title: PolIISer5_JQ1treated_Tcell_ChIPseq_pooled5donor

city: Singapore

first: Keh-chuang

last: Chin

address: Biopolis, 8A Biomedical Grove, #03-06 Immunos

department: Laboratory of Gene Regulation

country: Singapore

institute: Singapore Immunology Network

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT031_CD4TCell_JQ1_PolII4H8_rmdup.bed: hg18
CHT031_CD4TCell_JQ1_PolII4H8.wig.gz: hg18
CHT031_CD4TCell_JQ1_PolII4H8_normalized_48.73.wig.gz: hg18

source_name: CD4+ T cells

growth_protocol: CD4+ T-cells were purified from normal human peripheral blood using the human CD4+ T-cell Isolation Kit II (Miltenyl Biotech).

extract_protocol: ChIP DNA ends were repaired using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase), and T4 polynucleotide kinase (PNK). The 3' to 5' exonuclease activity of these enzymes removes 3' overhangs and the polymerase activity fills in the 5' overhangs. This is followed by treatment with Klenow fragment (3' to 5' exo minus) to generate an overhanging 3  adenine base for adaptor ligation to adapters which have a single  T  base overhang at their 3' end. Size Selection of 300bp fragment were done using the Invitrogen EGel system, followed by enrichment with 15 PCR cycles. The amplified DNA was purified by Ampure beads before validation on the Agilent Bionanlyser.

treatment_protocol:
Isolated human CD4+ T cells were pooled from five different donors and used for side-by-side experiments of BRD4, Pol II Ser2, Pol II Ser5 and total Pol II (4H8) treated with or without 500nM JQ1 for 24hr.
Freshly isolated human CD4+ T-cells treated with or without 500nM JQ1 for 24hr

tag: cell type

value: CD4+ T cells

value: PolIISer5 [Abcam, Cat no. ab5131, Lot no. 949433]

tag: treatment

value: JQ1 treated


title: Digital Genomic Footprinting assay of flow sorted CD4+ Cells; DGF.DS17881

status: Public on Nov 14 2012

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17881
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7018
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM1036374_UW.CD4_Primary_Cells.Digital_Genomic_Footprinting.RO_01701.DGF.DS17881.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17881.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on CD4 Primary Cells, Donor RO 01701, Library DGF.DS17881 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.15144
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 118,253,141
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.481
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4805
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4583
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1036374_UW.CD4_Primary_Cells.Digital_Genomic_Footprinting.RO_01701.DGF.DS17881.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17881.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  CD4 Primary Cells, Donor RO 01701, Library DGF.DS17881 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.15155
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD4 DGF 01 81
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells Digital Genomic Footprinting Donor RO 01701 Library DGF.DS17881 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 118,253,141
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.481
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4805
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4583
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: flow sorted CD4+ Cells, year 37; DGF.DS17881

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD4 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Male

value: Hispanic

value: Digital Genomic Footprinting

value: Qiagen minElut


title: TAF5-H9wt-rep1

status: Public on Nov 19 2012

type: genomic

city: Worcester

first: Michael

middle: R.

last: Green

state: MA

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description:
ChIP-chip for TAF5 vs No Antibody in wild-type H9 cells
platform design id: 100718_HG18_Refseq_Prom_ChIP

hyb_protocol: The labeled experimental and control ChIP DNA (20 pmol of each label) was precipitated with 0.1 volume 5M NaOAc and 2 volume ethanol, and hybridized using Nimblegen Hybridization kit according to recommended protocol. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed using Nimblegen wash kit reagents and protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Agilent High Resolution C Scanner (G2505-60502) at 5µ resolution

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 ChIP data extraction.

source_name: TAF5 ChIP DNA from H9 wt cells

label_protocol: 500 ng of purified ChIP or control (No Antibody) DNA were blunted by using the End-IT kit (Epicenter) and adapters (annealed oligos oJW102: 5’-GCGGTGACCCGGGAGATCTGAATTC and oJW103: 5’-GAATTCCAGATC) ligated to the fragment ends using the Fast-Link DNA ligation kit (Epicenter).  Ligated fragments were then amplified by pcr for 15 rounds with a primer directed against the adapter, gel-purified to a size range of 400-600 bp, and then amplified a second time for 30 rounds using either Cy5-dCTP (ChIP experiment) or Cy3-dCTP (Control chIP).  Amplified products were purified on Qiaquick columns to remove unincorporated label, and quantitated on a Nanodrop.

extract_protocol: 5x10E7 cells were rinsed with PBS, scraped, and pelleted in a 50 mL conical tube.  The cells were then fixed with 1.5 mM EGS in 90% PBS/10% DMSO for 30 minutes, then also with  1% formaldehyde for an additional 10 minutes at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50 mM HEPES pH8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na-Deoxycholate, 1 mM EDTA, 1 mM PMSF plus protease inhibitor cocktail) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 18 30-second pulses using a Misonix 3000 sonicator on power level 6 with 90 seconds rests between pulses while sample is immersed in icewater. The lysate was then centrifuged to remove cell debris, and the chromatin was quantified using BCA assay. The chromatin (500 µg) was pre-cleared with 25 µl protein G agarose beads (pre-absorbed with BSA) for 4 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein G agarose beads (80 µl) overnight at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; twice with lysis  buffer, once with high-salt lysis buffer (lysis buffer adjusted to 1 M NaCl) three times in LiCl buffer (250 mM LiCl, 50 mM HEPES pH8.0, 0.5% Na deoxycholate, 0.5% NP40) and once in TEN (50 mM Tris pH8.0, 10 mM EDTA, 50 mM NaCl). The protein-DNA complexes were eluted from the beads in 200 µl elution buffer (1% SDS, 100 mM NaHCO3) at 68C for 15 min followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

value: wild-type pluripotent H9 embryonic stem cell line

tag: chip antibody

value: TAF5, Sigma-Aldrich HPA006474

source_name: No Antibody control ChIP DNA from H9 wt cells

value: None, No Antibody control


title: TAF3-H9wt-rep1

description:
ChIP-chip for TAF3 vs No Antibody in wild-type H9 cells
platform design id: 090618_HG18_Refseq_Prom_ChIP

source_name: TAF3 ChIP DNA from H9 wt cells

value: TAF3, Bethyl A302-359A


title: TAF11-H9wt-rep2

description:
ChIP-chip for TAF11 vs No Antibody in wild-type H9 cells
platform design id: 100718_HG18_Refseq_Prom_ChIP

source_name: TAF11 ChIP DNA from H9 wt cells

value: TAF11, Dr. Robert Roeder, Rockefeller University


title: PolIISer5_untreated_Tcell_ChIPseq_pooled5donor

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT030_CD4TCell_JQ1_PolIISer5_rmdup.bed: hg18
CHT030_CD4TCell_JQ1_PolIISer5.wig.gz: hg18
CHT030_CD4TCell_JQ1_PolIISer5_normalized_41.66.wig.gz: hg18

value: CD4+ T cells

value: untreated


title: ChIP-Seq Input of Fetal Thymus; Histone.DS21508

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21508
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14537
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1036258_UW.Fetal_Thymus.Input.H-24644.Histone.DS21508.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21508-Histone.DS21508.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Thymus, Donor H-24644, 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.16881
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: 34,002,809
FINDPEAKS_SCORE: 0.0027
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0027
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0291
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1036258_UW.Fetal_Thymus.Input.H-24644.Histone.DS21508.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21508-Histone.DS21508.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Thymus, Donor H-24644, 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.16977
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: FT Input 44 08
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus ChIP-Seq Input Donor H-24644 Library Histone.DS21508 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,002,809
FINDPEAKS_SCORE: 0.0027
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0027
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0291
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Thymus primary tissue, day 110; Histone.DS21508

value: Fetal Thymus

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

value: Primary Tissue

value: UW

value: fetal

value: day 110

value: Female

value: ChIP-Seq Input

value: Diagenode Bioruptor

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

value: Input


title: TAF11-H9wt-rep1

description:
ChIP-chip for TAF11 vs No Antibody in wild-type H9 cells
platform design id: 090618_HG18_Refseq_Prom_ChIP

value: wild-type pluripotent H9 embryonic stem cell line

value: TAF11, from Dr. Robert Roeder, Rockefeller University


title: PolIISer2_JQ1treated_Tcell_ChIPseq_pooled5donor

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT029_CD4TCell_JQ1_PolIISer2_rmdup.bed: hg18
CHT029_CD4TCell_JQ1_PolIISer2.wig.gz: hg18
CHT029_CD4TCell_JQ1_PolIISer2_normalized_44.06.wig.gz: hg18

value: PolIISer2 [Abcam, Cat no. ab5095, Lot no. 782031]

