValue FDR 1.5
processed data file:
kkrb_h3k4me1_normal_a_1p5_glitr.tla
TessLA tool MergeOverlappingSpans: Regions of enrichment identified by GLITR where merged if their adjacent end-points were close enough to each other.  The coordinates of the resulting region run from the start of the first region to the end of the last region.  Regions that are not close enough to any other regions are included as is.
ParameterValue MaxGapBp 500
processed data file:
kkrb_h3k4me1_normal_a_1p5_glitrm.tla

value: abcam cat no# ab8895


title: [E-MTAB-189] A06-Input

data_processing:
Flow cell and pre-filled reagants are placed in the Genome Analyzer according to manufacturer's protocol.  The Analyzer successively images nucleotides. Single-end reads of lengh 36.
ParameterValue Version 1.0.8
Automated base calls, alignment and polymorphism detection using the Genome Analyzer Software.
ParameterValue Version 1.0.8
ELAND alignment were performed against an UNMASKED version of human genome hg18. Using the ELAND alignments, we selected all reads that had a unique best alignment for further processing.
ParameterValue Version 1.0.8
In-House scripts: ELAND output was processe to select reads with a unique best match, i.e., where the match with the fewest mismatches was to a single location.  The position of the read is converted to UCSC-style coordinate where the start position is 0-based and the end position is 1-based.  The reads are given their unique ids from the Illumina run which includes the run, lane, tile and x,y coordinates in the tile.
IDOM Functional Genomics Core Pipeline: All reads from all of the replicates for each factor value, i.e., antibody or input, were pooled to create the set of reads for further analysis.
Normalization Name: Input pool
GLITR: Regions of enrichment were identifying using GLITR (Tuteja et al NAR 2008). The unique position/strand pairs for all reads were compared to in similarly-processed reads for the input pool.  Regions with an FDR less than or equal to a cutoff were selected. The columns in the GLITR files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - GLITR fold change which is median average fold change of peak to input* Name - position* PValue - left blank* FDR - GLITR FDR percent, should always be less than 1.5* ExtraContent - left blankThe columns in the merged GLITR region files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - total GLITR fold change for merged regions* Name - position* PValue - left blank* FDR - left blank* ExtraContent - left blank
ParameterValue version JS-1
ParameterValue FDR 1.5
processed data file:
kkrb_Input_normal_a_1p5_glitr.tla


title: [E-MTAB-189] A06-H3K4me3-ChIP

data_processing:
Flow cell and pre-filled reagants are placed in the Genome Analyzer according to manufacturer's protocol.  The Analyzer successively images nucleotides. Single-end reads of lengh 36.
ParameterValue Version 1.0.8
Automated base calls, alignment and polymorphism detection using the Genome Analyzer Software.
ParameterValue Version 1.0.8
ELAND alignment were performed against an UNMASKED version of human genome hg18. Using the ELAND alignments, we selected all reads that had a unique best alignment for further processing.
ParameterValue Version 1.0.8
In-House scripts: ELAND output was processe to select reads with a unique best match, i.e., where the match with the fewest mismatches was to a single location.  The position of the read is converted to UCSC-style coordinate where the start position is 0-based and the end position is 1-based.  The reads are given their unique ids from the Illumina run which includes the run, lane, tile and x,y coordinates in the tile.
IDOM Functional Genomics Core Pipeline: All reads from all of the replicates for each factor value, i.e., antibody or input, were pooled to create the set of reads for further analysis.
Normalization Name: H3K4me3 pool
GLITR: Regions of enrichment were identifying using GLITR (Tuteja et al NAR 2008). The unique position/strand pairs for all reads were compared to in similarly-processed reads for the input pool.  Regions with an FDR less than or equal to a cutoff were selected. The columns in the GLITR files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - GLITR fold change which is median average fold change of peak to input* Name - position* PValue - left blank* FDR - GLITR FDR percent, should always be less than 1.5* ExtraContent - left blankThe columns in the merged GLITR region files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - total GLITR fold change for merged regions* Name - position* PValue - left blank* FDR - left blank* ExtraContent - left blank
ParameterValue version JS-1
ParameterValue FDR 1.5
processed data file:
kkrb_h3k4me3_normal_a_1p5_glitr.tla
TessLA tool MergeOverlappingSpans: Regions of enrichment identified by GLITR where merged if their adjacent end-points were close enough to each other.  The coordinates of the resulting region run from the start of the first region to the end of the last region.  Regions that are not close enough to any other regions are included as is.
ParameterValue MaxGapBp 1000
processed data file:
kkrb_h3k4me3_normal_a_1p5_glitrm.tla

