title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Lung Tissue; renlab.H3K4me3.STL002LG.01.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY133
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12270
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12247
****************
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: GSM915336_UCSD.Lung.H3K4me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL002LG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Lung H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Lung, Donor STL002, 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.13553
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,903,739
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.166
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2289
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2995
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM915336_UCSD.Lung.H3K4me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL002LG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Lung H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Lung, Donor STL002, 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.13673
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: Lung H3K4me3 02 33
BROWSER_TRACK_DESCRIPTION: UCSD Lung Histone H3K4me3 Donor STL002 Library AY133 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,903,739
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.166
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2289
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2995
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Lung

value: genomic DNA

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Left Ventricle Tissue; renlab.H3K4me3.STL001LV.01.01

status: Public on Mar 05 2014

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK337
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11840
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM906406_UCSD.Left_Ventricle.H3K4me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL001LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Left Ventricle, Donor STL001, 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.13509
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,868,204
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3775
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4289
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9999
IROC_PERCENTILE: 83
POISSON_SCORE: 0.3995
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM906406_UCSD.Left_Ventricle.H3K4me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL001LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Left Ventricle, Donor STL001, 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.13629
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: LV H3K4me3 01 37
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K4me3 Donor STL001 Library AK337 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,868,204
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3775
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4289
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9999
IROC_PERCENTILE: 83
POISSON_SCORE: 0.3995
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Left Ventricle tissue; renlab.H3K4me3.STL001LV.01.01

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

tag: sample alias

tag: sample common name

value: Left Ventricle

tag: molecule

tag: disease

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American


title: 9wk: 228

status: Public on Mar 04 2014

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

data_processing:
library strategy: Sequence of PCR amplification of bisulfite converted genomic DNA of numerous loci
We aligned all reads to the mouse genome and determined the methylation status of each CpG for every read covering this position using Bismark
We then error corrected the overlapping portion of the read using a custom perl script, keeping the base call with the highest base quality
We summarized methylation data using the bismark methylation_extractor and a custom perl script
We summarized data for each CpG using custom scripts in R
Genome_build: mm9
Supplementary_files_format_and_content: SerreLocusSpecificCountsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are data, with two consecutive columns per sample. The first is the total number of methylated reads at that position, and the second is the total number of reads at that position.
Supplementary_files_format_and_content: SerreLocusSpecificPercentsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are the percent methylation at each locus for each sample, with one column per sample.

organism: Mus musculus

source_name: maternal-High fat_adult-Low fat

extract_protocol:
We extracted DNA from the liver of all 9-week-old males using the DNeasy Blood and Tissue kit (Qiagen Inc., Valencia, CA, USA).
We bisulfite treated 2 µg of DNA from each of the 40 liver tissues using the MethylCode Bisulfite Conversion kit (Invitrogen, Carslbad, CA, USA) and PCR amplified 22 loci. We pooled all PCR products generated from a single individual to prepare a sequencing library incorporating a unique barcode.

tag: strain

tag: age

value: nine weeks

tag: gender

value: male

tag: maternal diet

value: High fat

tag: adult diet

value: Low fat

tag: tissue

value: liver


title: 9wk: 200

source_name: maternal-Low fat_adult-High fat


title: JAG wild-type replicate 3

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

country: United Kingdom

institute: JIC

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were mapped to TAIR10 whole genome using SOAPv2 -r 0
CSAR (default parameter except backg=20) was used for the peak calling step
Genome_build: TAIR10
Supplementary_files_format_and_content: csv; significant binding sites

organism: Arabidopsis thaliana

source_name: JAG wild-type

growth_protocol: Plants were grown under long day conditions (16 h light and 8 h dark) at 18° C day temperature and at 20° C night temperature at 80% humidity.

extract_protocol:
pJAG:JAG-GFP jag-2 and wild-type L-er control plants were used. 1300-1500 mg  (fresh weight) of inflorescence apices per sample were fixed in 35 ml fixation buffer (0.4 M sucrose, 10mM Tris pH 8, 1 mM EDTA pH 8.5, 1% formaldehyde, 100 µM PMSF) under vacuum for 20 min on ice. Cross-linking was stopped with 100 µM  glycine for 10 min on ice. After two washes with sterile water, the tissue was blotted dry and frozen in liquid nitrogen. Nuclei were purified as described [Gomez-Mena et al., 2005, Development 132: 429-438] and resupended in 1 ml of sonication buffer containing 500 mM Hepes, 150 mM NaCl, 5 mM MgCl2, 10% TRITON X-100 and ½ a tablet of protease inhibitor cocktail complete Mini, EDTA-free (Roche). Sonication was performed in a Bioruptor waterbath sonicator at 4°C (2 x 5 min high power level with 30 sec on/30sec off cycles) resulting in an average fragment size of 500 bp.  After centrifugation, the supernatant was mixed with 500 ul of immunoprecipitation buffer containing 0.5M Hepes, 150 mM NaCl, 5 mM MgCl2 , 10% TRITON X-100, 1 mg/ml BSA and 25 µl of anti-GFP µMACS Microbeads (Milteyi Biotec), incubated on ice for 30 min and loaded on a µ Column (Milteyi Biotec) that had been equilibrated with 200 µl immunoprecipitation buffer and placed into a magnetic µMACS separator (Milteyi Biotec). After washing twice with 400 µl and twice with 200 µl of immunoprecipitation buffer, then twice with 200 µl TE buffer (100 mM Tris pH 8, 10 mM EDTA pH 8), DNA was eluted once with 20 µl and twice with 50 µl of preheated (96° C) elution buffer containing 50 mM Tris pH8, 10 mM EDTA, 50 mM DTT and 1% SDS. 100 µl of TE-buffer and 9 µl of 25 mg/ml Proteinase K (Sigma) were added to the eluted samples and to the input control samples. Crosslinking was reverted in eluted and input samples at 37°C overnight, followed by addition of 9 µl of 25 mg/ml Proteinase K and 8 h incubation at 65° C, phenol-chloroform extraction and precipitation with ethanol overnight at -20° C. After washing in 70% EtOH, the air-dried DNA was resuspended in 100 µl PCR-grade water (Roche), purified using a PCR purification Kit (18104, Qiagen) and stored at -80° C.
Illumina TruSeq ChIP-Seq libraries (three pJAG: JAG-GFP replicates and three wild-type controls) were produced as described [Kaufmann et al, 2009, PLoS Biology 7: e90.]

tag: genotype/variation

value: wt

value: inflorescence tips (only unopened buds)


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Left Ventricle Tissue; renlab.H3K27me3.STL001LV.01.01

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK236
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12176
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
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: GSM908952_UCSD.Left_Ventricle.H3K27me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL001LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Left Ventricle, Donor STL001, 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.13477
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,806,639
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0445
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1585
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.8038
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3137
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM908952_UCSD.Left_Ventricle.H3K27me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL001LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Left Ventricle, Donor STL001, 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.13597
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: LV H3K27me3 01 36
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K27me3 Donor STL001 Library AK236 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,806,639
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0445
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1585
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.8038
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3137
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Left Ventricle tissue; renlab.H3K27me3.STL001LV.01.01

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Histone H3K27me3


title: 9wk: 199


title: 9wk: 183

source_name: maternal-High fat_adult-High fat


title: 9wk: 182


title: 9wk: 181


title: 9wk: 174


title: 9wk: 177


title: 9wk: 173


title: FLER-DS13348

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: cultured erythroid cells derived from human fetal liver, replicate 1

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Illumina chastity filtered reads were aligned to the Human GRCh37/hg19 reference with bowtie version 0.12.7 with the following parameter equivalents: bowtie -p <nodes> -n 2 -m 1 --best --phred33-quals
Nucleotide cleavage signal was generated across the genome by summing the 5' read positions at each location where reads mapped , using the bedmap utility from the BEDOPS suite: https://github.com/bedops/bedops
per base bigWig files were generated with bedGraphToBigWig (UCSC)
FDR 1% Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration for 36mer mappability
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Signal, bigWig; Peaks, bed

source_name: fetal livers cells

growth_protocol: FL cells (50–100-day gestation) were obtained from the fetal tissue repository (University of Washington Birth Defects Research Laboratory). MPB CD34+ cells and dissociated FL cells were cultured in an erythroid induction medium to generate adult- and fetal-type erythroid cells composed of Stemline hematopoietic stem cell growth and expansion medium (Sigma-Aldrich) supplemented with 2 mM L-glutamine, 1× penicillin/streptomycin, 0.1 mM MEM nonessential amino acids (all from Mediatech), 0.1 mM β-mercaptoethanol, 200 μg/mL iron-saturated transferrin,10 μM ethanolamine, 10 μg/mL insulin (all from Sigma-Aldrich), 6 U/mL erythropoietin, 50 ng/mL stem cell factor (both from Amgen, Thousand Oakes, CA), 20 ng/mL interleukin-3, 20 ng/mL interleukin-6, 40 ng/mL insulin-like growth factor-1, 10 ng/mL vascular endothelial growth factor (all from Peprotech, Rocky Hill, NJ), 5% protein-free hybridoma medium, 1 × insulin-transferrin–selenium (both from Invitrogen), and 1 × EX-CYTE (Millipore, Billerica, MA). At the end of the culture, cell composition was determined by flow cytometry. Fourteen days after culture, staining with anti-glycophorin-A antibody (DAKO, Glostrup, Denmark) revealed that ~50% of cells where erythroid cells, expressing glycophorin-A, FLERs were enriched to over 95% purity using MACS system as per the manufacturer's instruction (Miltenyi Biotec, Auburn, CA). The surface expression of CD71 or CD36 by glycophorin-A+ erythroblasts was also analyzed by flow cytometry using Fluorescein isothiocyanate-conjugated anti-CD71 or Allophycocyanin-conjugated anti-CD36 antibodies (both from BD Biosciences, San Jose, CA). Cells were acquired using FACScalibur (BD Biosciences), and the results were analyzed with Flowjo X (Tree Star Inc., Ashland, OR). Gatings were set according to isotype controls.