value: JQ1 treated


title: Digital Genomic Footprinting assay of Fetal Intestine, Large; DGF.DS17313

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17313
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14559
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7041
****************
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: GSM1036260_UW.Fetal_Intestine_Large.Digital_Genomic_Footprinting.H-23769.DGF.DS17313.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17313.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Intestine Large, Donor H-23769, Library DGF.DS17313 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.15147
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 434,089,248
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4415
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.4231
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.99
IROC_PERCENTILE: 36
POISSON_SCORE: 0.4787
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1036260_UW.Fetal_Intestine_Large.Digital_Genomic_Footprinting.H-23769.DGF.DS17313.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17313.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Fetal Intestine Large, Donor H-23769, Library DGF.DS17313 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.15158
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FIL DGF 69 13
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Digital Genomic Footprinting Donor H-23769 Library DGF.DS17313 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 434,089,248
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4415
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.4231
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.99
IROC_PERCENTILE: 36
POISSON_SCORE: 0.4787
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 108; DGF.DS17313

value: Fetal Intestine, Large

value: genomic DNA

value: day 108

value: Male

value: Digital Genomic Footprinting

value: Qiagen minElut


title: PolII4H8_JQ1treated_Tcell_ChIPseq_pooled5donor

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT027_CD4TCell_PolII4H8_rmdup.bed: hg18
CHT027_TCell_PolII4H8.wig.gz: hg18
CHT027_TCell_PolII4H8_normalized_45.08.wig.gz: hg18

value: CD4+ T cells

value: PolII4H8 [Abcam, Cat no. ab5408, Lot no. 722997]


title: RNAPII_0hours_DLD23_rep2

status: Public on Nov 15 2012

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DL23ntRNAPIIn37.txt: hg19

growth_protocol: DLD1 colon carcinoma cell line and DL23 clone containing pcDNA3-HA-FOXO33-ER or pcDNA3-ER-DBD-NLS were grown on RPMI-1640 medium with 10% FCS and standard supplements.

extract_protocol: Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD/AB sequencer to produce 50-bp long reads.

treatment_protocol: 4-hydroxy-tamoxifen (4OHT) was Sigma, was dissolved in ethanol and added to cells at a final concentration of 1uM. Cells were treated with LY 294002 at a concentration of 10 µM.

tag: cell line

value: DL23 cell line with pcDNA3-HA-FOXO33-ER

value: anti RBP1 (PB-7C2) antibody

tag: chip antibody vendor

value: Euromedex


title: TAF3-H9wt-rep2

value: TAF3, Bethyl A302-359A

value: None, No Antibody control


title: TBP-H9wt-rep1

description:
ChIP-chip for TBP vs No Antibody in wild-type H9 cells
platform design id: 090618_HG18_Refseq_Prom_ChIP

source_name: TBP ChIP DNA from H9 wt cells

value: wild-type pluripotent H9 embryonic stem cell line

value: TBP, santa cruz sc-273


title: K-562 truseq 30ng

city: Cambridge

first: Nataly

middle: Moran

last: Cabili

address: 7  Cambridge Center

institute: Broad Institute ;  Harvard University

library_source: transcriptomic

data_processing: All files were mapped against Hg19 using TopHat 1.1.4

molecule: total RNA

source_name: K-562 cell line

extract_protocol:
Illumina TruSeq RNA sample prep kit used with these changes:  SuperScript III instead of SuperScript II & optimization of PCR cycle number
RNA purchased from Ambion/ABI

value: immortalised chronic myelogenous leukemia (CML)

tag: sample type

value: K-562 truseq 30ng

tag: average insert size

tag: std. dev. insert size


title: K-562 truseq 50ng

value: K-562 truseq 50ng


title: BRD4_JQ1treated_Tcell_ChIPseq_pooled5donor

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT025_CD4TCell_PolIISer2_rmdup.bed: hg18
CHT025_CD4TCell_PolIISer2.wig.gz: hg18
CHT025_CD4TCell_PolIISer2_normalized_52.90.wig.gz: hg18

value: BRD4 [Abcam, Cat no. ab46199, Lot no. 613288]

value: JQ1 treated


title: K-562 truseq 100ng

value: K-562 truseq 100ng


title: TBP-H9wt-rep2


title: K-562 truseq 250ng

value: K-562 truseq 250ng


title: K-562 truseq 3000ng

value: K-562 truseq 3000ng


title: K-562 truseq 1000ng

value: K-562 truseq 1000ng


title: TAF7-H9wt-rep1

description:
ChIP-chip for TAF7 vs No Antibody in wild-type H9 cells
platform design id: 090618_HG18_Refseq_Prom_ChIP

source_name: TAF7 ChIP DNA from H9 wt cells

value: TAF7, Santa cruz sc101167


title: BRD4_untreated_Tcell_ChIPseq_pooled5donor

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT024_CD4TCell_BRD4_rmdup.bed: hg18
CHT024_CD4Tcell_BRD4.wig.gz: hg18
CHT024_CD4TCell_BRD4_normalized_49.33.wig.gz: hg18

value: CD4+ T cells

value: untreated


title: TAF7-H9wt-rep2

description:
ChIP-chip for TAF7 vs No Antibody in wild-type H9 cells
platform design id: 100718_HG18_Refseq_Prom_ChIP


title: K-562 truseq 10000ng

value: K-562 truseq 10000ng


title: K-562 std gel sized

molecule: polyA RNA

extract_protocol:
Standard Illumina cDNA library preparation as per Levin et al. (2010) Nature Methods , v. 7, pp.709-715
RNA purchased from Ambion/ABI

value: K-562 std gel sized


title: air1-Δ rrp6-Δ rep2

city: Rochester

first: J. Scott

last: Butler

state: NY

address: 601 Elmwood Ave Box 672

department: Department of Microbiology and Immunology

institute: University of Rochester Medical Center

data_processing:
sequences reads were aligned to S.cerevisiae genome with Bowtie (version 0.12.7) using parameters "--all -f -e 70 --tryhard --sam --color --best"
SAMtools was used to sort and index the maping results
Reads unambiguously mapped inside a single gene were counted and used as weights to divide each multi-mapped read to all of the genes to which it mapped.
The Bioconductor package edgeR (version 2.2.5) was used for TMM (trimmed mean of M values) normalization followed by the statistical testing to find genes differentially expressed
Genome_build: Saccharomyces Genome Database (July 2011 version)
Supplementary_files_format_and_content: wig file; tab-delimited read counts for each gene of each sample; excel file with statistically tested differential gene expression data.
Supplementary_files_format_and_content: wig.tgz; tar gzipped wig file format
Supplementary_files_format_and_content: all.count; tab-delimited raw read counts for each gene
Supplementary_files_format_and_content: differential.xlsx; excel file with differential expression calculated from edgeR

organism: Saccharomyces cerevisiae

source_name: liquid culture

growth_protocol: A single colony of each strain was inoculated into 100mls of YPD, and grown with agitation at 30° C to an OD600 of ~2.5.

extract_protocol:
Total RNA was isolated using chloroform phenol extraction and ethanol precipitation. Polyadenylated RNAs were selected on poly(U) sepharose, and was eluted in elution buffer at 45°C for 5 minutes. The supernatant was gradually concentrated and desalted into sterile ddH2O using an Amicon Ultra-4 Centrifugal Filter Device (Millipore).
RNA libraries were prepared for sequencing using standard SOLiD protocols

tag: genotype

value: MAT-alpha his3D1 leu2D0 lys2D0 ura3D0 rrp6::LEU2 air1::bleR


title: BY4742 (WT) rep2

value: MAT-alpha his3D1 leu2D0 lys2D0 ura3D0


title: BY4742 (WT) rep1


title: air2-Δ rrp6-Δ rep1

value: MAT-alpha his3D1 leu2D0 lys2D0 ura3D0 rrp6::LEU2 air2::bleR


title: air1-Δ rrp6-Δ rep1


title: rrp6-Δ rep1

value: MAT-alpha his3D1 leu2D0 lys2D0 ura3D0 rrp6::LEU2


title: mRNA_JQ1treated_Tcell_RNAseq

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained.
Sequence reads were obtained and mapped to the human (hg18) genomes using ELAND of the Illumina Genome Analyzer pipeline. All reads with at most two ambiguous base calls and mapping with two or fewer mismatches were retained.   Refseq transcript level expression [RPKM data not submitted] estimation was performed using the Partek Genomics SuiteTM RNA-seq workflow (Partek(r) software, version 6.5 build 6.11.0121 Copyright (c) 2010).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purified by RNeasy mini-kit (Qiagen, Valencia, USA). Poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The cDNA fragments were then subjected to an end repair process of addition of a single 'A' base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Freshly isolated human CD4+ T-cells treated with or without 500nM JQ1 for 24hr


title: POL2-H9wt-rep2

description:
ChIP-chip for RNA Pol2 vs No Antibody in wild-type H9 cells
platform design id: 090618_HG18_Refseq_Prom_ChIP

source_name: RNA Polymerase II ChIP DNA from H9 wt cells

value: wild-type pluripotent H9 embryonic stem cell line

value: RNA Polymerase II (8WG16, Covance)

value: None, No Antibody control


title: air2-Δ rrp6-Δ rep2


title: BRD4_untreated_hESC_ChIPseq

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using ELAND of the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.01 using the landerwaterman algorithm.
Normalization (wig normalized files): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)

source_name: Embryonic Stem Cells

extract_protocol: ChIP DNA ends were repaired using PNK and Klenow enzyme followed by treatment with Taq polymerase to generate an overhanging 3’ adenine base for adaptor ligation. The repaired ends were then ligated to a pair of Solexa adaptors and ChIP DNA was amplified for 17 cycles using adaptor primers. The amplified DNA was separated using an agarose gel and DNA fragments around 220bp were isolated and purified.