value: abcam cat no# ab8580


title: [E-MTAB-189] A04-H3K27me3-ChIP

data_processing:
Flow cell and pre-filled reagants are placed in the Genome Analyzer according to manufacturer's protocol.  The Analyzer successively images nucleotides. Single-end reads of lengh 36.
ParameterValue Version 1.3.2
Automated base calls, alignment and polymorphism detection using the Genome Analyzer Software.
ParameterValue Version 1.3.2
ELAND alignment were performed against an UNMASKED version of human genome hg18. Using the ELAND alignments, we selected all reads that had a unique best alignment for further processing.
ParameterValue Version 1.3.2
In-House scripts: ELAND output was processe to select reads with a unique best match, i.e., where the match with the fewest mismatches was to a single location.  The position of the read is converted to UCSC-style coordinate where the start position is 0-based and the end position is 1-based.  The reads are given their unique ids from the Illumina run which includes the run, lane, tile and x,y coordinates in the tile.
IDOM Functional Genomics Core Pipeline: All reads from all of the replicates for each factor value, i.e., antibody or input, were pooled to create the set of reads for further analysis.
Normalization Name: H3K27me3 pool
GLITR: Regions of enrichment were identifying using GLITR (Tuteja et al NAR 2008). The unique position/strand pairs for all reads were compared to in similarly-processed reads for the input pool.  Regions with an FDR less than or equal to a cutoff were selected. The columns in the GLITR files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - GLITR fold change which is median average fold change of peak to input* Name - position* PValue - left blank* FDR - GLITR FDR percent, should always be less than 1.5* ExtraContent - left blankThe columns in the merged GLITR region files are as follows:* Genome - always hg18 for this data* Chromosome* Begin - 1-based position* End - 1-based position* Strand - always '+', but actually strandless* Score - total GLITR fold change for merged regions* Name - position* PValue - left blank* FDR - left blank* ExtraContent - left blank
ParameterValue version JS-1
ParameterValue FDR 1.5
processed data file:
kkrb_h3k27me3_normal_a_1p5_glitr.tla
TessLA tool MergeOverlappingSpans: Regions of enrichment identified by GLITR where merged if their adjacent end-points were close enough to each other.  The coordinates of the resulting region run from the start of the first region to the end of the last region.  Regions that are not close enough to any other regions are included as is.
ParameterValue MaxGapBp 5000
processed data file:
kkrb_h3k27me3_normal_a_1p5_glitrm.tla

value: Millipore cat no# 07-449


title: [E-MTAB-189] A05-H3K27me3-ChIP

value: Hispanic


title: [E-MTAB-189] A05-H2K4me2-ChIP


title: [E-MTAB-189] A05-H2K4me1-ChIP


title: [E-MTAB-189] A04-H2K4me2-ChIP


title: [E-MTAB-189] A03-H3K27me3-ChIP

value: Asian


title: [E-MTAB-189] A05-Input


title: cycle 13 male

value: Canton-S

value: His2Av-mRFP III.1 (Bloomington 23650)


title: [E-MTAB-387] E_coli_K12_MG1655_RNAseq_LB_Transition_to_stationary

description: Provider: EMBL_Heidelberg

data_processing: Sequences obtained from the Illumina Genome Analyzer were mapped to both strands of the E. coli K12 MG1655 genome using BLAT allowing no gaps and up to two mismatches. Only reads which mapped to a single region of the genome were considered for further analysis. For each base position on the genome, the number of reads that mapped to that position was calculated.

organism: Escherichia coli

growth_protocol: grow | The E. coli K-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth.

extract_protocol:
nucleic_acid_extraction | To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at -80C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).
sequencing | Standard Illumina protocol for cDNA sequencing

tag: strainorline

value: K-12 substr. MG1655

tag: genotype

tag: growth condition

value: transition-to-stationary-phase


title: [E-MTAB-189] A02-Input

value: pancreatic islet


title: [E-MTAB-189] A02-H3K27me3-ChIP


title: [E-MTAB-189] A07-H3K4me3-ChIP


title: [E-MTAB-332] rpo delhns mid-exponential

description: Provider: EMBL_Heidelberg

data_processing: Sequences obtained from the Illumina Genome Analyzer were mapped to both strands of the E. coli K12 MG1655 genome using BLAT allowing no gaps and up to two mismatches. Each alignment was extended to 200bp the approximate average length of DNA fragments on the 3' end. Only reads which mapped to a single region of the genome were considered for further analysis. For each base position on the genome, the number of reads that mapped to that position was calculated.