extract_protocol:
Refer to the Nuclei isolation section of John et.al. Current Protocols in Molecular Biology PMID: 23821440
Illumina TruSeq v2

tag: developmental stage

value: Fetal (50–100-day gestation)

tag: cell type

value: fetal liver derived erythroid cells

tag: replicate


title: 9wk: 134

source_name: maternal-Low fat_adult-Low fat


title: 9wk: 172


title: 9wk: 133


title: 9wk: 128


title: 9wk: 127


title: 9wk: 227


title: 9wk: 126


title: 9wk: 201


title: 9wk: 123


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Sigmoid Colon Tissue; renlab.H3K4me3.STL001SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK333
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13322
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
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: GSM956024_UCSD.Sigmoid_Colon.H3K4me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL001SG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Sigmoid Colon, Donor STL001, 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.16441
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,621,862
FINDPEAKS_SCORE: 0.1592
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2442
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9999
IROC_PERCENTILE: 56
POISSON_SCORE: 0.2658
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM956024_UCSD.Sigmoid_Colon.H3K4me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL001SG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Sigmoid Colon, Donor STL001, 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.16595
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SC H3K4me3 01 33
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K4me3 Donor STL001 Library AK333 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,621,862
FINDPEAKS_SCORE: 0.1592
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2442
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9999
IROC_PERCENTILE: 56
POISSON_SCORE: 0.2658
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Sigmoid Colon tissue; renlab.H3K4me3.STL001SG.01.01

value: Sigmoid Colon

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: 9wk: 109

value: nine weeks

value: male

value: High fat

value: Low fat

value: liver


title: 9wk: 122


title: 9wk: 97


title: 9wk: 99


title: 9wk: 100


title: 9wk: 108


title: 9wk: 102


title: 9wk: 101


title: 9wk: 54


title: 9wk: 55


title: 9wk: 24


title: 9wk: 52


title: 9wk: 23


title: 9wk: 13


title: 9wk: 14


title: 9wk: 227 [RRBS]

data_processing:
We aligned all reads to the mouse genome and determined the methylation status of each CpG for every read covering this position using Bismark
We summarized methylation data using the bismark methylation_extractor and a custom perl script
We summarized data for each CpG using custom scripts in R
Genome_build: mm9
Supplementary_files_format_and_content: SerreRRBSCountsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are data, with two consecutive columns per sample. The first is the total number of methylated reads at that position, and the second is the total number of reads at that position.
Supplementary_files_format_and_content: SerreRRBSPercentsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are the percent methylation at each locus for each sample, with one column per sample.

extract_protocol:
We extracted DNA from the liver of all 9-week-old males using the DNeasy Blood and Tissue kit (Qiagen Inc., Valencia, CA, USA).
Briefly, we digested genomic DNA with MspI before preparing barcoded libraries according to the Illumina protocol. We then size selected DNA molecules of 150-600 bp and bisulfite converted the DNA libraries.

tag: Sex

value: Male


title: 9wk: 228 [RRBS]


title: 9wk: 211 [RRBS]


title: 9wk: 210 [RRBS]


title: 9wk: 208 [RRBS]


title: PGP1 primary fibroblasts

city: Boston

first: Je

middle: Hyuk

last: Lee

state: MA

address: 3 Blackfan Circle, CLSB 528

department: Wyss Institute

institute: Harvard Medical School

description:
Sample 3
Grown  in 10% FBS DMEM.

library_source: transcriptomic

data_processing:
Read trimming: fastq-mcf -o /pgp1/fastq-mcf/s_1_1.fq -o pgp1/fastq-mcf/s_1_2.fq adaptors.fasta /pgp1/s_1_1_sequence.txt /pgp1/s_1_2_sequence.txt
Alignment (http://bio-bwa.sourceforge.net/bwa.shtml): bwa mem bwa-master/bwarefseq /pgp1/fastq-mcf/s_1_1.fq /pgp1/fastq-mcf/s_1_2.fq > /pgp1/bwa/s_1_pe.sam
Sort SAM>BAM files: samtools view -bS /pgp1/fastq-mcf/s_1_pe_aln.sam > /pgp1/bwa/s_1_pe_aln.bam
Sort SAM>BAM files: samtools sort -n -m 500000000 /pgp1/bwa/s_1_pe_aln.bam /pgp1/bwa/s_1_pe_aln_sorted
Gene expression (eXpress 1.4.0): express -o /pgp1/express/s_2/ refMrna.fa /pgp1/bwa/s_2_pe_aln_sorted.bam
Genome_build: NCBI human RefSeq-release 59
Supplementary_files_format_and_content: Tab delimited text containing genes, counts, fpkm.

molecule: total RNA

source_name: Dermal primary fibroblasts

extract_protocol:
RNeasy (Quagen)
Ovation RNA-seq kit (NuGen)

treatment_protocol: no treatment

tag: disease state

value: normal

value: adult

value: Dermal primary fibroblasts


title: 9wk: 209 [RRBS]


title: 9wk: 124


title: PGP1 lymphocytes

description:
Sample 2
Grown in 10% FBS DMEM.

source_name: Immortalized B-cells

value: Immortalized B-cells


title: PGP1 hiPSC

description:
Sample 1
Grown in mTeSR1 media.

source_name: IPS cells

value: IPS cells


title: 9wk: 207 [RRBS]


title: 9wk: 183 [RRBS]


title: 9wk: 199 [RRBS]


title: 9wk: 201 [RRBS]


title: 9wk: 182 [RRBS]


title: 9wk: 174 [RRBS]


title: 9wk: 173 [RRBS]


title: 9wk: 181 [RRBS]


title: 9wk: 133 [RRBS]


title: 9wk: 172 [RRBS]


title: 9wk: 134 [RRBS]


title: 9wk: 128 [RRBS]


title: 9wk: 127 [RRBS]


title: 9wk: 126 [RRBS]


title: 9wk: 124 [RRBS]


title: 9wk: 123 [RRBS]


title: JAG wild-type replicate 1

value: wt

value: inflorescence tips (only unopened buds)


title: 9wk: 108 [RRBS]


title: 9wk: 122 [RRBS]


title: 9wk: 109 [RRBS]


title: 9wk: 102 [RRBS]


title: 9wk: 101 [RRBS]


title: 9wk: 99 [RRBS]


title: 9wk: 100 [RRBS]


title: 9wk: 177 [RRBS]


title: 9wk: 55 [RRBS]


title: 9wk: 97 [RRBS]


title: 9wk: 54 [RRBS]


title: 9wk: 52 [RRBS]


title: 9wk: 24 [RRBS]


title: 9wk: 23 [RRBS]


title: 9wk: 13 [RRBS]


title: 9wk: 15 [RRBS]


title: 9wk: 200 [RRBS]


title: rhesus_monkey_lung

status: Public on Mar 03 2014

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

country: China

institute: Peking University

data_processing:
RNA-Seq data were mapped to genome (rheMac2) tophat (v1.2.0)
RPKM was calculated as previously described
Genome_build: rheMac2
Supplementary_files_format_and_content: Table format. The gene and transcript ID, RPKM, reads number mapped to this gene, the length of exon and the position were listed in order.

organism: Macaca mulatta

source_name: lung

extract_protocol:
Trizol method
Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions. A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.

value: lung

tag: library type

value: strand-specific, dUTP protocal


title: rhesus_monkey_cerebellun

source_name: cerebellum

value: cerebellum


title: strain B6 Influenza infection at 148 hours, repeat 1

city: Tel-Aviv

first: Irit

last: Gat-Viks

address: Tel-Aviv

department: Department of Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

data_processing:
All reads were aligned to the mouse reference genome (NCBI 37, MM9) using the TopHat aligner
The raw expression levels of the genes were calculated using Scripture, an ab-initio software which reconstruct transcriptomes.
Normalization was done using DESeq based on the negative binomial distribution and a local regression model
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file which includes RefSeq ID and normalized read counts for each sample.

extract_protocol:
For RNA isolation, each organ was cut into small pieces in the presence of QIAzol, homogenized using SPEX CertiPrep homogenizer, and total RNA was extracted using miRNeasy Mini Kit (Qiagen). The RNA integrity number (RIN) was determined using the TapeStation System (Agilent Technologies). Quantity was determined by Qubit Fluorometric Quantitiation (Life Technologies).
For preparation of RNA-seq libraries, total RNA was fragmented into average size of 300 nucleotides by chemical heat (95Oc) treatment for 4:30 minutes (NEBNext Magnesium RNA Fragmentation Module). The 3’ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen). Strand specific cDNA was synthesized using a poly T-VN oligo (18 T) and Affinity Script RT enzyme (Agilent). Double strand DNA was obtained using Second strand synthesis kit (NEB). DNA ends were repaired using T4 polynucleotide kinase and T4 polymerase (NEB-Next). After addition of an adenine base residue to the 5’ end using Klenow enzyme (NEB-Next), a barcode Illumina compatible adaptor (IDT) was ligated to each fragment. The washed DNA fragment was amplified by PCR (12 cycles) using specific primers (IDT) to the ligated adaptors. The quality of the library was analyzed by Tapestation (Agilent).

tag: infection

value: influenza

tag: time

value: 148 hours

value: 5 weeks


title: strain B6 Influenza infection at 149 hours, repeat 2

value: 149 hours


title: strain B6 Influenza infection at 122 hours, repeat 1

value: 122 hours


title: strain B6 Influenza infection at 75 hours, repeat 2

value: 75 hours


title: strain B6 Influenza infection at 50 hours, repeat 2

value: 50 hours


title: strain B6 Influenza infection at 49 hours, repeat 1

value: 49 hours


title: strain B6 Influenza infection at 12 hours, repeat 2

value: 12 hours


title: strain B6 Influenza infection at 32 hours, repeat 1

value: 32 hours


title: strain B6 Influenza infection at 28 hours, repeat 2

value: 28 hours


title: strain B6 Influenza infection at 74 hours, repeat 1

value: 74 hours


title: strain B6 Influenza infection at 26 hours, repeat 1

value: 26 hours


title: strain B6 Influenza infection at 98 hours, repeat 1

value: 98 hours


title: strain B6 Influenza infection at 11 hours, repeat 1

value: 11 hours

value: lung


title: strain B6 Influenza infection at 4 hours, repeat 2

value: 4 hours


title: 9wk: 14 [RRBS]