value: Embryonic Stem Cells

value: BRD4 (Abcam; Cat no. ab46199; Lot no. 613288)


title: PolIISer2_JQ1treated_Tcell_ChIPseq

value: PolIISer2 (Abcam; Cat no. ab5095; Lot no. 782031)

value: JQ1 treated


title: PolII4H8_JQ1treated_Tcell_ChIPseq

value: PolII4H8 (Abcam; Cat no. ab5408; Lot no. 722997)


title: BRD4_JQ1treated_Tcell_ChIPseq


title: rrp6-Δ rep2


title: BRD4_untreated_Tcell_ChIPseq


title: ovary

status: Public on Nov 13 2012

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

data_processing:
Following removal of the adaptor sequences from the sequence reads, high quality reads with >= 36 nt in length were selected as previous (PMID: 21685128).
For each predicted Ascaris gene (mRNA), their expression level (RPKM) was calculated using tophat/cufflinks.
Genome_build: Ascaris suum (Ohio) germline genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Ascaris suum

source_name: ovary germinal zone

growth_protocol: Ascaris fertilized eggs were harvested from female uteri by treatment with 0.5 N NaOH, followed by extensive washing in water, and then stored at 4 °C with 5 volumes of PBS (pH 2.0). For embryonation, the fertilized eggs from final proximal region of the uterus (Zygote-4 = 0 hr embryos) were incubated at 30 °C in PBS (pH 2.0) with constant (100 rpm) shaking for the desired time. The outer shell/membranes were de-coated with 0.4 N KOH/1.4% sodium hypochlorite at 4 °C (zygotes from regions 1-4) or 30°C (developing embryos and larvae) for 180 or 90 minutes, respectively, prior to RNA preparation. RNA from early embryos were extracted directly with Trizol (Invitrogen). Frozen testis, ovary, larvae, intestine, muscle, male carcass and female carcass samples were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.

extract_protocol: cDNA libraries were prepared from polyadenylated RNA (2x oligo-dT purified using μMACS™ mRNA Isolation Kit, Miltenyi Biotec). RNA was treated for 75-150 sec with RNA fragmentation buffer (Ambion) at 70°C to generate RNA fragments 150-400 nt in length. First stand cDNA was prepared by random priming (3-6 µg random hexamers/1 µg of A+ RNA) and second stranded cDNA synthesis was carried out using a SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen).  Solexa paired-end adaptors were added to the blunt cDNA as described by Illumina, cDNA fragments of 300-400 bp in length were gel purified, the fragments amplified using 17 PCR cycles, and sequencing reads were generated as described on the Illumina GAII or HiSeq2000.

tag: strain

value: North American wild population

tag: developmental stage

value: adult

tag: gender

value: female

tag: tissue

value: ovary


title: testis

source_name: testis germinal zone

value: male

value: testis


title: intestine

source_name: intestine

growth_protocol: Ascaris fertilized eggs were harvested from female uteri by treatment with 0.5 N NaOH, followed by extensive washing in water, and then stored at 4 °C with 5 volumes of PBS (pH 2.0). For embryonation, the fertilized eggs from final proximal region of the uterus (Zygote-4 = 0 hr embryos) were incubated at 30 °C in PBS (pH 2.0) with constant (100 rpm) shaking for the desired time. The outer shell/membranes were de-coated with 0.4 N KOH/1.4% sodium hypochlorite at 4 °C (zygotes from regions 1-4) or 30°C (developing embryos and larvae) for 180 or 90 minutes, respectively, prior to RNA preparation. RNA from early embryos were extracted directly with Trizol (Invitrogen). Frozen larvae, intestine, muscle, male carcass and female carcass samples were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.

value: intestine


title: muscle

source_name: muscle (and hypodermis)

value: muscle


title: larvae

source_name: 7 days - Larvae L2

value: larvae


title: mRNA_untreated_Tcell_RNAseq

data_processing: Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained.

source_name: CD4+ T cells

extract_protocol: Poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The cDNA fragments were then subjected to an end repair process of addition of a single 'A' base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final cDNA library.

tag: cell type

value: CD4+ T cells


title: 64hr

source_name: 64hr (2-4-cell) embryos

value: embryo

tag: timepoint

value: 64 hr


title: male carcass

source_name: muscle, hypodermis, pharynx, and neurons

value: carcass


title: female carcass


title: 46hr

source_name: 46hr (1-2-cell) embryos

value: 46 hr


title: Lmd2_ChIPSeq

city: Bethesda

first: Brian

last: Busser

state: Md

address: 10 Center Drive

institute: NHLBI/NIH

data_processing:
Basecalls performed using CASAVA version 1.8.1
ChIP-seq reads were aligned to the dm3 genome assembly using Burrows-Wheeler Aligner
Genome_build: dm3
Supplementary_files_format_and_content: wig files: peaks were called using MACS with the following setting: p-value (10-5) and mfold (2)
Supplementary_files_format_and_content: bed file: dm3 genomic coordinates for the overlap of regions called enriched by MACS from Lmd1_ChIPSeq compared to input and Lmd2_ChIPSeq compared to input

organism: Drosophila melanogaster

growth_protocol: Embryos were collected spanning a two-hour window from stage 11 through early stage 12; following embryo collection, cells were dissociated on ice and fixed in 1.8% formaldehyde (15 min) prior to cell sorting

extract_protocol: Immunoprecipiated DNA was end-repaired (END-IT kit from Epicentre), A-tailed (Epicentre), ligated with barcoded Illumina paired-end Y-linker, PCR-amplified for 16 cycles and library fragments of 300-500 bp were selected on 2% agarose E-gel and gel-purified.

value: Lmd2 [Cunha et al. 2010 PLoS Genet 6(7):e1001014]

value: sorted primary mesodermal

value: 2 hour embryo collection spanning late stage 11 to early stage 12


title: input

source_name: input

value: none (input)


title: 24hr

source_name: 24hr (1-cell) embryos

value: North American wild population

value: 24 hr


title: Lmd1_ChIPSeq

value: Lmd1 [Cunha et al. 2010 PLoS Genet 6(7):e1001014]


title: PolII4H8_untreated_Tcell_ChIPseq_pooled5donor

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT026_CD4TCell_PolIISer5_rmdup.bed: hg18
CHT026_CD4TCell_PolIISer5.wig.gz: hg18
CHT026_CD4TCell_PolIISer5_normalized_40.19.wig.gz: hg18

value: PolII4H8 [Abcam, Cat no. ab5408, Lot no. 722997]

tag: treatment

value: untreated


title: endogenous small RNAs from heterozygous; 2 day recovery, 12 day old, male, whole body minus testis

status: Public on Nov 12 2012

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

data_processing:
Linkers and barcode sequences were extracted from the raw tags. Remaining tags were imported into Galaxy (http://main.g2.bx.psu.edu/), converted into Sanger reads (groomer tool) and mapped to the Drosophila genome assembly (dm3) using, Bowtie. Mapped reads were subsequently filtered for Drosophila tRNAs sequences using LASTZ pairwise sequence alignment.
Genome Build:
wt_male_soma_2R_counts.txt: Drosophila melanogaster (Dm3)

source_name: heterozygous; 2 day recovery, male, whole body minus testis

growth_protocol: Flies were cultured on standard fly food in a humidified incubator (60% humidity) at a 12/12 hour day-night light cycle

extract_protocol: Germ line (testes) was separated from carcasses (soma) and RNA was extracted from soma using Trizol. 200 µg of total RNA per experiment were depleted of 2S rRNA using biotinylated DNA-oligos and streptavidin magnetic beads. 25- to 70-nt small RNAs from depleted total RNA were gel extracted from a 15% denaturing acrylimide gel (0.5´ TBE, 0.42 g/ml urea, 15% 19:1 acrylimide:bisacrylimide). After elution from the gel (twice incubated at 4°C in 0.4 M NaCl for 12 hours), RNAs were precipitated using ethanol and further processed for bar-coded RNA sequencing (6 barcodes) using the TrueSeq small RNA sample preparation kit (Illumina). Sequencing of samples was performed on a HighSeq platform (Illumina).