source_name: rpo, delhns, ME

growth_protocol: grow | The E. coli K-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1); MG1655 hns (hns::Kanr); MG1655 fis (fis::Kanr); MG1655 hns-FLAG (hns::3xFLAG::Kanr); MG1655 fis-FLAG (fis::3xFLAG::Kanr). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth. Where needed, ampicillin, kanamycin, and chloramphenicol were used at final concentrations of 100, 30, and 30 ug/ml respectively.

extract_protocol:
nucleic_acid_extraction | ChIP was performed as previously described (Grainger et al, 2004) with some modifications to the protdegree Col. Cells were grown aerobically at 37degree C to the desired OD600 and formaldehyde was added to a final concentration of 1%. After 20 min of incubation, glycine was added to a final concentration of 0.5 M to quench the reaction and incubated for a further 5 min. Cross-linked cells were harvested by centrifugation and washed twice with ice-cold TBS (pH 7.5). Cells were resuspended in 1 ml of lysis buffer (10 mM Tris [pH 8.0], 20% sucrose, 50 mM NaCl, 10 mM EDTA, 20 mg/ml lysozyme and 0.1 mg/ml RNase A) and incubated at 37degree C for 30 min. Following lysis, 3 ml immunoprecipitation (IP) buffer (50 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% sodium dodecyl sulfate [SDS] and PMSF [final concentration 1 mM]) was added and the lysate passed through a French pressure cell twice. 2 ml aliquots were removed and the DNA sheared to an average size of ~200 bp using a Bioruptor (Diagenode) with 30 cycles of 30 sec on/off at high setting. Insoluble cellular matter was removed by centrifugation for 10 min at 4degree C, and the supernatant was split into two 800 microl aliquots. The remaining 400 microl was kept to check the size of the DNA fragments.

Each 800 microl aliquot was incubated with 20 microl Protein A/G UltraLink Resin (Pierce) on a rotary shaker for 45 min at room temperature to get rid of complexes binding to the resin non-specifically. The supernatant was then removed and incubated with either no antibody (mdegree Ck-IP), FLAG mouse mondegree Clonal antibody (Sigma-Aldrich) or RNAP Beta subunit mouse mondegree Clonal (Nedegree Clone) and 30 microl Protein A/G UltraLink Resin, pre-incubated with 1mg/ml bovine serum albumin (BSA) in TBS, on a rotary shaker at 4degree C overnight (FLAG antibody) or at room temperature for 90 min (RNAP Beta subunit antibody). Samples were washed once with IP buffer, twice with IP buffer + 500 mM NaCl, once with wash buffer (10 mM Tris [pH 8.0], 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet P-40 and 0.5% sodium deoxycholate) and once with TE (pH 7.5). Immunoprecipitated complexes were eluted in 100 microl elution buffer (10 mM Tris [pH 7.5], 10 mM EDTA and 1% SDS) at 65degree C for 20 min.
sequencing| Immunoprecipitated samples and the sheared DNA following the Bioruptor were de-crosslinked in 0.5x elution buffer containing 0.8 mg/ml Pronase at 42degree C for 2 h followed by 65degree C for 6 h. DNA was purified using a PCR purification kit (QIAGEN). Prior to sequencing, the DNA fragment sizes were checked and gene-specific quantitative PCR (qPCR) was carried out. Prior and post library construction, the concentration of the immunoprecipitated DNA samples was measured using the Qubit HS DNA kit (Invitrogen). Library construction and sequencing was done using the ChIP-Seq Sample Prep kit, Reagent Preparation kit and Cluster Station kit (Illumina). Samples were loaded at a concentration of 10 pM.

value: del-hns

value: mid-exponential

tag: chip antibody

value: RNAP beta subunit antibody


title: Unlabelled DNA rep1

value: unlabelled


title: [E-TABM-828] CTCF_breast_ab992_hsa_CTCFkd 2

description: Provider: CRUK-CRI

source_name: CTCF_breast_ab992_hsa_CTCFkd 2

growth_protocol: growth | MCF7 human breast cancer cells were grown as previously described (Neve et al. 2006). Unless otherwise stated, during all experiments oestrogen was added at a final concentration of 100 nM for 45 minutes (ChIP) or 24 hours (cell cycle analysis). HepG2 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
immunoprecipitate | ChIP experiments were performed with well-characterized antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) and MED12 (abcam, ab70842). ChIP-seq experiments were performed as recently described (Schmidt et al. 2009)
sequencing | The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.