value: nine weeks

value: Male

value: Low fat

value: liver


title: strain B6 Influenza infection at 3 hours, repeat 1

value: influenza

value: 3 hours

value: 5 weeks


title: strain B6 uninfected, repeat 2

source_name: strain B6 uninfected, repeat 2


title: strain B6 uninfected, repeat 3

source_name: strain B6 uninfected, repeat 3


title: strain B6 Influenza infection at 7 hours, repeat 1

value: 7 hours


title: strain B6 Influenza infection at 8 hours, repeat 2

value: 8 hours


title: rhesus_monkey_kidney

source_name: kidney

value: kidney

value: male

value: strand-specific, dUTP protocal


title: strain B6 uninfected, repeat 1

source_name: strain B6 uninfected, repeat 1


title: strain B6 uninfected, repeat 4

source_name: strain B6 uninfected, repeat 4


title: strain B6 Influenza infection at 123 hours, repeat 2

value: 123 hours


title: CD8+ pDC, strain B6 Influenza infection at day 5, repeat 2

extract_protocol:
For sorting dendritic cells from lungs, the lungs from infected and control uninfected C57BL/6J mice were immersed in cold PBS, cut into small pieces in 5 ml DMEM media containing 10% Bovine Fetal Serum, the cell suspensions were grinded using 1ml syringe cup on a 70 μm cell strainers (BD Falcon). The cells were washed with ice cold PBS. Remaining red blood cells were lysed using ammonium chloride solution (Sigma). Cells were harvested, immersed 1ml FACS buffer [PBS+2% FBS, 1mM EDTA], Fc receptors were blocked with anti-mouse CD16/CD32, washed with FACS buffer and divided into two tubes for sorting cDC and pDC cells. For sorting cDC, the cells were stained with antibodies against multiple surface antigens: Percp cy5.5 conjugated anti CD45 (clone –F11), APC conjugated CD11c (clone N418), PB conjugated anti I-A/IE (clone M5/114.15.2), PE conjugated anti CD103 (clone 2E7) and FITC conjugated CD11b (clone M1/70). The cDC cells were identified as CD45 positive, CD11c high, MHC-II positive, and were gated as CD103 negative CD11b positive and CD103 positive CD11b negative. For pDC sorting, the cells were stained with the following antibodies: Percp cy5.5 conjugated anti CD45 (clone –F11), APC conjugated CD11C (clone N418), APC CY7 conjugated CD45R/B220, (clone RA3-6B2), PE conjugated anti PDCA-1 (clone129c1) and PE CY7 conjugated CD8  (clone 53-6.7). The pDC cells were identified as CD45 positive, CD11C intermediate, B220 positive, PDCA-1 positive, and gated as CD8  positive and CD8  negative. Flow cytometry was performed using SORP FACSAriaII Flow Cytometer (Becton Dickinson) and data were analyzed using WinMDI 2.8 software.
For preparation of RNA-seq libraries, total RNA was fragmented into average size of 300 nucleotides by chemical heat (95Oc) treatment for 4:30 minutes (NEBNext Magnesium RNA Fragmentation Module). The 3’ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen). Strand specific cDNA was synthesized using a poly T-VN oligo (18 T) and Affinity Script RT enzyme (Agilent). Double strand DNA was obtained using Second strand synthesis kit (NEB). DNA ends were repaired using T4 polynucleotide kinase and T4 polymerase (NEB-Next). After addition of an adenine base residue to the 5’ end using Klenow enzyme (NEB-Next), a barcode Illumina compatible adaptor (IDT) was ligated to each fragment. The washed DNA fragment was amplified by PCR (12 cycles) using specific primers (IDT) to the ligated adaptors. The quality of the library was analyzed by Tapestation (Agilent).

value: day 5

value: lung dendritic cell


title: strain B6 Influenza infection at 99 hours, repeat 2

value: 99 hours

value: lung


title: CD8+ pDC, strain B6 Influenza infection at day 5, repeat 1


title: CD8+ pDC, strain B6 Influenza infection at day 3, repeat 1

value: day 3


title: CD8+ pDC, strain B6 uninfected, repeat 2


title: CD8+ pDC, strain B6 uninfected, repeat 1


title: CD8- pDC, strain B6 Influenza infection at day 5, repeat 1


title: CD8- pDC, strain B6 Influenza infection at day 5, repeat 2


title: CD8- pDC, strain B6 Influenza infection at day 3, repeat 1


title: CD8- pDC, strain B6 Influenza infection at day 3, repeat 2


title: CD8- pDC, strain B6 Influenza infection at day 1, repeat 2

value: day 1


title: CD8- pDC, strain B6 uninfected, repeat 1


title: CD8- pDC, strain B6 uninfected, repeat 2


title: CD103-CD11b+ cDC, strain B6 Influenza infection at day 5, repeat 1


title: CD103+CD11b- cDC, strain B6 Influenza infection at day 5, repeat 1


title: CD103+CD11b- cDC, strain B6 Influenza infection at day 3, repeat 2


title: CD103+CD11b- cDC, strain B6 Influenza infection at day 1, repeat 1


title: CD103+CD11b- cDC, strain B6 Influenza infection at day 1, repeat 2


title: CD8- pDC, strain B6 Influenza infection at day 1, repeat 1


title: CD103-CD11b+ cDC, strain B6 Influenza infection at day 1, repeat 2


title: CD103+CD11b- cDC, strain B6 Influenza infection at day 3, repeat 1


title: CD103-CD11b+ cDC, strain B6 Influenza infection at day 3, repeat 1


title: CD103-CD11b+ cDC, strain B6 uninfected, repeat 2


title: CD103-CD11b+ cDC, strain B6 uninfected, repeat 1


title: CD103+CD11b- cDC, strain B6 uninfected, repeat 1


title: CD8+ pDC, strain B6 Influenza infection at day 1, repeat 1


title: CD8+ pDC, strain B6 Influenza infection at day 3, repeat 2


title: BMDM-RNAseq-mu

status: Public on Mar 02 2014

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: no treatment

data_processing:
RNA-Seq: Reads were aligned to the mouse mm9 genome (NCBI Build 37) using STAR (v2.0.3e). RNA-Seq experiments were normalized and visualized by using HOMER (http://biowhat.ucsd.edu/homer/) to generate custom tracks for the UCSC Genome Browser (http://genome.ucsc.edu/). Gene expression values were generating for RefSeq annotated transcripts using HOMER and differential expression calculations were performed using edgeR.
RNA-Seq RPKM tab-delimited text file is available on series record. Columes: 1: RefSeq ID, 2: chr, 3: gene start, 4: gene end, 5: strand, 6: mRNA length, 7: Copies of gene in genome, 8: Annotation information, 9-18: RPKM gene expression values
Genome_build: mm9

molecule: polyA RNA

source_name: Primary Bone Marrow Derived Macrophages (mu HTT Q175/175)

growth_protocol: Murine microglial BV2 cells, primary mouse microglia, mouse astrocyte maintained with DMEM (Cellgro) supplemented with 10% FBS (low endotoxin, Hyclone) and penicillin/streptomycin (Invitrogen).  Adult microglia Purification: Cortex, striatum, and hippocampus were extracted and gently homogenized in staining buffer (HBSS (Life Technologies, 14175-095), 1% BSA, 1mM EDTA) on ice using a 2 ml polytetrafluoroethylene pestle (Wheaton), first in a 14 ml round-bottom tube (BD Falcon, 352059) and then in a 2 ml grinder chamber (Wheaton, 358029). Homogenates were filtered onto a 70 ?m cell strainer (BD Falcon, 352350) and centrifuged for 10 min at 400g. Cell pellets were resuspended in 6 ml of 37% isotonic Percoll (Sigma, P4937) and then underlayed with 5 ml of 70% isotonic Percoll in a 15ml centrifuge tube (Corning, 430790). Tubes were then centrifuged at 600g for 40 min at 18°C, with no acceleration or decelaration. Cells at the 37?70% Percoll interface were recovered and washed once in 15 ml HBSS. Cell were then incubated in staining buffer on ice with CD16/CD32 (eBioscience, clone 93) antibody for 25 min, and then with CD11b-PE (BioLegend 101208, clone M1/70) and CD45- Alexa488 (BioLegend 103122, clone 3-F11) antibodies for 30 min. Cells were then washed once and filtered onto a 40 ?m cell strainer (BD Falcon, 352340). Sorting was performed on a BD Influx cell sorter. Microglia were defined as singlets, CD11b+CD45Low events, and emcompassed 90-95% of all CD11b+ events. BMDM Isolation: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion). Subsequently, RNA was treated with TURBO DNase (Ambion), fragmented with RNA Fragmentation Reagents (Ambion) and purified by a P-30 column (Biorad).
Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs) heat inactivated and precipitated over-night. Poly(A)-tailing and cDNA synthesis was performed as previously described. For reverse transcription, oligos with custom barcodes (underlined) were used: 5′-Phos-CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTT TTTTTTTTTTTTTTTTVN-3′. Subsequently, exonuclease was used to remove the excess oligo. After heat-inactivation, RNA was hydrolyzed by alkaline treatment (100mM NaOH) and heat at 95°C for 25 min. The cDNA fragments of 50–150 nucleotides were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 12 cycles, and gel purified as previously described. The library was sequenced on Illumina sequencers according to the manufacturer's instructions.

treatment_protocol: pCDH, Nwt, and Nmu Constructs: N-terminus human wild-type and N-terminus mutant huntingtin have been cloned from pCAG-Htt19550-15Q and pCAG-Htt1955-128Q respectively into MCS of pCDH-CMV-MCS-EF1-Puro (System Bioscience) using EcoRI and NotI. Lentiviral production and BV2 cells transduction were performed according to the manufacturer's protocol. Control cell line was generated by transducing BV2 cells with Lentivirus obtained from pCDH-CMV-MCS-EF1-Puro (empty vector). Validation of plasmids used in this study was performed by Western blotting.

value: macrophages

tag: htt status

value: mutant  HTT Q175/175


title: Microglia-RNAseq-mu

description: no treatment

source_name: Primary Microglia (mu HTT Q175/175)

value: microglial


title: Microglia-RNAseq-wt

description: no treatment

source_name: Primary Microglia (wt HTT Q7/7)

value: wildtype HTT Q7/7


title: Input3

first: R. Anthony

last: Barnitz

address: 450 Brookline Ave.

department: Department of Pediatric Oncology

institute: Dana-Farbert Cancer Institute, Harvard Medical School

data_processing:
Basecalls and demultiplexing were performed using CASAVA v1.8.2
ChIP-Seq reads were aligned to the mouse NCBI37/mm9 reference genome using bowtie (PubMed ID: 19261174) v0.12.7 using the following parameter: (-n 1 -m 1 --best --strata)
Reads were sorted using samtools (PMID: 19505943) and deduplicated using picard (http://picard.sourceforge.net/)
SPP (PMID: 19029915) and MACS2 (PMID: 18798982) were both used for peak finding.  Regions from both peak callers were combined with mergeBed (PMID: 20110278).  Quality rating for the merged regions was assigned based on the maximum significance from either source.
Genome_build: mm9
Supplementary_files_format_and_content: SPP was used to generated BigWig visualization tracks for ChIP reads corrected for background (Input, IgG, or total H3, as appropriate)

source_name: In vitro effector CD8+ T cells

growth_protocol: Primary P14 TCR transgenic CD8+ T cells were isolated using CD8 negative selection magnetic-activated cell sorting (MACS) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 10mM HEPES, 50 U/ml of Penicillin, 50 mg/ml of Streptomycin, and 50 mM b-mercaptoethanol.