treatment_protocol: Male flies were heat-shocked (37 C for one hour) in a water bath, followed by a recovery period of a) 5 hours at RT or b) 2 days before extracting total RNA

value: adult males, 12 days

value: whole body without testis

tag: rna fraction

value: small RNAs (25-70 nucleotides)


title: endogenous small RNAs from heterozygous; heat shock, 10 day old, male, whole body minus testis

data_processing:
Linkers and barcode sequences were extracted from the raw tags. Remaining tags were imported into Galaxy (http://main.g2.bx.psu.edu/), converted into Sanger reads (groomer tool) and mapped to the Drosophila genome assembly (dm3) using, Bowtie. Mapped reads were subsequently filtered for Drosophila tRNAs sequences using LASTZ pairwise sequence alignment.
Genome Build:
wt_male_soma_hs_counts.txt: Drosophila melanogaster (Dm3)

source_name: heterozygous; heat shock, male, whole body minus testis

value: adult males, 10 days


title: endogenous small RNAs from heterozygous; control, 10 day old, male, whole body minus testis

data_processing:
Linkers and barcode sequences were extracted from the raw tags. Remaining tags were imported into Galaxy (http://main.g2.bx.psu.edu/), converted into Sanger reads (groomer tool) and mapped to the Drosophila genome assembly (dm3) using, Bowtie. Mapped reads were subsequently filtered for Drosophila tRNAs sequences using LASTZ pairwise sequence alignment.
Genome Build:
wt_male_soma_ctrl_counts.txt: Drosophila melanogaster (Dm3)

source_name: heterozygous; control, male, whole body minus testis


title: endogenous small RNAs from Dnmt2 mutants; control, 10 day old, male, whole body minus testis

data_processing:
Linkers and barcode sequences were extracted from the raw tags. Remaining tags were imported into Galaxy (http://main.g2.bx.psu.edu/), converted into Sanger reads (groomer tool) and mapped to the Drosophila genome assembly (dm3) using, Bowtie. Mapped reads were subsequently filtered for Drosophila tRNAs sequences using LASTZ pairwise sequence alignment.
Genome Build:
mut_male_soma_ctrl_counts.txt: Drosophila melanogaster (Dm3)

source_name: Dnmt2 mutants; control, male, whole body minus testis

value: w1118; Dnmt2 mutant/Dnmt2 mutant;+/+


title: endogenous small RNAs from Dnmt2 mutants; 2 day recovery, 12 day old, male, whole body minus testis

data_processing:
Linkers and barcode sequences were extracted from the raw tags. Remaining tags were imported into Galaxy (http://main.g2.bx.psu.edu/), converted into Sanger reads (groomer tool) and mapped to the Drosophila genome assembly (dm3) using, Bowtie. Mapped reads were subsequently filtered for Drosophila tRNAs sequences using LASTZ pairwise sequence alignment.
Genome Build:
mut_male_soma_2R_counts.txt: Drosophila melanogaster (Dm3)

source_name: Dnmt2 mutants; 2 day recovery, male, whole body minus testis


title: endogenous small RNAs from Dnmt2 mutants; heat shock, 10 day old, male, whole body minus testis

data_processing:
Linkers and barcode sequences were extracted from the raw tags. Remaining tags were imported into Galaxy (http://main.g2.bx.psu.edu/), converted into Sanger reads (groomer tool) and mapped to the Drosophila genome assembly (dm3) using, Bowtie. Mapped reads were subsequently filtered for Drosophila tRNAs sequences using LASTZ pairwise sequence alignment.
Genome Build:
mut_male_soma_hs_counts.txt: Drosophila melanogaster (Dm3)

source_name: Dnmt2 mutants; heat shock, male, whole body minus testis


title: Environmental DNA form contaminated aquifer_Sep. 08_7.15m

status: Public on Nov 11 2012

city: Neuherberg

first: Giovanni

last: Pilloni

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz-Centre Munich

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

data_processing: Sequence data processing was performed using mothur, with binning of denoised and quality-trimmed sequences into operational taxonomic units (OTUs) at a 97% similarity cutoff.

molecule: other

organism: aquifer metagenome

source_name: Aquifer Sediment

extract_protocol: Nucleic acids extracted with a bead beating-phenol/chloroform protocol from sediment samples were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads from 2 runs were furhter trimmed for quality and lenght (>250 bp).

tag: sampling time

value: September 2008

tag: depth

value: 7.1 m below ground

tag: plume zone

value: Lower fringe


title: Environmental DNA form contaminated aquifer_Jun. 09_7.25m

value: June 2009

value: 7.25 m below ground

value: Lower fringe/deeper zone


title: Environmental DNA form contaminated aquifer_Jun. 09_6.85m

value: 6.85 m below ground

value: Plume core/lower fringe


title: Environmental DNA form contaminated aquifer_Sep. 08_6.9m

value: 6.9 m below ground


title: Environmental DNA form contaminated aquifer_Jun. 09_6.55m

value: 6.55 m below ground

value: Upper fringe


title: Environmental DNA form contaminated aquifer_Sep. 08_8.3m

value: 8.3 m below ground

value: Deeper zone


title: Environmental DNA form contaminated aquifer_Sep. 08_6.7m

value: 6.7 m below ground

value: Plume core


title: Environmental DNA form contaminated aquifer_Jun. 09_7.15m

value: 7.15 m below ground


title: Environmental DNA form contaminated aquifer_Jun. 09_8.35m

value: 8.35 m below ground


title: Environmental DNA form contaminated aquifer_Feb. 06_8.1m

value: February 2006

value: 8.1 m below ground


title: Environmental DNA form contaminated aquifer_Feb. 06_6.9m

value: Lower fringe


title: Environmental DNA form contaminated aquifer_Feb. 06_7.1m

value: 7.1 m below ground


title: Environmental DNA form contaminated aquifer_Feb. 06_6.65m

value: 6.65 m below ground


title: Environmental DNA form contaminated aquifer_Feb. 06_6.5m

value: 6.5 m below ground


title: A INPUT phenobarbital donor2021

status: Public on Nov 10 2012

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

data_processing:
base calling with CASAVA 1.8 for single-end and GERALD v1.52.6.1 for paired-end
for the paired-end data, mapping of reads with bowtie 0.12.7: bowtie --solexa1.3-quals -v 3 --best --strata -S -m 100 -5 11 -3 3 -I 0 -X 400
for the single-end data mapping was done with bowtie 0.12.5: bowtie --solexa1.3-quals -n 3 -l 36 --best --chunkmbs 512 --strata -S -m 100 -5 3
alignments were post-processed with samtools to create sorted and indexed BAM files
redundant alignments were removed (same alignment with same mismatches and genomic mapping)
the target genome was binned into 500 base pairs bins and reads counted per bin
the log2 fold change of IP (per sample and histone mark) over the input (background) is calculated
regions are further summarized (e.g. promotors, gene body), see supplementary file histoneMarkREsults3.txt
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files of enrichment (log2 library size normlaized read counts of IP over background) in bins of 500 base pairs; tab delimited enrichment (normalized by library size) of histone marks in different gene regions

organism: Mus musculus

source_name: whole liver extract

growth_protocol: 29–32 days old male B6C3F1/Crl (C57BL/6 ♂ x C3H/He ♀) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups of five animals each. Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behaviour and sacrificed on the last day of dosing (day 28)

extract_protocol:
Extraction according to Thomson et al. Genome Biology 2012: Dynamic changes in liver 5‐ hydroxymethylcytosine profiles upon non‐ genotoxic carcinogen exposure
Library construction according to Thomson et al. Genome Biology 2012: Dynamic changes in liver 5‐ hydroxymethylcytosine profiles upon non‐ genotoxic carcinogen exposure

tag: age

tag: chip antibody

value: INPUT

tag: treament

value: phenobarbital

value: liver

tag: animal id

tag: experiment id

value: A

value: B6C3F1/Crl (C57BL/6 male x C3H/He female)


title: A INPUT vehicle donor1024

treatment_protocol: Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days

value: vehicle


title: A INPUT vehicle donor1021


title: A H3K36me3 phenobarbital donor2024


title: A INPUT phenobarbital donor2024


title: A H3K36me3 vehicle donor1024


title: A H3K36me3 phenobarbital donor2021


title: R53-L6-Input-Sequences

city: Irvine

first: Amelia

middle: Soto

last: Hopkin

state: CA

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California Irvine

data_processing:
Base-calls were made using RTA  version 1.12.4.2.
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using macs14, with input aligned sequences as the control file, m fold of 8,30, and p-value 1e-7
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: Human hg19
Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations

source_name: Human neonatal epidermis_input

growth_protocol: NHEK cells were grown in DermaLife medium (LifeLine Cell Technologies) at 37C, 5%CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 24 ug of sonicated chromatin was used for each IP. The following antibodies were used : Grhl3 (Andersen Lab), WDR5 (AbCam cat#ab56919)
Sequencing libraries were generated for the GRHL3, WDR5, and Input samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [PMID 19275939]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.