value: cell

tag: cellline

value: female

value: breast

value: CTCF

tag: chip antibody catalog

value: Millipore, 07-729

tag: compound

value: oestrogen

tag: sirna knockdown

value: mock


title: [E-TABM-828] CTCF_breast_ab992_hsa_CTCFkd 1

description: Provider: CRUK-CRI

source_name: CTCF_breast_ab992_hsa_CTCFkd 1

tag: material type

tag: organismpart


title: [E-MTAB-332] rpo wt mid-exponential

description: Provider: EMBL_Heidelberg

source_name: rpo, wt, ME


title: [E-MTAB-332] H-NS stationary

description: Provider: EMBL_Heidelberg

source_name: H-NS, S

value: stationary

value: FLAG antibody


title: [E-TABM-828] CEBPA_liver_sc9314_hsaHepG2CRI 2

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
CEBPA.gff

source_name: CEBPA_liver_sc9314_hsaHepG2CRI 2

tag: Sex

value: male

value: liver

value: CEBPA

value: santa cruz, sc-9314

value: not applicable


title: [E-TABM-828] Input_liver_none_hsaHepG2CRI 1

description: Provider: CRUK-CRI

source_name: Input_liver_none_hsaHepG2CRI 1


title: [E-MTAB-189] A05-H3K2me3-ChIP

value: pancreatic islet

tag: phenotype

value: Hispanic

tag: diseasestate

value: normal

value: abcam cat no# ab8580


title: [E-MTAB-332] H-NS transition-to-stationary

description: Provider: EMBL_Heidelberg

source_name: H-NS, TS

value: K-12 substr. MG1655

value: transition-to-stationary


title: [E-MTAB-189] A04-H2K4me1-ChIP

value: female

value: African American

tag: antibody

value: abcam cat no# ab8895

tag: antibody target


title: [E-MTAB-332] H-NS early-exponential

description: Provider: EMBL_Heidelberg

source_name: H-NS, EE

value: early-exponential


title: [E-MTAB-332] H-NS mid-exponential

description: Provider: EMBL_Heidelberg

source_name: H-NS, ME

value: mid-exponential


title: [E-TABM-828] CTCF_liver_07729upstate_hsaHepG2CRI 2

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
CTCF.gff

source_name: CTCF_liver_07729upstate_hsaHepG2CRI 2

value: cell

value: CTCF

value: Millipore, 07-729


title: [E-MTAB-189] A03-H3K4me3-ChIP

value: male

tag: age

value: Asian


title: [E-MTAB-189] A03-H2K4me1-ChIP


title: [E-TABM-828] Rad21_liver_ab992_hsaHepG2CRI 2

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
Rad21.gff
Cohesin.gff

source_name: Rad21_liver_ab992_hsaHepG2CRI 2

value: liver

value: abcam, ab992

value: not applicable


title: [E-TABM-828] CEBPA_liver_sc9314_hsaHepG2CRI 1

description: Provider: CRUK-CRI

source_name: CEBPA_liver_sc9314_hsaHepG2CRI 1

value: CEBPA

value: santa cruz, sc-9314


title: [E-TABM-828] HNF4a_liver_ARP31046_hsa 1

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
HNF4a.gff

source_name: HNF4a_liver_ARP31046_hsa 1


title: [E-TABM-828] SA1_liver_ab4457_hsaHepG2CRI 2

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
SA1.gff
Cohesin.gff

source_name: SA1_liver_ab4457_hsaHepG2CRI 2


title: [E-TABM-828] CTCF_liver_07729upstate_hsaHepG2CRI 1

description: Provider: CRUK-CRI

source_name: CTCF_liver_07729upstate_hsaHepG2CRI 1


title: [E-MTAB-332] fis mid-exponential

description: Provider: EMBL_Heidelberg

source_name: Fis, ME

value: K-12 substr. MG1655

value: FLAG antibody


title: [E-TABM-828] SA1_liver_ab4457_hsaHepG2CRI 1

description: Provider: CRUK-CRI