extract_protocol:
In vitro effector CD8+ T cells were fixed with 1% formaldehyde and flash frozen at -80°C.  The fixed cells were lysed and the chromatin was sheared using a Covaris E210 Ultrasonicator.  Transcription factor-DNA and histone-DNA complexes were immunoprecipitated and then eluted from magnetic beads.  The formaldehyde crosslinks were reversed, and the ChIP DNA fragments were purified.
ChIP DNA was prepared for high-throughput Illumina sequencing using the NEBNext ChIP-Seq Library Master Mix Set for Illumina kit and the NEBNext Multiplex Oligos for Illumina kit according to a modified manufacturer's protocol.  For each ChIP or input sample, 10-50 ng of DNA was used to prepare a sequencing library.  The DNA fragments were end-repaired, dA-tailed, and ligated to illumina adaptors according th the kit instructions.  DNA fragments of 150-600 bp in length were then selected using Pippin Prep 2% Agarose Gel Cassettes and the Pippin Prep DNA Size Selection System.  The ChIP DNA was then amplified with 12 PCR cycles using the NEBNext Multiplex Oligos.  Amplifed DNA was purfied using a 1:1 ratio of DNA to Agencort AMPure XP beads.

treatment_protocol: Naïve CD8+ T cells were stimulated with plate-bound anti-CD3 (4 mg/ml, clone 2C11, BD Pharmingen) and anti-CD28 (4 mg/ml, clone 37.51, BD Pharmingen) in the presence of recombinant human IL-2 (100 U/ml, R&D Systems) for 3 days to generate in vitro effector CD8+ T cells.

value: Day 3 in vitro activated effector CD8+ T cells

tag: mouse strain

value: P14 TCR transgenic C57Bl/6

tag: chip antibody

tag: nebnext index for illumina barcode

value: NEBNext Index 1 (ATCACG)


title: Input2

value: NEBNext Index 2 (CGATGT)


title: Input

value: NEBNext Index 8 (ACTTGA)


title: IgG

value: Normal Rabbit IgG (Life Technologies, 10500C, Lot 939223A)


title: CD103-CD11b+ cDC, strain B6 Influenza infection at day 3, repeat 2

value: influenza

tag: age

value: 5 weeks

tag: strain


title: Total H3 replicate

value: Total H3 (Abcam, ab1791, Lot GR82485)


title: H3K36me3 replicate

value: NEBNext Index 3 (TTAGGC)


title: CD103-CD11b+ cDC, strain B6 Influenza infection at day 1, repeat 1

value: lung dendritic cell


title: Total H3

value: NEBNext Index 11 (GGCTAC)


title: H3K36me3

value: NEBNext Index 6 (GCCAAT)


title: H3K4me1 replicate

value: H3K4me1 (Abcam, ab8895, Lot GR61280)


title: H3K27me3


title: H3K4me3 replicate

value: H3K4me3 (Abcam, ab8580, Lot GR33084)

value: NEBNext Index 9 (GATCAG)


title: H3K4me1

value: NEBNext Index 12 (CTTGTA)


title: BMDM-RNAseq-wt

description: no treatment

source_name: Primary Bone Marrow Derived Macrophages (wt HTT Q7/7)

value: macrophages

value: wildtype HTT Q7/7


title: cJun

value: Day 3 in vitro activated effector CD8+ T cells

value: P14 TCR transgenic C57Bl/6

value: cJun (N) (Santa Cruz, sc-45, Lot K3010)


title: H3K27ac

value: H3K27ac (Abcam, ab4729, Lot GR52136)

value: NEBNext Index 4 (TGACCA)


title: H3K27me3 replicate

value: NEBNext Index 8 (ACTTGA)


title: IRF4 replicate

value: IRF4 (M-17) (Santa Cruz, sc-6059, Lot C2712)


title: JunB

value: JunB (210) (Santa Cruz, sc-73, Lot D2610)


title: H3K27ac replicate

value: NEBNext Index 5 (ACAGTG)


title: H3K4me3


title: IRF4 1


title: BATF

value: BATF (Brookwood Biomedical, PAB4003, Lot 004)

value: NEBNext Index 1 (ATCACG)


title: JunD

value: JunD (329) (Santa Cruz, sc-74, Lot I1510)

value: NEBNext Index 10 (TAGCTT)


title: BATF replicate

value: NEBNext Index 2 (CGATGT)


title: siCTL_RNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description:
siCTL
polyA RNA

data_processing:
87,975,078 (siCTL) and 83,661,413 (siER) 50bp single-end reads were generated by sequencing.
Initially, Differentially Expressed genes (DE genes) were called using Illumina RegionMiner algorithm selecting 0.01 as P-Value score cut-off and 1.5 as absolute siCTL/siER fold change threshold. We considered only transcripts associated with at least 10 reads in one of two conditions.
Subsequently, each FastQ file was aligned again using Tophat version 2.0.6. Hg19 was used as reference genome assembly and Gencode 14 as reference transcriptome database. About 96% of reads for both the dataset were aligned by the algorithm (84,929,381, siCTL; 80,694,174, siERα). Count tables were created using HT-Seq algorithm in union modality and them were subjected to differential expression analysis using EdgeR and DESeq. EdgeR was applied using estimateGLMCommonDisp function with options method=“deviance”, robust=TRUE and subset=NULL. Instead, DESeq analysis was performed estimating expression variance using blind method and sharing mode fit-only.
We considered only genes detected as differerential expression by all algorithms. P-value scores computed were combined using the Fisher method.
Genome_build: hg19
Supplementary_files_format_and_content: Tabular file of  DE genes list sorted by increasing P-value.

source_name: mammary gland, adenocarcinoma

growth_protocol: MCF7 were routinely grown in DMEM containing 10% heat-inactivated FBS, 2mM L-glutamine, 50 U/ml penicillin and 50 μg/ml streptomycin. Before to perform any experiments, MCF7 cells were grown in phenol red-free DMEM supplemented with 5% charcoal-dextran-treated serum for 3 days.

extract_protocol:
Total RNA was extracted from MCF7 cells using RNAeasy mini kit (QIAGEN), with on-column DNase treatment to remove contaminating genomic DNA. mRNA was purified from 5 μg of total RNA using poly-T oligo-attached  magnetic beads
Extracted RNA was converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the manufacturer recommendations using the Illumina TruSeq RNA SamplePreparation Kit.

treatment_protocol: Cells were transfected with siRNA using Lipofectamine2000 (Invitrogen) on day 2, according to the manufacture protocol. Stealth RNAiTM siRNAs (ESR1HSS103376, ESR1HSS103377, ESR1HSS176619) from Invitrogen were used to target ERα. Stealth RNAiTM siRNA Negative Control LO GC from Invitrogen was used as a negative control.

tag: cell line

tag: transfection

value: siCTL


title: 9wk: 15

source_name: maternal-Low fat_adult-Low fat

value: nine weeks

tag: gender

value: male

tag: maternal diet

value: Low fat

tag: adult diet

tag: tissue

value: liver


title: siERα_ChIP-Seq

data_processing:
A total of 53,673,423 (siCTL), 49,388,965 (siERα) and 53,543,845 (IgG) 36 bp single-end reads were obtained by sequencing. The reads were mapped against human genome assembly Hg19 (GRCh37) using ELANDv2 algorithm allowing up to 2 mismatch in the first 32 read position
Mapping process resulted in 35,077,717 (siCTL, 65.4%), 34,258,440 (siERα, 69.4%) and 35,456,783 (IgG, 66.2%) unique aligned reads.
ChIP-seq peak identification and quality control were performed using RegionMiner. Peaks having a p-value minor than 0.00001 in siCTL/IgG condition were selected.
These 4,232 peaks are associated also to a p-value computed using siERα sample as control.
Genome_build: hg19
Processed data reported the ChIP-Seq peaks

extract_protocol:
Cells were crosslinked by adding 1% formaldehyde, immunoprecipitation was performed as described using antibodies against ERα. DNA purification was achieved with Phenol:Chloroform:IAA (25:24:1) according to the manufacturer’s instructions.
ChIP-Seq was performed using 10ng of immunoprecipitated DNA obtained from 240 μg of chromatin for each sample, followed by library amplification and Illumina sequencing.

value: ERα (Santa Cruz Biotechnology; sc-534X, sc-7207X)

value: siERα


title: siCTL_ChIP-Seq


title: IgG

value: Rabbit Control IgG ChIP Grade ab46540


title: BV2-ChIPseq-notx-CEBPb-Nwt

description: no treatment, 24h

data_processing:
ChIP-Seq: Reads were aligned to the mouse mm9 genome assembly (NCBI Build 37) using Bowtie allowing up to 2 mismatches. Only tags that mapped uniquely to the genome were considered for further analysis. ChIP-Seq experiments were normalized and visualized by using HOMER (http://biowhat.ucsd.edu/homer/) to generate custom tracks for the UCSC Genome Browser (http://genome.ucsc.edu/). Peak finding, motif finding, and peak annotation were performed using HOMER.
Genome_build: mm9

source_name: BV2 cells

extract_protocol:
20x10^6 cells were crosslinked in Formaldehyde/PBS 1% for 10 min at RT. After quenching the reaction by adding 125mM glycine, cells were washed 2X with PBS and were centrifuged (8 min, 800g, 4°C). Cells were resuspended in swelling buffer (10mM HEPES/KOH pH 7.9, 85mM KCl, 1mM EDTA, 0.5% IGEPAL CA-630, 1X protease inhibitor cocktail (Roche), 1mM PMSF) for 5 min. Cells were spun down and resuspended in 500μl lysis buffer (50mM Tris- HCl pH 7.4, 1% SDS, 0.5% EmpigenBB, 10mM EDTA, 1X protease inhibitor cocktail (Roche), 1mM PMSF) and chromatin was sheared to an average DNA size of 300–400bp by administering 5 pulses of 10 sec duration at 10 W power output with 30 sec pause on ice using a Misonix 3000 sonicator. The lysate was cleared by centrifugation (5 min, 16000g, 4°C), and supernatant was diluted 2.5-fold with 750μl dilution buffer (20mM Tris-HCl pH 7.4, 100mM NaCl, 0.5% Triton X-100, 2mM EDTA, 1X protease inhibitor cocktail (Roche)). The diluted lysate was pre-cleared by rotating for 2h at 4°C with 120μl 50% rProtein A sepharose Fast Flow (GE Healthcare). The beads were discarded, and 1% of the supernatant were kept as ChIP input. The protein of interest was immunoprecipitated by rotating the supernatant with 2.5 μg antibody overnight at 4°C, then adding 50μl blocked rProtein A sepharose and rotating the sample for an additional 1h at 4°C. The beads were pelleted (2 min, 1000g, 4°C), the supernatant discarded, and the beads were transferred in 400μl wash buffer I (WBI) (20mM Tris-HCl pH 7.4, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA) into 0.45 μm filter cartridges (Ultrafree MC, Millipore), spun dry (1 minute, 2200g, 4°C), washed one more time with WBI, and twice each with WBII (20mM Tris-HCl pH 7.4, 500mM NaCl, 1% Triton X-100, 2mM EDTA), WBIII (10mM Tris-HCl pH 7.4, 250mM LiCl, 1% IGEPAL CA-630, 1% Na-deoxycholate, 1mM EDTA), and TE. Immunoprecipitated chromatin was eluted twice with 100 μl elution buffer each (100mM NaHCO3, 1% SDS) into fresh tubes for 20 min. Eluates were pooled, the Na+ concentration was adjusted to 300mM with 5M NaCl and crosslinks were reversed overnight at 65°C in a hybridization oven. The samples were sequentially incubated at 37°C for 2h each with 0.33mg/ml RNase A and 0.5mg/ml proteinase K. The DNA was isolated using the QiaQuick PCR purification kit (Qiagen).
DNA from chromatin immunoprecipitation (10–50ng) was adapter-ligated and PCR amplified according to the manufacturer’s protocol (Illumina).