treatment_protocol: Medium containing high calcium levels (1.8mM) was used to induce differentiation in NHEK cells. Cells were collected 24 hours after the switch to high calcium medium

value: human differentited primary keratinocytes (NHEK)


title: R48-L2-Grhl3-Sequences

source_name: Human neonatal epidermis_Grhl3 ChIP

value: Grhl3 (Andersen Lab)


title: R53-L8-Wdr5-Sequences

source_name: Human neonatal epidermis_Wdr5_ChIP

value: Anti-WDR5 antibody

tag: chip antibody vendor

value: AbCam

tag: chip antibody cat. #


title: Environmental DNA form contaminated aquifer_Sep. 08_6.4m

value: September 2008

value: 6.4 m below ground

value: Upper fringe


title: C H3K27me3 phenobarbital donor14

value: C

tag: strain


title: C H3K27me3 phenobarbital donor17


title: C H3K27me3 vehicle donor5


title: C INPUT vehicle donor5


title: C INPUT vehicle donor10


title: B H3K4me2 phenobarbital donor15

value: B


title: C INPUT phenobarbital donor14


title: C INPUT phenobarbital donor17


title: B H3K4me2 vehicle donor7


title: B H3K4me2 vehicle donor1


title: C H3K27me3 vehicle donor10


title: A H3K36me3 vehicle donor1021


title: B H3K4me2 phenobarbital donor11


title: Col_ChIPseq

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: Wild-type plants not expressing CMT3-FLAG

data_processing:
Illumina base-called reads were mapped with Bowtie (Langmead et al, 2009 Genome Biology) allowing up to 2 mismatches. Only uniquely mapping reads were used for analyses. Reads mapping to indentical positions were collapsed into single reads.
Genome_build: TAIR8
Supplementary_files_format_and_content: Column1 = chromosome, Column2 = strand, Column3 =genomic coordinate (zero-based)

organism: Arabidopsis thaliana

source_name: flowers

growth_protocol: All plants were grown under long day conditions.

extract_protocol: 10 gram flower tissues were ground into   powder and suspended in 50 mL of low lysis buffer (50 mM Tris pH 7.5, 50 mM NaCl, 5 mM   MgCl2, 10% glycerol, 0.1% NP-40, 0.5 mM DTT, 1 µg/µl pepstatin, 1 mM PMSF and 1 protease   inhibitor cocktail tablet).  The crude extracts were incubated with Micrococcal Nuclease (Takara, K822AB) on ice for 30 minutes and stopped by adding EDTA to a final concentration of 25 mM.   Sodium salts were added to the extracts to obtain a final concentration of 150 mM before   incubation with beads. After centrifugation at 10,000 g for 20 min, the supernatant was   incubated with pre-washed Flag-Dynabeads at 4ºC for 2 hours with rotation. Beads were   washed two times with 40 mL of lysis buffer and four times with 1 mL of lysis buffer by gentle   mixing at 4ºC for 10 minutes each wash. Elution was performed three times by incubating with   250 µl of 100 µg/mL of 3xFlag peptide (Sigma, F4799) at room temperature for 15 minutes each   elution. The eluted protein-DNA complexes were treated by proteinase K followed by   phenol:chlorophorm purification. The enriched DNA was ethanol precipitated and subjected to   library generation following Illumina’s manufacturer instructions.

tag: antibody

value: flowers

tag: genotype/variation


title: B INPUT phenobarbital donor15

tag: tissue


title: B INPUT vehicle donor1


title: B INPUT vehicle donor7


title: ChIP-Seq_Mouse_Liver_ZT8_BMAL1

status: Public on Nov 09 2012

city: College Station

first: Jerome

middle: S

last: Menet

address: 301 Old Main Drive, Building 1530, ILSB

department: Dept of Biology

institute: Texas A&M University

data_processing:
Basecalls performed using CASAVA  v1.6
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with the following criteria: –p 6 –q –a –-best –m 1
Peaks were called using Macs with the following setting: –bw=80 –-gsize=1890000000 –-tsize=36 –-mfold=5
Genome_build: mm9
Supplementary_files_format_and_content: ChIPSeq_Mouse_Liver_Processed_data_Table1.txt: table with all significant CLK and BMAL1 peaks, their genomic location and relevant information. [Linked as supplementary file on Series record.]
Supplementary_files_format_and_content: ChIPSeq_Mouse_Liver_BMAL1peaks_Macs_Analysis.txt: Output file from Macs analysis for peak calling
Supplementary_files_format_and_content: ChIPSeq_Mouse_Liver_CLKpeaks_Macs_Analysis.txt: Output file from Macs analysis for peak calling

source_name: Liver

extract_protocol: Formaldehyde cross-linked mouse liver nuclei were sonicated. Chromatin was immunoprecipitated with specific antibodies against CLK or BMAL1. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Mouse were exposed to a 12h light: 12h dark cycle (LD12:12) for at least 2 weeks before the experiment

value: Liver

value: Adult (3-6months)

tag: time


title: ChIP-Seq_Mouse_Liver_ZT8_CLK

value: anti-CLK (Novus Biological; #NB100-126; lot B1)


title: Nascent-Seq_Mouse_Liver_Rep2_ZT4

description: Nascent RNA

data_processing:
Basecalls performed using CASAVA v1.7
Nascent-Seq reads were aligned to the mm9 genome assembly using tophat with the following criteria: -m 1 -F 0 -g 1 --microexon-search --no-closure-search. Reads that map uniquely to the genome were only considered for analysis.
For each gene, reads mapped to exons were summed and normalized to the length of exons. The value, corresponding the read per base pair (rpbp) for any given gene, was normalized to the sequencing depth of each sample (time point).
Normalized rpbp were then used to assess for rhythmic expression. Rhythmically expressed genes with 24hr period were identified by Fourier transformation. The 24hr spectral power (F24) score and its significance (p-value; generated via comparison with a randomly permuted dataset) were obtained using a custom-written R code.
bedGraph files were generated using custom-written perl scripts for visualization purpose only.
Genome_build: mm9
Supplementary_files_format_and_content: NascentSeq_Mouse_Liver_NormalizedGeneSignal.txt, a tab-delimited text file, includes Normalized Reads per Base Pair values for each Sample.  [Linked as supplementary file on Series record.]
Supplementary_files_format_and_content: bedGraph files (generated using custom-written perl scripts) are provided for visualization on Genome Browsers

extract_protocol: Mouse liver nuclei were purified and lysed using NUN buffer as described in Wuarin and Schibler, 1994. Nascent RNA was extracted from DNA pellet using Trizol, DNase-treated and further purified by removing polyadenylated RNA.  Libraries were prepared according to Illumina's instructions. Briefly, Nascent RNA were fragmented using fragmentation reagents (Ambion #AM8740) and reverse transcribed using random primers. After second strand synthesis, dsDNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: rep


title: Nascent-Seq_Mouse_Liver_Rep2_ZT16

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep2_ZT8

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep2_ZT0

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep2_ZT20

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep2_ZT12

description: Nascent RNA


title: B INPUT phenobarbital donor11

value: INPUT

value: phenobarbital

value: liver


title: ChIP-Seq_Mouse_Liver_ZT8_Input

value: none (input)


title: Nascent-Seq_Mouse_Liver_Rep1_ZT16

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep1_ZT12

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep1_ZT0

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep1_ZT20

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep1_ZT4

description: Nascent RNA


title: Nascent-Seq_Mouse_Liver_Rep1_ZT8

description: Nascent RNA


title: 20dpi control

city: Beijing

first: Jie

last: Lu

address: Shuangqiaozhonglu

country: China

institute: CAIQ

data_processing:
*_TagCount.txt: Extraction of tags and tag counting were performed using the Illumina pipeline. To get the high quality tags that we used to analysis, we filtered the potentially erroneous tags (only one copy number, only adaptor sequences, or containing unknown sequences 'N') to get the clean tags. For mapping the clean tags to reference sequences, we get all the possible 17 bases length sequences next to the NlaIII restriction site of the reference sequences, then plus the 4 bases NlaIII recognition site to construct a reference database. The clean tag expression was normalized to TPM (transcripts per million clean tags).
Unigene.blast.Nr.xls, Unigene.blast.Swissprot.xls, Unigene.blast.kegg.xls, Unigene.blast.cog.xls: The Unigenes were analyzed by searching the protein databases like nr, Swiss-Prot, KEGG and COG using blastx (evalue < 0.00001) program. If results of different databases conflicted with each other, a priority order of nr, Swiss-Prot, KEGG and COG should be followed when deciding sequence direction of Unigenes.
Unigene.gene2GO.xls, Unigene.GO2gene.xls: Unigenes with nr annotation were further analyzed with Blast2go to get GO annotations.