source_name: SA1_liver_ab4457_hsaHepG2CRI 1


title: [E-TABM-828] do750_Input_breast_none_hsa_CTCF_mock 1

description: Provider: CRUK-CRI

source_name: do750_Input_breast_none_hsa_CTCF_mock 1

growth_protocol: knock_down | Cells were grown in phenol red-free DMEM supplemented with 5% charcoal dextran treated serum for at least three days (cell cycle analysis) or in full media (RNAi-ChIP-seq). Cells were transfected with siRNA for 48 hours using Lipofectamine2000 (Invitrogen, CA, USA). AllStars Negative Control siRNA (Qiagen) was used as negative (mock) controls. CTCF RNAi (Invitrogen Stealth, sense: GCGCUCUAA-GAAAGAAGAUUCCUCU, antisense: AGAGGAAUCUUCUUUCUUAGAGCGC). RAD21#1 (Invitrogen Stealth; sense: CAGCUUGAAUCAGAGUAGAGUGGAA, antisense: UUCCACUCUACUCUGAUUCAAGCUG) RAD21#2 (ON-TARGETplus SMARTpool L-006832).

value: female

value: breast

value: oestrogen

value: mock


title: [E-MTAB-332] fis early-exponential

description: Provider: EMBL_Heidelberg

source_name: Fis, EE

value: early-exponential


title: [E-TABM-828] Rad21_liver_ab992_hsaHepG2CRI 1

description: Provider: CRUK-CRI

source_name: Rad21_liver_ab992_hsaHepG2CRI 1

value: cell


title: [E-TABM-828] do748_Input_breast_none_hsa_CTCF_kd 1

description: Provider: CRUK-CRI

source_name: do748_Input_breast_none_hsa_CTCF_kd 1

value: CTCF


title: [E-MTAB-387] E_coli_K12_MG1655_RNAseq_LB_Early_exponential

description: Provider: EMBL_Heidelberg


title: [E-MTAB-332] rpo delfis mid-exponential

description: Provider: EMBL_Heidelberg

source_name: rpo, delfis, ME

value: del-fis

value: mid-exponential

value: RNAP beta subunit antibody


title: [E-TABM-828] Rad21_breast_ab992_hsa_CTCFkd 1

description: Provider: CRUK-CRI

source_name: Rad21_breast_ab992_hsa_CTCFkd 1


title: [E-TABM-828] SA1_breast_ab4457_hsa_CTCF_kd 1

description: Provider: CRUK-CRI

source_name: SA1_breast_ab4457_hsa_CTCF_kd 1


title: [E-TABM-828] Rad21_breast_ab992_hsaMCF7_vehicle 2

description: Provider: CRUK-CRI

source_name: Rad21_breast_ab992_hsaMCF7_vehicle 2

value: vehicle


title: [E-TABM-828] SA1_breast_ab4457_hsa_CTCF_mock 1

description: Provider: CRUK-CRI

source_name: SA1_breast_ab4457_hsa_CTCF_mock 1


title: [E-TABM-828] Rad21_breast_ab992_hsaMCF7_vehicle 1

description: Provider: CRUK-CRI

source_name: Rad21_breast_ab992_hsaMCF7_vehicle 1

value: abcam, ab992


title: [E-TABM-828] Rad21_breast_ab992_hsa_CTCF_mock 1

description: Provider: CRUK-CRI

source_name: Rad21_breast_ab992_hsa_CTCF_mock 1


title: [E-TABM-828] MCF7_CTCF_E45_rep1 2

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
CTCF_treat.gff

source_name: MCF7_CTCF_E45_rep1 2

value: Millipore, 07-729

value: not applicable


title: [E-TABM-828] SA1_breast_ab4457_hsaMCF7_vehicle 2

description: Provider: CRUK-CRI

source_name: SA1_breast_ab4457_hsaMCF7_vehicle 2

value: abcam, ab4457


title: [E-TABM-828] SA1_breast_ab4457_hsaMCF7_vehicle 1

description: Provider: CRUK-CRI

source_name: SA1_breast_ab4457_hsaMCF7_vehicle 1


title: [E-TABM-828] MCF7_CTCF_E45_rep1 1

description: Provider: CRUK-CRI

source_name: MCF7_CTCF_E45_rep1 1


title: [E-TABM-828] Rad21_breast_ab992_hsaMCF7_treat 2

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
Rad21_treat.gff
Cohesin_treat.gff