tag: cell type

value: microglial

value: wildtype Human Htt overexpression

value: CEBPb (sc-150)

tag: expression construct

value: Nwt (HTT wt)


title: BV2-ChIPseq-notx-CEBPb-Nmu

description: no treatment, 24h

value: mutant Human Htt overexpression

value: Nmu (HTT mutant)


title: BV2-ChIPseq-notx-CEBPa-Nmu

description: no treatment, 24h

value: CEBPa (sc-61)


title: BV2-ChIPseq-notx-CEBPb-pCDH

description: no treatment, 24h

value: no Human Htt overexpression

value: pCDH (empty)


title: BV2-ChIPseq-notx-PU.1-Nmu

description: no treatment, 24h


title: BV2-ChIPseq-notx-CEBPa-Nwt

description: no treatment, 24h


title: BV2-ChIPseq-notx-H3K4me2-Nwt

description: no treatment, 24h

value: H3K4me2 (Millipore 07-030)


title: BV2-ChIPseq-notx-H3K4me2-pCDH

description: no treatment, 24h


title: siERα_RNA-Seq

description:
siERα
polyA RNA


title: BV2-ChIPseq-notx-H3K4me2-Nmu

description: no treatment, 24h


title: BV2-ChIPseq-notx-PU.1-pCDH

description: no treatment, 24h


title: BV2-RNAseq-notx-24h-Nmu

description: no treatment, 24h


title: BV2-ChIPseq-notx-PU.1-Nwt

description: no treatment, 24h


title: BV2-RNAseq-notx-48h-Nmu

description: no treatment, 48h


title: BV2-RNAseq-notx-48h-Nwt

description: no treatment, 48h


title: BV2-RNAseq-notx-48h-pCDH

description: no treatment, 48h


title: BV2-RNAseq-notx-24h-pCDH

description: no treatment, 24h


title: later developmental stage of primary roots

status: Public on Mar 01 2014

city: Jinan

first: Xiangpei

last: Kong

address: 27 Shanda South Road

institute: Shandong University

data_processing:
clean reads were aligned to the maize B73 RefGen_V2 genome using SOAP2
The sequences were used in a BLASTN search of the Rfam database (http://rfam.sanger.ac.uk/) and NCBI to remove the rRNAs, tRNAs, snRNAs and snoRNAs.
The unique small RNA sequences were used to do a Blastn search against the miRNA database
Genome_build: B73 RefGen_V2
Supplementary_files_format_and_content: Relative expression level (TPM)

organism: Zea mays

source_name: roots

growth_protocol: Maize seedlings (Zea mays L. cv Zhengdan 958) were grown in Hoagland’s solution (pH 6.0) under greenhouse conditions at 28°C/25°C (day/night) with a photosynthetic active radiation of 300 μmol m-2 s-1, 60% relative humidity and a photoperiod of 16/8 h (day/night) for 2 weeks. The solution was renewed every 2 days.

extract_protocol: Total RNA was extracted from the shoots and roots with TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). Total RNAs were purified by electrophoretic separations on a 15% TBE-Urea denaturing PAGE gel. The sRNA regions corresponding to 18- to 30-nucleotide bands were excised and recovered. Subsequently, those sRNAs were 5' and 3' RNA adapter-ligated using T4 RNA ligase. RT-PCR was performed for 18 cycles, and the products were purified and sequenced using an Illumina/Solexa Genome Analyzer at the Beijing Genomics Institute,Shenzhen, China.

treatment_protocol: Early developmental stage of primary root (PRY) (3 days after germination), early developmental stage of seminal root (SR) (7 days after germination), early developmental stage of crown root (CR) (15 days after germination) and later developmental stage of primary root (PRO) (15 days after germination) were harvested with lengths of 1 cm from root tip. PRY, SR and CR with lengths of approximately 3 to 5 cm were selected for the experiments.

tag: developmental stage

value: PRO

value: 15 days after germination

tag: cultivar

value: Zhengdan 958


title: BV2-RNAseq-notx-24h-Nwt

description: no treatment, 24h


title: crown roots

value: CR


title: early developmental stage of primary roots

value: PRY

value: 3 days after germination


title: seminal roots

value: SR

value: 7 days after germination


title: Arabidopsis thaliana Zu-0 X Edi-0 seedling, biological replicate 3

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
zu-0_x_edi-0_br_3
PolyA RNA

data_processing:
Reads from FASTQ files that were the output of the Illumina pipeline were aligned to the genome and processed with TopHat 2.0.9, Bowtie2 2.1.0, SAMtools 0.1.19-44428cd, and Cufflinks 2.1.1 for calculation of gene expression levels with the TAIR10 annotation.
Genome_build: TAIR10
Supplementary_files_format_and_content: A single text file per biological replicate with the output of Cufflinks 2.1.1. The files are tab delimited.

source_name: Seedling, Zu-0 X Edi-0 F1

growth_protocol: Plants were germinated on soil and grown for approximately 10 or 11 days under standard long day conditions (16 hours light, 8 hours dark, at 20C) for collection of aerial seedlings at the emergence of the fourth true leaf.

extract_protocol:
Tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477:419-23 (see Supplementary Information Section 7).
Libraries were prepared using the 'NEBNext mRNA Library Prep Master Mix Set for Illumina' protocol. Modifications to the workflow to create directional data included the incorporation of a nucleotide analogue (dUTP) at second strand reverse transcription and an enzymatic digest of the pre-PCR libraries. Custom indexed primers incorporated barcodes at PCR to enable sequencing in 9-plex pools per Illumina lane.