organism: Nicotiana tabacum

source_name: mock-inoculated tobacco leaves

growth_protocol: Tobacco plants (Nicotiana tabacum cv. Xanthi nc) were grown in a greenhouse at a cycle of 16 h light and 8 h dark.

extract_protocol: The systemically infected leaves and mock-inoculated leaves were harvested at 6, 9, 11, 13, 16 and 20 days post-inoculation (dpi), respectively. In order to average out variation of different plants, five leaves from five different plants were mixed to prepare every RNA sample. The collected leaf tissues were frozen in liquid nitrogen and stored at -80â until RNA extraction. Total RNAs of leaf tissues were extracted using TRIzolÂ® Reagent and then treated with DNase I. For DGE profiling, twelve individual tag libraries of samples (six infected samples and six mock-inoculated samples) were constructed in parallel. Sequence tags were prepared using Illumina Gene Expression Sample Prep Kit following the manufacturer's instructions. Magnetic beads with oligo(dT) were used to purify poly(A)-containing mRNA and oligo-dT primer was used to sythesize double-stranded cDNA. The bead-bound cDNAs were then digested by endonuclease NlaIII, which recognizes and cuts CATG sites, to generate sticky 5' ends. The cut-off fragments were washed away and the bead-bound fragments were ligated to the Illumina adaptor 1 through the sticky 5' end. The bead-bound fragments with adaptor 1 were then digested by MmeI, which cuts at 17bp downstream of CATG site. After that, the bead-bound fragments without adaptor 1 were removed by magnetic beads precipitation, and the tags with adaptor 1 were purified and ligated to Illumina adaptor 2 through the 3' end of the tag. After 15 cycles of linear PCR amplification, 95bp fragments were purified by 6% TBE polyacrylamide gel electrophoresis to obtain the final tag libraries. After denaturation, the single-stranded DNAs were fixed onto the Illumina Sequencing Chip (flowcell). Four types of nucleotides labeled by four colors were used and sequencing was performed with the method of sequencing by synthesis (SBS) using Illumina HiSeqâ¢ 2000.

treatment_protocol: The systemically infected leaves of M-CMV infected plants were harvested and immediately homogenized to prepare viral inoculum. Approximately 0.5 g leaves were homogenized with kieselguhr in 1 ml water. The viral inoculum was rub-inoculated by a latex-gloved finger onto the top two leaves of tobacco plants having four to six fully expanded leaves. The mock inoculum was prepared from leaves of healthy plants and applied in the same way as viral inoculum.

tag: plant variety

value: cv. Xanthi nc

value: leaves

tag: viral infection

value: control


title: 16dpi control


title: mock and infected tobacco RNA-Seq

description: 200 bp average insert size

source_name: mock-inoculated and virus-infected tobacco leaves

value: mixture of uninfected and Cucumber mosaic virus M strain infected leaves


title: 16dpi infected

source_name: virus-infected tobacco leaves

value: Cucumber mosaic virus M strain


title: 20dpi infected


title: 9dpi infected


title: 6dpi control


title: 13dpi control


title: 11dpi infected


title: 13dpi infected


title: 9dpi control


title: 11dpi control


title: PolIISer2_untreated_Tcell_ChIPseq_pooled5donor

data_processing:
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained. For ChIP-seq, only unique reads were retained (for reads with duplicates,one read was retained).
Peaks (wig files): Peak detection was performed with FindPeaks4 (Fejes et al., 2008) with an extension of sequence tags to 200bp and a false discovery rate of 0.0000001 using the landerwaterman algorithm.
Normalization (wig normalized files ): Wig files of peaks detected were normalized for comparison between ChIP-seq libraries before and after JQ1 treatment. Tag counts in each position were normalized by a multiplication factor of 10/(Number of million mapped tags in the particular library to 2 decimal places)
Genome Build:
CHT028_CD4TCell_JQ1_BRD4_rmdup.bed: hg18
CHT028_CD4TCell_JQ1_BRD4.wig.gz: hg18
CHT028_CD4TCell_JQ1_BRD4_normalized_48.40.wig.gz: hg18

source_name: CD4+ T cells

extract_protocol: ChIP DNA ends were repaired using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase), and T4 polynucleotide kinase (PNK). The 3' to 5' exonuclease activity of these enzymes removes 3' overhangs and the polymerase activity fills in the 5' overhangs. This is followed by treatment with Klenow fragment (3' to 5' exo minus) to generate an overhanging 3  adenine base for adaptor ligation to adapters which have a single  T  base overhang at their 3' end. Size Selection of 300bp fragment were done using the Invitrogen EGel system, followed by enrichment with 15 PCR cycles. The amplified DNA was purified by Ampure beads before validation on the Agilent Bionanlyser.

tag: cell type

value: CD4+ T cells

value: PolIISer2 [Abcam, Cat no. ab5095, Lot no. 782031]

tag: treatment

value: untreated


title: 6dpi infected


title: K-562 truseq 500ng

data_processing: All files were mapped against Hg19 using TopHat 1.1.4

source_name: K-562 cell line

extract_protocol:
Illumina TruSeq RNA sample prep kit used with these changes:  SuperScript III instead of SuperScript II & optimization of PCR cycle number
RNA purchased from Ambion/ABI

value: immortalised chronic myelogenous leukemia (CML)

tag: cell line

tag: sample type

value: K-562 truseq 500ng

tag: average insert size

tag: std. dev. insert size


title: CD4+ T cells, WT, biological rep10

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.CGGTG_zwt1

data_processing:
Before data was deposited in GEO it was demultiplexed and the degenerate barcode from the index read was appended to the beginning of the read (it is the first six nucleotides of the reads deposited here).
The 3' ends of reads were trimmed until the base quality score was >20. FASTX-Toolkit: fastq_quality_trimmer  -t 20 -l 20
3' Linker sequences were clipped (linker1= GTGTCTTTACACAGCTACGGCGTCG; linker2= GTGTCACTGATAGCAACCCGGTGCT). FASTX-Toolkit: fastx_clipper -a GTGTCTTTACACAGCTACGGCGTCG -l 20 -M 4; fastx_clipper -a GTGTCACTGATAGCAACCCGGTGCT -l 20 -M 4
Remove any reads with adapter sequence fragments (custom perl script): CGACCAGCAT, GTGTCTTTAC, GTGTCACTGA
Reads were consolidated -- that is we merged identical reads with identical barcodes in nt. pos. 1-6 of each read.
We aligned reads (starting with the seventh nucleotide to avoid the degenerate barcode) uniquely to the mm9 Mouse genome with up to one mismatch. (Bowtie 0.12.7): mm9 -5 6 -v 1 --tryhard -a -m 1 --best --strata
UTR mapping, normalization, peak calling and detection of differential binding was performed using custom tools.  See supplementry computational methods (linked to Series record as supplementary file) for details.
Supplementry computational methods also available from: http://homes.uchicago.edu/~aakhan/clip_supplemental.pdf
Genome_build: mm9
Supplementary_files_format_and_content: File clip_peaks.txt contains all 3'UTR peaks called from the data--all called peaks had binding in at least 7 out of 12 wild type or 155KO replicates.  File clip_peaks.txt is linked as a supplementary file on the Series record.

source_name: In vitro activated CD4+ T cells from spleen and lymph nodes

growth_protocol: CD4+ T cells were isolated using CD4 dynabeads (Invitrogen) according to the manufacture's instructions.

extract_protocol:
Cells were lysed and treated with limiting RNAse.  AGO-RNA complexes were immunoprecipitated with AGO2 antibody.  Immunoprecipitated samples were separated by SDS-PAGE and transferred to nitrocellulose.  Libraries were constructed from complexes that ran at ~100-150kD.
3' RNA linkers were ligated while Ago complexes were complexed to IP beads.  5' RNA linkers were ligated following proteinase K digestion of nitrocellulose bound complexes.  Reverse transcription was performed with a primer containing a 5nt multiplexing index and 6nt degenerate barcode.  Following library amplification, libraries were size selected on agarose gels to enrich for inserts.