source_name: Rad21_breast_ab992_hsaMCF7_treat 2


title: [E-TABM-828] Era_breast_sc543_hsaMCF7_treat 1

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
Era_treat.gff

source_name: Era_breast_sc543_hsaMCF7_treat 1

value: Era

value: santa cruz, sc-543


title: [E-TABM-828] Rad21_breast_ab992_hsaMCF7_treat 1

description: Provider: CRUK-CRI

source_name: Rad21_breast_ab992_hsaMCF7_treat 1

value: female


title: [E-TABM-828] SA1_breast_ab4457_hsaMCF7_treat 1

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
SA1_treat.gff
Cohesin_treat.gff

source_name: SA1_breast_ab4457_hsaMCF7_treat 1

value: breast


title: [E-TABM-828] Input_breast_none_hsamcf7 2

description: Provider: CRUK-CRI

source_name: Input_breast_none_hsamcf7 2

value: oestrogen


title: [E-TABM-828] Input_breast_none_hsamcf7 1

description: Provider: CRUK-CRI

source_name: Input_breast_none_hsamcf7 1


title: Chromatin accessibility assay of CD14+ Primary cells; DS17215

status: Public on Feb 02 2011

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17215
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5356
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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: Various levels of processed data files will be made available as this project proceeds.

source_name: flow sorted CD14+ Cells,year 21; DS17215

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD14 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 21

value: Male

value: Caucasian

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of CD4+ Primary cells; DS17212

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17212
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5346
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
****************

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

ANALYSIS FILE NAME: GSM665839_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17212.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD4 Primary Cells, Donor RO 01679, Library DS17212 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6369
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4851
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.489
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4804
POISSON_PERCENTILE: 59

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

ANALYSIS FILE NAME: GSM665839_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17212.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD4 Primary Cells, Donor RO 01679, Library DS17212 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6408
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CD4 DNase 21 12
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS17212 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4851
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.489
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4804
POISSON_PERCENTILE: 59

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

source_name: flow sorted CD4+ Cells,year 21; DS17212

value: CD4 Primary Cells


title: Chromatin accessibility assay of CD3+ Primary cells; DS17198

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17198
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5323
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5322
****************
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: GSM665837_UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17198.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD3 Primary Cells, Donor RO 01679, Library DS17198 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6384
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4798
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.4876
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9973
IROC_PERCENTILE: 95
POISSON_SCORE: 0.4584
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM665837_UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17198.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD3 Primary Cells, Donor RO 01679, Library DS17198 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6423
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CD3 DNase 21 98
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS17198 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4798
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.4876
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9973
IROC_PERCENTILE: 95
POISSON_SCORE: 0.4584
POISSON_PERCENTILE: 54

source_name: flow sorted CD3+ Cells,year 21; DS17198

value: CD3 Primary Cells


title: Chromatin accessibility assay of CD56+ Primary cells; DS17189

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17189
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5359
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5358
****************
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: GSM665836_UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01679.DS17189.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17189.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD56 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD56 Primary Cells, Donor RO 01679, Library DS17189 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6379
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6182
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6307
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9975
IROC_PERCENTILE: 97
POISSON_SCORE: 0.5813
POISSON_PERCENTILE: 87

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

ANALYSIS FILE NAME: GSM665836_UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01679.DS17189.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17189.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD56 Primary Cells, Donor RO 01679, Library DS17189 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6418
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CD56 DNase 21 89
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS17189 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6182
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6307
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9975
IROC_PERCENTILE: 97
POISSON_SCORE: 0.5813
POISSON_PERCENTILE: 87

source_name: flow sorted CD56+ Cells,year 21; DS17189

value: CD56 Primary Cells


title: Chromatin accessibility assay of Fetal Kidney_Left Tissue; DS16579

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16579
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5382
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5381
****************
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: GSM665829_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23604.DS16579.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16579.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-23604, Library DS16579 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6387
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3242
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.325
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9891
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4351
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM665829_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23604.DS16579.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16579.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Left, Donor H-23604, Library DS16579 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6426
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FKL DNase 04 79
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-23604 Library DS16579 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3242
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.325
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9891
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4351
POISSON_PERCENTILE: 46