tag: strain/background

value: Zu-0 X Edi-0 F1 cross progeny

value: aerial seedling

value: emergence of fourth true leaf


title: Arabidopsis thaliana Zu-0 X Edi-0 seedling, biological replicate 2

description:
zu-0_x_edi-0_br_2
PolyA RNA


title: Arabidopsis thaliana Zu-0 X Edi-0 seedling, biological replicate 1

description:
zu-0_x_edi-0_br_1
PolyA RNA


title: Arabidopsis thaliana Wu-0 X Rsch-4 seedling, biological replicate 2

description:
wu-0_x_rsch-4_br_2
PolyA RNA

source_name: Seedling, Wu-0 X Rsch-4 F1

value: Wu-0 X Rsch-4 F1 cross progeny


title: Arabidopsis thaliana Wu-0 X Rsch-4 seedling, biological replicate 3

description:
wu-0_x_rsch-4_br_3
PolyA RNA


title: Arabidopsis thaliana Wu-0 X Rsch-4 seedling, biological replicate 1

description:
wu-0_x_rsch-4_br_1
PolyA RNA


title: BV2-ChIPseq-notx-CEBPa-pCDH

description: no treatment, 24h

value: microglial

tag: htt status


title: Arabidopsis thaliana Ws-0 X Oy-0 seedling, biological replicate 2

description:
ws-0_x_oy-0_br_2
PolyA RNA

source_name: Seedling, Ws-0 X Oy-0 F1

value: Ws-0 X Oy-0 F1 cross progeny


title: Arabidopsis thaliana Ws-0 X Oy-0 seedling, biological replicate 3

description:
ws-0_x_oy-0_br_3
PolyA RNA


title: Arabidopsis thaliana Ws-0 X Oy-0 seedling, biological replicate 1

description:
ws-0_x_oy-0_br_1
PolyA RNA


title: Arabidopsis thaliana Wil-2 X No-0 seedling, biological replicate 3

description:
wil-2_x_no-0_br_3
PolyA RNA

source_name: Seedling, Wil-2 X No-0 F1

value: Wil-2 X No-0 F1 cross progeny


title: Arabidopsis thaliana Mt-0 X Tsu-0 seedling, biological replicate 3

description:
mt-0_x_tsu-0_br_3
PolyA RNA

source_name: Seedling, Mt-0 X Tsu-0 F1

value: Mt-0 X Tsu-0 F1 cross progeny


title: Arabidopsis thaliana Wil-2 X No-0 seedling, biological replicate 1

description:
wil-2_x_no-0_br_1
PolyA RNA


title: Arabidopsis thaliana Sf-2 X Can-0 seedling, biological replicate 3

description:
sf-2_x_can-0_br_3
PolyA RNA

source_name: Seedling, Sf-2 X Can-0 F1

value: Sf-2 X Can-0 F1 cross progeny


title: Arabidopsis thaliana Mt-0 X Tsu-0 seedling, biological replicate 1

description:
mt-0_x_tsu-0_br_1
PolyA RNA


title: Arabidopsis thaliana Ler-0 X Kn-0 seedling, biological replicate 3

description:
ler-0_x_kn-0_br_3
PolyA RNA

source_name: Seedling, Ler-0 X Kn-0 F1

value: Ler-0 X Kn-0 F1 cross progeny


title: Arabidopsis thaliana Wil-2 X No-0 seedling, biological replicate 2

description:
wil-2_x_no-0_br_2
PolyA RNA


title: Arabidopsis thaliana Hi-0 X Ct-1 seedling, biological replicate 3

description:
hi-0_x_ct-1_br_3
PolyA RNA

source_name: Seedling, Hi-0 X Ct-1 F1

value: Hi-0 X Ct-1 F1 cross progeny


title: Arabidopsis thaliana Sf-2 X Can-0 seedling, biological replicate 1

description:
sf-2_x_can-0_br_1
PolyA RNA


title: Arabidopsis thaliana Hi-0 X Ct-1 seedling, biological replicate 2

description:
hi-0_x_ct-1_br_2
PolyA RNA


title: Arabidopsis thaliana Sf-2 X Can-0 seedling, biological replicate 2

description:
sf-2_x_can-0_br_2
PolyA RNA


title: Arabidopsis thaliana Ler-0 X Kn-0 seedling, biological replicate 2

description:
ler-0_x_kn-0_br_2
PolyA RNA


title: Arabidopsis thaliana Hi-0 X Ct-1 seedling, biological replicate 1

description:
hi-0_x_ct-1_br_1
PolyA RNA


title: Arabidopsis thaliana Bur-0 X Col-0 seedling, biological replicate 2

description:
bur-0_x_col-0_br_2
PolyA RNA

source_name: Seedling, Bur-0 X Col-0 F1

value: Bur-0 X Col-0 F1 cross progeny


title: Arabidopsis thaliana Bur-0 X Col-0 seedling, biological replicate 1

description:
bur-0_x_col-0_br_1
PolyA RNA


title: Arabidopsis thaliana Mt-0 X Tsu-0 seedling, biological replicate 2

description:
mt-0_x_tsu-0_br_2
PolyA RNA


title: SR-salt.fq

first: Maolin

last: Zhang

state: Shandong

address: No.27 Shanda South Road

data_processing:
The reads were perfectly mapped to the maize (Zea mays) genome (B73 RefGen_v2, release 5b.60) using SOAP.
The reads were mapped to reference genes using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi)
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads). Statistical analysis of differentially expressed genes (DEGs) was conducted using the probability (P) value and FDR (False Discovery Rate).

source_name: root

growth_protocol: Maize seedlings (Zea mays L. cv Chang 7-2) were grown in Hoagland’s solution (pH 6.0) under greenhouse conditions at 28°C/25°C (day/night) with a photosynthetic active radiation of 300 μmol m-2 s-1, 60% relative humidity and a photoperiod of 16/8 h (day/night)

extract_protocol:
Root tips were cut, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
Total RNA was extracted from the shoots and roots with TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

treatment_protocol: Each types of roots (5-8 cm) were treated with Hoagland's solution containing 100 mM NaCl for 24 h. Three biological replicates were collected for each root type.

tag: root type

value: seminal root

value: root tip

tag: length


title: SR.fq


title: PR.fq

value: primary root


title: Arabidopsis thaliana Ler-0 X Kn-0 seedling, biological replicate 1

description:
ler-0_x_kn-0_br_1
PolyA RNA


title: Arabidopsis thaliana Bur-0 X Col-0 seedling, biological replicate 3

description:
bur-0_x_col-0_br_3
PolyA RNA


title: CR-salt.fq

value: crown root


title: BF3h_2

city: Athens

first: Judy

last: Willis

state: GA

address: 302 Biological Sciences Building

department: Cell Biology

institute: University of Georgia

description: blood fed

data_processing:
Processed at Hudson Alpha (Alabama) using Illumina pipeline (CASAVA-1.8.0a16)
Tuxedo Pipeline run with blacktie: all associated log files including version numbers for tophat/cufflinks/etc found and cited here: http://dx.doi.org/10.6084/m9.figshare.768500
Genome_build: Assembly: AgamP3, gene-build: AgamP3.7
Supplementary_files_format_and_content: http://cufflinks.cbcb.umd.edu/manual.html#gtfout

organism: Anopheles gambiae

source_name: females

growth_protocol: Mosquitoes were maintained at the University of Georgia in a humidified insectary kept at 28⁰C and a 16:8 L:D photoperiod and fed powdered Tetramin Fish food. Males and females were kept together after eclosion and provided with 8% fructose.

extract_protocol:
RNA was isolated following the Trizol protocol and DNA removed with Turbo DNA-free (Invitrogen). RNA integrity was monitored with an Agilent 2100 Bioanalyzer.
The eight libraries were prepared using the Illumina True-Seq RNA Sample Prep kit and analyzed with HiSEQ paired-end reads of 50 nt according to Illumina standard protocols.

treatment_protocol: Females, five days after eclosion, were moved to a small chamber for feeding either directly or after 20 min exposure to 9⁰C. Feeding was on a human arm, over a 10 min period. Non-blood fed control females in a similar small chamber had access to water-soaked wicks. Feeding took place 4 h after light on. Three hours later, all animals were chilled for 20 min and then groups of five females were placed in 500µl Trizol and immediately placed on dry ice. Tubes were subsequently moved to -80⁰C until processed.

value: whole body

value: adult 5-day-old

tag: treatment

value: sacrified 3h after the blood meal


title: BF3h_3

description: blood fed

tag: age


title: BF3h_4

description: blood fed

tag: strain


title: PR-salt.fq


title: BF3h_1

description: blood fed


title: NBF_4 (water)

description: non-blood fed

value: sacrified at the same time as BF3h


title: NBF_2 (water)

description: non-blood fed


title: NBF_1 (water)

description: non-blood fed


title: NBF_3 (water)

description: non-blood fed


title: PH-1_mycelium_R3

city: Wageningen

first: Theo

last: van der Lee

address: Building no.107 Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen university

description: Mycelium Rep_3

data_processing:
RNA-Seq reads were mapped to transcript sequences of Fusarium graminearum using software available in the CLC Genomics Workbench
RPKM values were calculated to evaluate gene expression level in CLC Genomics Workbench
Genome_build: ASM24013v3
Supplementary_files_format_and_content: Tab-delimited .txt file includes RPKM values for each Sample

organism: Fusarium graminearum PH-1

source_name: Mycelium

growth_protocol: To prepare spores, isolate PH-1 was grown in 400 ml liquid mung bean medium for 3 days to produce spores (25 °C, 200 rpm).To prepare mycelium. 10e5 spores of PH-1 were transferred to 400 ml liquid complete medium and subsequently incubated for 30 h to produce mycelium (25 °C, 200 rpm).

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen, Cat. No. 15596-018) according to manufacturer’s instructions.
Isolated RNA was enriched for mRNA by using oligo dT Dynabeads (Invitrogen) according to the manufacturer’s instructions and fragmented into fragments of 200-700 nucleotides by incubating at 70 °C for 15 min in fragmentation buffer (Ambion). Fragmentation of mRNA was terminated by adding stop solution (Ambion) and used as template to synthesize the first strand cDNA by using random hexamers (Invitrogen). Subsequently dNTPs, RNase and DNA polymerase were added to the reaction solution to synthesize the second strand cDNA. The synthesized cDNA was purified by Qiaquick PCR kits and blunted by an End Repair reaction. Subsequently a single “A” base was added to the 3’ end of cDNA by using dATP and Klenow Exo Fragment. Later Illumina adaptors were linked to the cDNA ends. The adapted cDNA was run on agrose gel and ~200 bp cDNA fragments were selected. Finally, the cDNA was amplified and the obtained cDNA pool was subjected to high-throughput sequencing by Illumina HiSeqTN 2000.

value: Mycelium

tag: medium

value: Complete medium


title: PH-1_mycelium_R2

description: Mycelium Rep_2


title: PH-1_spores_R3

description: Spores Rep_3

source_name: Spores

value: Spores

value: Mung bean


title: PH-1_spores_R2

description: Spores Rep_2


title: CR.fq


title: IPSC.fastq.gz

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on an Illumina GAIIx using the default RTA analysis software.
Quality control of raw sequence data was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and trimming using TrimGalore (v0.3.5, parameters: --rrbs, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Sequence alignment and methylation calls were performed using Bismark (v0.10.1, default options).
Genome_build: NCBI m37
Supplementary_files_format_and_content: The coverage output files are tab delimited text files describing the methylation at measured positions in the genome (using 1-based genomic coordinates). The columns are: 1) chromosome 2) start position 3) end position 4) methylation percentage 5) count methylated 6) count non-methylated

source_name: IPSC

extract_protocol:
genomic DNA from E14.5 mdDA neurons, Nestin-GFP positive precursors and iPSC-derived DA neurons was purified using QIAamp Micro kit (Qiagen) according to manufacturer guidelines
RRBS was performed as described earlier (Smallwood et al., 2012, Methods Mol Biol;925:187-97. doi: 10.1007/978-1-62703-011-3_12.). Briefly, genomic DNA was digested with MspI, then end-repair/A-tailing and ligation (T4 Ligase) of 5mC-adapters (Illumina) were performed in Tango1X buffer without intermediate purification of the enzymatic reactions. Bisulfite conversion was performed (Imprint DNA modification, Sigma) and converted DNA was amplified (6 cycles) using uracil stalling free polymerase (Pfu Turbo Cx, Stratagene) followed by size selection (150-450bp, Qiaquick, Qiagen) and a second round of amplification (10-12 cycles, Platinium, Pfx polymerase, Invitrogen).

value: IPSC

value: Pitx3 Gfp/+


title: Primary_neurons.fastq.gz

source_name: Primary dopaminergic neurons

value: Primary neurons


title: PH-1_mycelium_R1

description: Mycelium Rep_1


title: PH-1_spores_R1

description: Spores Rep_1


title: IPSC_derived.fastq.gz

source_name: IPSC-derived dopaminergic neurons

value: IPSC-derived neurons


title: Nestin.fastq.gz

source_name: Nestin-GFP neurons

value: Nestin-GFP neurons

value: Nestin Gfp/+


title: Whole Cell Extracts in DND-41 persisters

first: Jiang

last: Zhu

address: 185 Cambridge Street

institute: Massachusetts General Hospital, Harvard Medical School and Broad Institute

data_processing:
ChIP DNA and input controls were sequenced with the Hi-Seq Illumina Genome Analyzer.
ChIP-seq reads were aligned to the reference genome (hg19) using SOAP2 allowing at most two mismatches. Positions were randomly selected for reads with multiple hits. Reads aligned to the same position and strand were only counted once.
Aligned reads were extended by 250 bp to approximate fragment sizes and then a 25-bp resolution density map was derived by counting the number of fragments overlapping each position.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated in 25-bp step based on UCSC definition and converted into bigWig files using UCSC utilities.

source_name: DND-41 persister cells

growth_protocol: The human T-cell leukemia cell lines DND-41 and KOPT-K1 were grown in RPMI 1640 containing 10% FCS at 37°C with 5% CO2. Cells were maintained between a density of 5 x 105 cells/ml and 2 x 106 cells/ml.