treatment_protocol: CD4+ T cells were activated upon culture in the presence of 1ug/mL CD3 and CD28 antibodies in 20U/mL IL-2 for 4 days at 37C, 5% CO2.

value: WT

value: CD4+ T cells [activated]

value: anti-AGO2 (a custom rabbit polyclonal antibody generated with the following peptide:MYS GAG PVL ASP APT TSP IPG YAFKC)

tag: 3' linker

value: 3' Linker 1


title: CD4+ T cells, WT, biological rep11

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.CAACT_zwt2


title: CD4+ T cells, WT, biological rep9

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.GCACA_dwt4


title: Nascent-Seq_Mouse_Liver_Rep1_ZT20_Strand_Specific

description:
Nascent RNA
Nascent-Seq (strand-specific)

data_processing:
Basecalls performed using CASAVA v1.7
Nascent-Seq reads were aligned to the mm9 genome assembly using tophat with the following criteria: -m 1 -F 0 -g 1 --microexon-search --no-closure-search. Reads that map uniquely to the genome were only considered for analysis.
bedGraph files were generated using custom-written perl scripts for visualization purpose only.
Determination of signal abundance (rpbp) has not been performed.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files (generated using custom-written perl scripts) are provided for visualization on Genome Browsers.

extract_protocol: Mouse liver nuclei were purified and lysed using NUN buffer as described in Wuarin and Schibler, 1994. Nascent RNA was extracted from DNA pellet using Trizol, DNase-treated and further purified by removing polyadenylated RNA.  Libraries were prepared according to Illumina's instructions. Briefly, Nascent RNA were fragmented using fragmentation reagents (Ambion #AM8740) and reverse transcribed using random primers. cDNA was then purified and second strand synthesis was performed using a dNTP mix comntaining dUTP instead of dTTP. dsDNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was treated with USER enzyme (NEB) and then PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPURE XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

value: Liver

tag: age

value: Adult (3-6months)


title: CD4+ T cells, WT, biological rep12

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.ACGCC_zwt3


title: Nascent-Seq_Mouse_Liver_Rep1_ZT16_Strand_Specific


title: CD4+ T cells, WT, biological rep5

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.CCGGT_wt5

value: 3' Linker 2


title: Nascent-Seq_Mouse_Liver_Rep1_ZT12_Strand_Specific


title: CD4+ T cells, WT, biological rep7

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TAGCG_ewt1


title: CD4+ T cells, WT, biological rep6

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.CACTA_wt6


title: CD4+ T cells, WT, biological rep8

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.GCACA_ewt4


title: CD4+ T cells, WT, biological rep4

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.CGTCC_wt4


title: Nascent-Seq_Mouse_Liver_Rep1_ZT8_Strand_Specific


title: Nascent-Seq_Mouse_Liver_Rep1_ZT4_Strand_Specific


title: CD4+ T cells, WT, biological rep2

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TCCAC_wt2


title: Nascent-Seq_Mouse_Liver_Rep1_ZT0_Strand_Specific


title: CD4+ T cells, WT, biological rep3

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.CTAAG_wt3


title: CD4+ T cells, WT, biological rep1

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TGATT_wt1


title: RNASeq_Mouse_Liver_Rep2_ZT22

data_processing:
Basecalls performed using CASAVA v1.8
RNA-Seq reads were aligned to the mm9 genome assembly using tophat with the following criteria: -m 1 -F 0 -g 1 --microexon-search --no-closure-search. Reads that map uniquely to the genome were only considered for analysis.
For each gene, reads mapped to exons were summed and normalized to the length of exons. The value, corresponding the read per base pair (rpbp) for any given gene, was normalized to the sequencing depth of each sample (time point).
Normalized rpbp were then used to assess for rhythmic expression. Rhythmically expressed genes with 24hr period were identified by Fourier transformation. The 24hr spectral power (F24) score and its significance (p-value; generated via comparison with a randomly permuted dataset) were obtained using a custom-written R code.
bedGraph files were generated using custom-written perl scripts for visualization purpose only.
Genome_build: mm9
Supplementary_files_format_and_content: RNASeq_Mouse_Liver_NormalizedGeneSignal.txt (a tab-delimited text file) includes Normalized Reads per Base Pair values for each Sample [Linked as supplementary file on Series record.]
Supplementary_files_format_and_content: bedGraph files (generated using custom-written perl scripts) are provided for visualization on Genome Browsers.

extract_protocol: Mouse liver were removed, cut into small pieces, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used with 4 ug of total RNA for the construction of sequencing libraries.


title: RNASeq_Mouse_Liver_Rep2_ZT18


title: RNASeq_Mouse_Liver_Rep2_ZT10


title: RNASeq_Mouse_Liver_Rep2_ZT14


title: CD4+ T cells, 155KO, biological rep9

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TGATT_dko2

value: miR-155 KO


title: CD4+ T cells, 155KO, biological rep11

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.AGTGT_zko1


title: CD4+ T cells, 155KO, biological rep10

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TTTGA_dko3


title: RNASeq_Mouse_Liver_Rep2_ZT6


title: RNASeq_Mouse_Liver_Rep1_ZT22


title: RNASeq_Mouse_Liver_Rep2_ZT2


title: CD4+ T cells, 155KO, biological rep5

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.ACTTG_ko5


title: CD4+ T cells, 155KO, biological rep6

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.AAAGC_ko6


title: RNASeq_Mouse_Liver_Rep1_ZT18


title: RNASeq_Mouse_Liver_Rep1_ZT14


title: CD4+ T cells, 155KO, biological rep4

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.ATCCT_ko4


title: RNASeq_Mouse_Liver_Rep1_ZT10


title: RNASeq_Mouse_Liver_Rep1_ZT2


title: CD4+ T cells, 155KO, biological rep7

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TTTGA_eko1


title: CD4+ T cells, 155KO, biological rep2

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.GTGTC_ko1


title: RNASeq_Mouse_Liver_Rep1_ZT6


title: CD4+ T cells, 155KO, biological rep12

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.AACAG_zko3


title: CD4+ T cells, 155KO, biological rep8

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TGATT_eko3


title: Dpse_WPP_CTCF_Input_2

status: Public on Nov 08 2012

first: Kevin

middle: P.

last: White

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

department: Institute for Genomics and Systems Biology

data_processing:
Alignment: Sequence reads were obtained and mapped to multiple drosophila genomes using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the QuEST 2.0 algorithm (http://mendel.stanford.edu/SidowLab/downloads/quest/)

organism: Drosophila pseudoobscura

source_name: white prepupae

growth_protocol: The four sequenced inbred fly lines for the different Drosophila species are grown in room temperature on standard fly food. The white prepupa whole animals are collected within 15 min time interval

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

treatment_protocol: No Treatment

tag: developmental stage

value: white prepupae

tag: fraction

value: input


title: Dpse_WPP_CTCF_Input_1


title: Dpse_WPP_CTCF_ChIPSeq_1, 2 and 3

tag: antibody name

value: CTCF-C

tag: antibody manufacturer

value: Renkawitz Lab

tag: antibody lot/batch#

tag: antibody catalog

value: Custom

value: ChIP


title: β-cat.siRNA+2h GnRH_2

city: New York

first: Maria

last: Chikina

address: Annenberg 14-88 One Gustave Levy Pl

institute: Mount Sinai School of Medicine

description: b-cat.siRNA+2h GnRH_2

data_processing:
We used the RUM runner 2.0 pipeline with all the default options with the mm9 index that comes with the software.
Genome_build: mm9
Supplementary_files_format_and_content: text, RPKM values for transcripts and exons

source_name: β-cat.siRNA+2h GnRH

growth_protocol: LβT2 cells were routinely maintained at 37°C  in a humidified air atmosphere of 5% CO2 in DMEM (Mediatech, Herndon, VA) supplemented with 10% fetal bovine serum (FBS) (Gemini, Calabasas, CA) and L-glutamine (Gibco Invitrogen, Carlsbad, CA).

extract_protocol:
Total RNA was isolated using Stratagene Absolutely 96 RNA microprep kit (Stratagene, La Jolla, CA).
RNA libraries were prepared for RNA-Sequencing using standard Illumina protocols.

treatment_protocol: LβT2 cells were transfected with either scrambled or β-catenin siRNA for 48 h, serum starved overnight, and stimulated with vehicle or 5nM GnRH for either 45 min or 2 h.