source_name: Fetal Kidney, Left primary tissue, day 110; DS16579

value: Fetal Kidney, Left

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

value: Primary Tissue

value: UW

value: fetal

value: day 110

value: Female


title: Chromatin accessibility assay of Fetal Lung_Right Tissue; DS16790

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16790
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5378
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5377
****************
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: GSM665832_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23640.DS16790.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16790.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-23640, Library DS16790 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6375
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4185
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4037
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9916
IROC_PERCENTILE: 26
POISSON_SCORE: 0.4651
POISSON_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM665832_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23640.DS16790.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16790.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Right, Donor H-23640, Library DS16790 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6414
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FLR DNase 40 90
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-23640 Library DS16790 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4185
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4037
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9916
IROC_PERCENTILE: 26
POISSON_SCORE: 0.4651
POISSON_PERCENTILE: 56

source_name: Fetal Lung, Right primary tissue, day 115; DS16790

value: Fetal Lung, Right

value: genomic DNA

value: day 115


title: Chromatin accessibility assay of Fetal Heart Tissue; DS16582

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16582
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5279
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5278
****************
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: GSM665830_UW.Fetal_Heart.ChromatinAccessibility.H-23604.DS16582.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16582.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23604, Library DS16582 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6388
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6087
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.5893
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9965
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6457
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM665830_UW.Fetal_Heart.ChromatinAccessibility.H-23604.DS16582.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16582.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-23604, Library DS16582 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6427
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FH DNase 04 82
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23604 Library DS16582 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6087
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.5893
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9965
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6457
POISSON_PERCENTILE: 100

source_name: Fetal Heart primary tissue, day 110; DS16582

value: Fetal Heart


title: Chromatin accessibility assay of Fetal Intestine_Small Tissue; DS16559

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16559
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5414
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5413
****************
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: GSM665825_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23604.DS16559.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16559.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23604, Library DS16559 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6378
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3725
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.3599
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9956
IROC_PERCENTILE: 72
POISSON_SCORE: 0.4353
POISSON_PERCENTILE: 49

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

ANALYSIS FILE NAME: GSM665825_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23604.DS16559.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16559.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Small, Donor H-23604, Library DS16559 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6417
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FIS DNase 04 59
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23604 Library DS16559 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3725
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.3599
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9956
IROC_PERCENTILE: 72
POISSON_SCORE: 0.4353
POISSON_PERCENTILE: 49

source_name: Fetal Intestine, Small primary tissue, day 110; DS16559

value: Fetal Intestine, Small

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Lung_Left Tissue; DS16570

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16570
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5370
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5369
****************
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: GSM665828_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23604.DS16570.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16570.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23604, Library DS16570 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6383
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4611
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4467
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9939
IROC_PERCENTILE: 51
POISSON_SCORE: 0.5077
POISSON_PERCENTILE: 77

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

ANALYSIS FILE NAME: GSM665828_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23604.DS16570.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16570.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-23604, Library DS16570 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6422
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FLL DNase 04 70
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23604 Library DS16570 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4611
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4467
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9939
IROC_PERCENTILE: 51
POISSON_SCORE: 0.5077
POISSON_PERCENTILE: 77

source_name: Fetal Lung, Left primary tissue, day 110; DS16570

value: Fetal Lung, Left

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Heart Tissue; DS16500

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16500
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5283
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5282
****************
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: GSM665824_UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16500.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23589, Library DS16500 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6373
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4152
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3977
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.515
POISSON_PERCENTILE: 79

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

ANALYSIS FILE NAME: GSM665824_UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16500.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-23589, Library DS16500 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6412
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FH DNase 89 00
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23589 Library DS16500 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4152
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3977
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.515
POISSON_PERCENTILE: 79

source_name: Fetal Heart primary tissue, day 147; DS16500

value: day 147


title: Chromatin accessibility assay of Fetal Kidney_Left Tissue; DS16805

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16805
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5386
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5385
****************
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: GSM665834_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23640.DS16805.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16805.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-23640, Library DS16805 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6401
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6266
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.625
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9969
IROC_PERCENTILE: 87
POISSON_SCORE: 0.6388
POISSON_PERCENTILE: 97

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

ANALYSIS FILE NAME: GSM665834_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23640.DS16805.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16805.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Left, Donor H-23640, Library DS16805 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6440
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FKL DNase 40 05
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-23640 Library DS16805 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6266
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.625
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9969
IROC_PERCENTILE: 87
POISSON_SCORE: 0.6388
POISSON_PERCENTILE: 97

source_name: Fetal Kidney, Left primary tissue, day 115; DS16805

value: Fetal Kidney, Left

value: Male