extract_protocol:
Chromatin from formaldehyde-fixed cells (1 - 5 x 106 per histone mark, 107 for BRD4) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was isolated.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Cat #: FC-102-1001). Briefly, DNA was end-repaired using Epicentre’s End-it™ DNA-Repair Kit (Cat #: ER81050). The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated using Angencourt® Ampure® XP. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Persister cells were established by treating DND-41 or KOPT-K1 cells with 1 microM GSI for at least 7 weeks, replenishing the inhibitor every 3 - 4 days (Compound E, EMD4 Biosciences).

tag: cell line

value: T-cell acute lymphoblastic leukemia

tag: treated with

value: 1uM gamma Secretase inhibitor over 7wks

tag: chip antibody

tag: chip antibody vendor


title: H3K4me3 ChIP-seq in DND-41 persisters

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: H3K4me1 ChIP-seq in DND-41 persisters

tag: cell type

value: Abcam


title: BRD4 ChIP-seq in DND-41 persisters

value: Bethyl


title: H3K36me3 ChIP-seq in DND-41 persisters


title: Whole Cell Extracts in DND-41

source_name: DND-41 naïve cells

value: vehicle (naïve)


title: H3K27me3 ChIP-seq in DND-41 persisters


title: H3K36me3 ChIP-seq in DND-41


title: H3K4me1 ChIP-seq in DND-41


title: H3K27ac ChIP-seq in DND-41


title: BRD4 ChIP-seq in DND-41


title: H3K27me3 ChIP-seq in DND-41


title: H3K4me3 ChIP-seq in KOPT-K1 persisters

source_name: KOPT-K1 persister cells


title: H3K27me3 ChIP-seq in KOPT-K1 persisters


title: H3K4me1 ChIP-seq in KOPT-K1

source_name: KOPT-K1 naïve cells


title: H3K36me3 ChIP-seq in KOPT-K1 persisters


title: BRD4 ChIP-seq in KOPT-K1 persisters


title: H3K27ac ChIP-seq in KOPT-K1 persisters


title: H3K4me3 ChIP-seq in KOPT-K1


title: H3K4me3 ChIP-seq in DND-41


title: H3K36me3 ChIP-seq in KOPT-K1


title: H3K27ac ChIP-seq in DND-41 persisters


title: Whole Cell Extracts in KOPT-K1


title: H3K27ac ChIP-seq in KOPT-K1


title: BRD4 ChIP-seq in KOPT-K1


title: H3K4me1 ChIP-seq in KOPT-K1 persisters


title: LncRNA_CaptureSeq

city: Sydney

first: Tim

middle: R.

last: Mercer

state: New South Wales

address: 384 Victoria Street Darlinghurst NSW 2010

country: Australia

institute: Garvan

description:
CaptureSeq_LncRNAdesign
ribodepleted total RNA from three K562 biological replicates

data_processing:
Library strategy: CaptureSeq
Illumina Casava1.7 software used for basecalling.
Generating the .gtf file:
We have used bowtie/2.1.0, and  samtools/1.18 tophat/2.0.9 cufflinks/2.1.1 for alignment using the following parameters:
Genome assembly: ucsc hg19
Gene annotation (for guided assembly) GENCODE v18 basic annotation.gtf
Parameters are default:
tophat2 --library-type fr-firststrand -G gencode.v18.annotation.gtf \     –o Tophat_ouput hg19_index reads_1.fastq.gz reads_2.fq
cufflinks -o Cufflinks_output Tophat_ouput/accepted_hits.bam
Genome_build: hg19
Supplementary_files_format_and_content: Probe design (.bed) and abundance measurements (.gtf).  The .gtf column headers are default for cufflinks output (as explained at http://cufflinks.cbcb.umd.edu/manual.html#cufflinks_output).

growth_protocol: Human K562 were cultured in RPMI and DMEM respectively plus 10% fetal bovine serum and penicillin/streptomycin at 37°C, 5% C02. K562 cells were collected by centrifugation, washed with PBS, centrifuged again and lysed in TRIzol (Life Technologies). HeLa cells were lysed in TRIzol by scraping of the cell culture flask. A standard TRIzol extraction was conducted and RNA resuspended in 200ul of RNase free water. Purity was confirmed by NanoDrop (Thermo scientific). RNA was DNase treated with Turbo™ DNase (Life Technologies), repurified with phenol/chloroform, nanodroppped again and the integrity of the RNA confirmed by Agilent 2100 Bioanalyzer (Agilent Technologies). The DNA free nature of the RNA was confirmed by the absence of product from a PCR for a section of NEAT1 gDNA with 200ng of purified RNA for 35 cycles. Five microgram lots of high quality RNA were treated with Ribo-Zero™ (Epicentre) to remove rRNA, purified by RNeasy Minelute (Qiagen) with successful ribodepletion confirmed by Bioanalyzer Pico chip.

extract_protocol: Capture sequencing was performed by combining and modifying the NimbleGen SeqCap EZ Library SR User’s Guide V3.0 and the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery v3.2. RNA sequencing libraries of ribodepleted total RNA from three K562 biological replicates were created using the TruSeq® Stranded mRNA Sample Preparation Kit (Illumina). Different index adaptors (4,6,12) were added to each K562 biological replicate. Library input consisted of ribodepleted RNA from 5 μg original total RNA after quality checking. ERCC RNA Spike-In Control mix 1 (Invitrogen) was added to ribodepleted RNA to give a final ERCC concentration of 1% (replicate 1 and 2) and 1.08% (replicate 3). Library preparation was begun at the fragmentation step by the addition of 9 μl EPH buffer and the standard protocol followed until “Enrich DNA Fragments”. The 20 μl obtained at the end of the “Ligate Adaptors” step was increased to 21 μl with resuspension buffer and mixed well. One microliter of this solution was added to 19 μl resuspension buffer in a new 0.3ml PCR plate and mixed. This new plate was utilised for the “Enrich DNA Fragments” step to create amplified test libraries to guide PreCapture LMPCR with the remaining 20 μl. Precapture LMPCR and QIAquick PCR Purification Kit (Qiagen) were performed as described by the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. To test LMPCR yields K562 biological replicate 3 libraries were amplified for 8, 9 or 10 cycles, quantified on the bioanalyzer and then pooled. K562 biological replicate 1 and 2 libraries were thus amplified for 9 cycles and the yield quantified by bioanalyzer. Capture hybridization was modified from the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery V3.2. The NimbleGen Hybridization System was set to 42°C and allowed 3 h to equilibrate. Equal nanograms of library from each K562 biological replicate were pooled, some of pooled library was allocated for pre-capture sequencing and 1ug of the pooled library utilized for capture. The library for capture was mixed with 300 µg human Cot-1 DNA (Invitrogen) and 3.34 µl 100 μm TS-INV-HE (hybridisation enhancing) Index Oligos (IDT) to each index adaptor plus 1 µl 1000 μm TS-HE Universal Oligo 1 (IDT) in a 1.5 ml tube. Lid of tube was pierced with an 18 gauge needle and the sample dried at 60 °C in a vacuum concentrator. Once dry the tube was given a new lid to prevent contamination through the needle hole. Library/Cot/Oligo mix was resuspended in 11.2 µl of nuclease and nucleic acid free water, vortexed for 10 s and centrifuged at max speed for 10 s. Sample was solubilised at 70 °C for 10 m before repeating vortexing and centrifugation. Nimblegen 2 x SC Hybridization Buffer (18.5 µl) and SC Hybridization Component A (7.3 µl) were added and vortexing and centrifugation repeated. Sample was denatured at 95°C for 10 m. During this time the “Prepare Mixers” procedure from the NimbleGen Arrays User’s Guide was performed with the omission of the compressed gas step. After denaturation samples was vortexed for 10 s, centrifuged at max speed for 10 s and incubated at 42°C until ready to load onto the NimbleGen Hybridization system. The ‘Load and Hybridize Samples’ procedure from the NimbleGen Arrays User’s Guide was performed to begin array hybridization. Hybridization was conducted for ~3 days. The NimbleGen Arrays User’s Guide protocol was followed to prepare the elution chamber, disassemble, wash and elute the captured DNA from the microarray, with the following modifications. Gasket and elution chamber was setup in a DNA-free laminar flowhood. All washes were conducted with 50 ml buffer in 50 ml falcon tubes. Minelute purification (Qiagen) was conducted using a microfuge. Captured DNA was recovered with two 30 µl elutions from a Minelute column and the final volume adjusted to 60 µl. Post-capture LMPCR and cleanup was performed similar to the NimbleGen SeqCap EZ Library SR User’s Guide V3.0, with the following modifications. LMPCR was run using 5x Phusion buffer for 17 cycles. Each PCR contained 70 µl of master mix and 30 µl of captured DNA. Quantity and quality of amplified captured DNA was determined by bioanalyzer.  Enrichment of captured transcripts was measured by qPCR using SYBR Green PCR Master Mix and real time cyclers (Applied Biosystems). Enrichment was determined by the ratio of transcript abundance between the pre and post capture samples using equal nanograms of each. Enrichment was determined for three Nimblegen capture controls and 3 sequences captured specifically by the branchpoint array. Two transcripts not targeted by the capture array were also tested to examine the specificity of capture. Concentrations and volumes were as per the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. Precapture and post capture samples (3 K562 biological replicates) were each sequenced on a single lane of an Illumnia® HiSeq.

tag: protocol

value: Capture Sequencing

value: K562 (Human erythromyeloblastoid leukemia cell line)


title: input-DNA

first: Zhuqiang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 0.12.7 with only unique mapped reads were kept
Data were filtered using samtools to remove potential PCR duplicates
peaks were called using MACS (v1.4.2) with P-value < E-8
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 300 bp

source_name: Flag-Anp-HeLa

extract_protocol:
HeLa cells stably expressing Flag-Anp were used for ChIP-seq experiments, cells were crosslinked with 1% (v/v) formaldehyde for 10 min at room temperature and the reaction was quenched by adding glycine to 0.15 M. Cells were washed with PBS and then resuspended in 20 mM Tris, pH 8.0, 300 mM NaCl and 0.1% SDS and sonicated to 200- to 500-bp chromatin fragments using Bioruptor (Diagenode).
Sequencing libraries were generated according to Illumina recommendations by using NEBNext® DNA Library Prep Master Mix Set for Illumina®. The libraries were single-end sequenced with HiSeq 2000.

value: HeLa


title: H2A.Z-ChIPSeq

value: α-H2A.Z polyclonal antibody (Abcam, ab4174)


title: Whole Cell Extracts in KOPT-K1 persisters


title: TS1

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Trichoplax YAP S81A

data_processing:
Data was processed with CASAVA version 1.7.0
Sequence reads in fastq format were mapped to dm3 using tophat-1.0.14. Flybase transcripts (v5.29) were quantified and compared between control and each overexpression condition using cuffdiff v1.0.2.
Genome_build: dm3
Supplementary_files_format_and_content: The file FPKM.txt includes the FPKM values for each gene from each sample as determined by cufflinks. The file cuffdiff_ratio_data.txt includes the log2 ratios, and p-values for each gene for each replicate set of overexpressed variants relative to control as determined by cuffdiff. Also listed are the BH adjusted p-values, gene annotations. There is also a value called Amean, a very general abundance ranking factor, which is the average of the “A” values from each comparison where A is equal to the log2 of the geometric mean of the averaged FPKM values for both treatment and control.

organism: Drosophila melanogaster

source_name: eye imaginal disk

extract_protocol:
Total RNA was recovered from surgically-isolated GMR expression domains (GFP+) from 25 to 30 third instar eye discs using a RNeasy kit (Qiagen). For each genotype, total RNA extraction was conducted in triplicate.
TruSeq RNA Sample Preparation (Low Throughput (LT) Protocol) Part# 15015050, Rev A, November 2010

value: Overexpression

tag: phenotype

value: Differentiation defects + Strong ectopic proliferation

tag: genotype

value: GMR-Gal4; UAS-eGFP; UAS-TrichoplaxYAP S81A


title: DS2

description: Drosophila Yki S168A

value: Differentiation defects + Middle ectopic proliferation

value: GMR-Gal4; UAS-eGFP; UAS-DrosophilaYKI S168A


title: DS1

description: Drosophila Yki S168A


title: TS2

description: Trichoplax YAP S81A


title: TS3

description: Trichoplax YAP S81A


title: DS3

description: Drosophila Yki S168A


title: MT3

description: Monosiga YAP with human TEAD


title: MT2

description: Monosiga YAP with human TEAD


title: H3K27me3 ChIP-seq in KOPT-K1


title: M3

description: Monosiga YAP

value: Differentiation defects

value: GMR-Gal4; UAS-eGFP; UAS-MonosigaYAP


title: M2

description: Monosiga YAP


title: C3

description: wt

value: Normal eyes

value: GMR-Gal4; UAS-eGFP


title: C2

description: wt


title: Flag-Anp-ChIPSeq

value: α-Flag M2 Agarose (Sigma, F3165)


title: C1

description: wt


title: H3K27me3_ChIPSeq in brm rep2

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline.
ChIP-seq reads were aligned to the Arabidopsis genome (TAIR10) using BOWTIE version 0.12.7. Only perfect match was allowed. The reads mapped to more than one positions were removed.
The alignments were converted to WIG files using MACS.
The program SICER v1.1 (Zang et al. 2009) was used to identify ChIP-enriched domains (peaks) in histone modification signals.
The quantitative comparisons between WT and brm were performed using the ChIPDiff program.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bed files were generated using SICER.

source_name: Young seedlings, brm mutant, H3K27me3 ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei, and histone-DNA complexes were isolated with H3K27me3 antibody (07-449, Millipore).
Ten ng of ChIP DNA immuoprecipitated by anti-H3K27me3 antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Genome Analyser IIx was used for high-throughput sequencing of the ChIP-seq library.

value: brm mutant

tag: tissue

value: seedling

value: 14 days


title: Input in brm

source_name: Young seedlings, brm mutant, input


title: H3K27me3_ChIPSeq in wt rep2

source_name: Young seedlings, wt, H3K27me3 ChIP

value: wild-type


title: H3K27me3_ChIPSeq in wt rep1


title: Input in wt

source_name: Young seedlings, wt, input


title: Flag-ChIPSeq

source_name: wildtype-HeLa


title: pooled HD3 rep 2 [4C-Seq]

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description:
HD3_pooled_rep2
L fraction
S fraction

data_processing:
Library strategy: 4C-Seq
Basecalling with CASAVA 1.8.2 software
Merging the reads from L and S fractions where both fractions were sequenced (see library construction protocol)
Trimming read subsequences originating from the bait region. Leaving only one read from the pair, the subsequence after HindIII restriction site
Mapping to galGal4 genome with bowtie aligner
For every HindIII restriction fragment, summing up the number of reads mapped to the left and the right end of the fragment
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: bedGraph files containing the number of 4C reads (score column) per HindIII restriction fragment

organism: Gallus gallus

source_name: erythroblast cell line

growth_protocol: The avian erythroblastosis virus-transformed chicken erythroblast cell line HD3 (clone A6 of the line LSCC (Beug, 1979;Beug, 1979) and the DT40 lymphoid cell line (CRL-2111, ATCC) were grown in Dulbecco’s Modified Eagle Medium supplemented with 2% chicken serum and 8% fetal bovine serum at 37ºC with 5% CO2. In the case of DT40 cells, the medium additionally contained 50 μM β-mercaptoethanol.

extract_protocol:
PCR reactions were performed using the Expand Long Template PCR system (Roche). The 50 µl PCR reaction contained 120 ng of the DNA template, 1× PCR buffer 1, 0.3 µM of each of the primers, 0.35 mM of each of dNTPs, and 3.75 units of Hot start Taq DNA polymerase (SibEnzyme)Expand Long enzyme mix (Roche). The sequences of HindIII / DpnII 4C primers are as follows (5’-3’): TSR3 bait CACTCATCTCCCCGTACTTTG / AAGTTTCTTTTAATTTGGAGACTTTC; GENE-Des bait AATTTGTGAAGCAGTTGTATGTAGTC / TCTTCTCCACATAATCCCACACT; NPRL3 bait GCCAGGATATAGATTCTGCTTT / CCTCTGACATAATTGCCGATAG; TRAP1 bait CCAGAGATTCTCAAATCACAGCA / CTATGGGGACAAGTGAGGAACAG; PPL bait AAAGCATCTCCTCTCCCTGAAG / GTCTCCCACAGTCACTCCTCCT. PCR amplification was performed in the linear range as follows: initial denaturation for 2 min at 94°C; 30 cycles of 15 s at 94°C, 1 min at 57°C, and 3 min at 68°C; final elongation for 4 min at 68°C. PCR products were purified and concentrated using QIAquick PCR purification kit (Qiagen). After separation according to sizes in 1.5% agarose gel, two zones - 70-400 bp (S fraction) and 400-1500bp (L fraction) - were cut. After extraction with QIAquick gel extraction kit (Qiagen), the fragments of L-fraction were sonicated to reduce the fragment size to 100-500 nucleotides using Covaris S220 with following parameters: time 300 seconds, duty cycle 10%, peak power 23W. Then S and L fraction were processed using TruSeq DNA sample prep kit v.2 (Illumina) with post-PCR size selection on agarose gel (fragments with length 200-600 nucleotides were selected). After purification library concentrations were measured using Qubit fluorimeter (Invitrogen) and real-time PCR with primers complementary to distal regions of Illumina adapters (I-qPCR-1.1: AATGATACGGCGACCACCGAGAT and I-qPCR-2.1: CAAGCAGAAGACGGCATACGA). Then libraries from S and L fractions were combined in equal amounts, diluted to 2nM, denatured using 0.1M NaOH and diluted to final concentration 10 pM using HT1 buffer (Illumina).
Cluster generation was performed using cBot instrument and TruSeq PE Cluster Kit v3 reagents and sequencing - using HiSeq2000 instrument and TruSeq SBS Kit v3 reagents (Illumina) with read length 101 nucleotides from each end.

treatment_protocol: 1×107 cells were fixed with 2% formaldehyde in DMEM medium supplemented with 10% fetal bovine serum (FBS) for 10 min at room temperature, and then the reaction was stopped by the addition of glycine to 0.125 M. After washing with PBS/10% FBS, the fixed cells were incubated for 10 min in an ice-cold lysis solution (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% Nonidet P40, and a protease inhibitor cocktail (Fermentas)) at a concentration of 2×107 cells/ml to release the nuclei. The nuclei were harvested and suspended in 0.5 ml of 1.2× restriction buffer 2 (New England Biolabs). SDS was added to a final concentration of 0.3%, and the solution was incubated for 1 h at 37°C with shaking. Triton X-100 was added to 1.8%, and the solution was further incubated for 1 h at 37°C to sequester the SDS. The DNA was digested by overnight incubation with 800 units of HindIII (New England Biolabs) at 37°C with shaking. The restriction endonuclease was inactivated by the addition of SDS to a final concentration of 1.6% and incubation for 20 min at 65°C. The solution was diluted by adding 7 ml of 1× ligation buffer (Fermentas). Triton X-100 was added to 1%, and the solution was incubated at 37°C for 1 h while shaking. Next, 100 U of T4 DNA Ligase (Fermentas) was added, and the DNA was ligated for 4.5  h at 16°C and then for 30 min at room temperature with slow agitation. Cross-links were reversed by incubation at 65°C for 16 h in the presence of Proteinase K (40 μg/ml). After cross-link reversion, RNase A was added to a final concentration of 40 μg/ml, and RNA was digested for 45 min at 37°C. The DNA was purified by extraction with phenol followed by precipitation with ethanol. To further purify DNA, the samples were processed with QIAEX II Gel Extraction Kit (Qiagen). The concentration of DNA was determined using a fluorometric assay (Qubit, Invitrogen). 50 µg of a ligated 3C DNA template was digested overnight at a concentration of 100 ng/µl with 200 units of DpnII (New England Biolabs). The restriction endonuclease was inactivated by incubation for 20 min at 65°C, and the DNA was purified by phenol-chloroform extraction and ethanol precipitation. Next, the DNA was ligated with 100 units of T4 DNA Ligase (Fermentas) in 14 ml of 1× ligation buffer (Fermentas) for 4 h at 16°C. Ligation products were precipitated with ethanol and further purified using QIAquick PCR purification kit (Qiagen). To linearize the circles of interest, the DNA was treated with a tertiary restriction enzyme of choice: EcoNI for TSR3 bait; NcoI for GENE-Des desert bait, TRAP1 bait and PPL bait; and EcoRV for NPRL3 bait. Digested products were purified using QIAquick PCR purification kit (Qiagen).

value: HD3 erythroblast cell line

tag: cell line details

value: clone A6 of the line LSCC

tag: anchor(s)

value: TSR3, GENE-Des, TRAP1, PPL


title: pooled HD3 rep 1 [4C-Seq]

description:
HD3_pooled_rep1
L fraction
S fraction


title: NPRL3 DT40 rep 2 [4C-Seq]

source_name: lymphoid cell line

value: DT40 lymphoid cell line

value: CRL-2111, ATCC