tag: tissue

value: anterior pituitary

value: pituitary gonadotrope-derived cells

value: immortalized gonadotrope cells

tag: transfected with

value: β-catenin siRNA for 48 h

tag: stimulated with

value: 5nM GnRH for 2hr

tag: passages


title: β-cat.siRNA+0.75h GnRH_4

description: b-cat.siRNA+0.75h GnRH_4

source_name: β-cat.siRNA+0.75h GnRH

tag: cell type

value: 5nM GnRH for 45 min


title: β-cat.siRNA+vehicle_4

tag: cell line

value: vehicle


title: β-cat.siRNA+0.75h GnRH_3

description: b-cat.siRNA+0.75h GnRH_3


title: CMT3_ChIPseq

description: Transgenic plants expressing CMT3-FLAG

tag: antibody

value: flowers

tag: genotype/variation

value: Transgenic plants expressing CMT3-FLAG


title: β-cat.siRNA+vehicle_3


title: β-cat.siRNA+0.75h GnRH_1

description: b-cat.siRNA+0.75h GnRH_1


title: Scr.siRNA+2h GnRH_4

description: Scr.siRNA+2h GnRH_4

source_name: Scr.siRNA+2h GnRH

value: scrambled siRNA for 48 h


title: β-cat.siRNA+vehicle_2


title: Scr.siRNA+2h GnRH_3

description: Scr.siRNA+2h GnRH_3


title: CD4+ T cells, 155KO, biological rep3

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.GCACA_ko2

tag: strain

value: miR-155 KO

value: CD4+ T cells [activated]

value: anti-AGO2 (a custom rabbit polyclonal antibody generated with the following peptide:MYS GAG PVL ASP APT TSP IPG YAFKC)

value: 3' Linker 1


title: Scr.siRNA+0.75h GnRH_3

description: Scr.siRNA+0.75h GnRH_3

source_name: Scr.siRNA+0.75h GnRH


title: β-cat.siRNA+vehicle_1


title: Scr.siRNA+2h GnRH_2

description: Scr.siRNA+2h GnRH_2


title: CD4+ T cells, 155KO, biological rep1

description:
Nucleotides 1-6 of the read are degenerate barcode that were appended from an index read, the subsequent nucleotides correspond to the Argonaute bound RNA
read.TAGCG_koc

tag: 3' linker


title: Scr.siRNA+0.75h GnRH_4

description: Scr.siRNA+0.75h GnRH_4


title: Scr.siRNA+0.75h GnRH_1

description: Scr.siRNA+0.75h GnRH_1


title: Scr.siRNA+0.75h GnRH_2

description: Scr.siRNA+0.75h GnRH_2


title: β-cat.siRNA+2h GnRH_4

description: b-cat.siRNA+2h GnRH_4


title: Scr.siRNA+vehicle_3


title: β-cat.siRNA+2h GnRH_3

description: b-cat.siRNA+2h GnRH_3


title: β-cat.siRNA+2h GnRH_1

description: b-cat.siRNA+2h GnRH_1


title: Scr.siRNA+vehicle_2


title: β-cat.siRNA+0.75h GnRH_2

description: b-cat.siRNA+0.75h GnRH_2


title: Scr.siRNA+vehicle_1


title: TrueSeq RRBS APL_patient APL_patient_48untreated

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
Off-Line Basecaller (OLB) was used for bcl to qseq conversion
Illumina paired-end adapter sequences were removed using Cutadapt version 0.9.3
Reads were mapped using Bismark version 0.5
Methylation calls from Bismark were extracted with a modified methylation_extractor script which removed 3’-MspI-sites
The extracted methylation data was further analyzed in R/Bioconductor with the BiSeq package
Genome_build: hg19 for human samples and mm9 for mouse samples
Supplementary_files_format_and_content: Extracted CpG methylation call files were generated using R/Bioconductor with help of the BiSeq package. Each processed file contains a column for chromosome, position and extracted methylation data for the respective sample. For each CpG position observed the number of methylated / unmethylated reads is listed.

source_name: In-vitro APL blast mock treated

extract_protocol: TrueSeq RRBS: Briefly, 500 ng genomic DNA was digested with MspI, end-repaired and A-tailed with the Klenow-fragment enzyme, and then ligated with 5mC-methylated Illumina TruSeq adapters. We followed the general library preparation instructions from Illumina and purified fragments in a range of 40 to 220 bps insert size from a SYBR Gold prestained gel. Subsequently, the libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA). Next the Libraries were amplified using PfuTurboCx polymerase. Libraries were sequenced in a pool with other libraries using an Illumina HiScanSQ instrument with TruSeq SBS Kit v3 sequencing chemistry. After demultiplexing with the CASAVA 1.8.2 (Illumina), the reads were subject to the described standard analysis pipeline.

tag: disease state

value: 48h Mock treated APL blasts

tag: Sex

value: m

tag: age

tag: sample pairs

value: APL patient


title: TrueSeq RRBS APL_patient APL_patient_48ATRA

source_name: In-vitro ATRA treated APL blast

value: 48h ATRA treated APL blasts


title: TrueSeq RRBS APL_patient APL_patient_diagnosis

source_name: In-vitro APL blasts before treatment

value: APL blasts before treatment


title: RRBS remission bone marrow APL_11436

source_name: Density centrifuged bone marrow

extract_protocol: 0.3 – 1 µg of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with 5mC-methylated Illumina paired end sequencing adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 220 bps insert size were gel-purified (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). Each library was sequenced on a separate lane using an Illumina HiScanSQ instrument with version 2.5 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.

value: Remission bone marrow

value: f


title: RRBS remission bone marrow APL_11523


title: Scr.siRNA+2h GnRH_1

description: Scr.siRNA+2h GnRH_1

value: anterior pituitary

value: pituitary gonadotrope-derived cells

value: immortalized gonadotrope cells

value: 5nM GnRH for 2hr


title: RRBS remission bone marrow APL_10325


title: RRBS remission bone marrow APL_16


title: RRBS remission bone marrow APL_10961


title: ChiP-Seq IgG APL blast

source_name: APL bone marrow blasts

extract_protocol: ChIP-seq: Cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as previously described (Dietrich et al, PLOS Genetics 2012). Briefly, formaldehyde fixed chromatin was sonicated in IP buffer (IP buffer =2 volume SDS Buffer : 1 volume Triton Dilution Buffer; SDS Buffer-  100mM NaCl  50mM Tris-Cl, pH8.1, 5mM EDTA, pH 8.0, 0.2% NaN3, 2% SDS; Triton Dilution Buffer- 100mM Tris-Cl, pH 8.6, 100mM NaCl, 5mM EDTA, pH 8.0, 0.2% NaN3, 5.0% Triton X-100) using Branson Sonifier (4 cycles of 30 sec each at 20% amplitude). 15ug DNA (sonicated chromatin) was used for each ChIP in IP buffer. Antibodies used: Rabbit IgG (DAKO), rabbit anti-REST (Millipore, 07-579), anti-SUZ12 (Rabbit monoclonal, Cell signaling). Samples were incubated with antibodies overnight at 40C and immunocomplexes were precipitated with protein A-sepharose beads with 3 hr rotation at 40C. After subsequent washes the samples were decrosslinked overnight at 650C (shaking) in 1%SDS, 0.1M NaHCO3. Finally, ChIP DNA was purified using Qiagen PCR purification kit. The ChIPs were validated at REST and Polycomb target genes by qPCR. ChIP DNA from three parallel ChIPs were pooled and 10 ng was used for making ChIP-seq libraries. The libraries were prepared using “ChIP seq DNA sample preparation kit” from Illumina following manufacturer’s instructions. Individual samples were run in a single lane on HiSeq2000 (Illumina). Basecalls were performed using on-instrument real time analysis (RTA). Mapping was performed with bowtie allowing for <=2 mismatches and only including reads that were mapped to a single position to hg18. The number of reads in 100 bp sections of the genome were counted genome-wide. A normal distribution was fitted to the counts, and the distribution with the least root-mean-square deviation was used as model for the background in the datasets. Thresholds were set so that windows that scored positive had p-values < 0.001 compared to the background distribution. A ChIP-sequenced IgG-control was used as a negative control and handled in the same way. Only windows scoring positive for REST or Suz12, but not IgG, were included for downstream analysis. Also windows where the positive signal (normalized to dataset size) did not exceed the negative signal (normalized to dataset size) at least threefold were omitted from downstream analysis. Datasets were analyzed this way four times in 25 bp shifts, thereby reducing the number of regions that scored negative due to a division of the reads into neighboring sections. Overlapping positive windows and positive windows within 100bp for REST and 500bp for Suz12 of each other were merged. The position of the border was refined by shifting the window in one bp steps until the window scored positive (without scoring positive in the negative control sample) starting at a distance of one window-size from the regions border. Genomic positions were transferred to hg19 using the UCSC liftover tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver).

value: Primary diagnosis


title: Scr.siRNA+vehicle_4

value: scrambled siRNA for 48 h

value: vehicle


title: RRBS hematopoietic progenitor cells Promyelocyte_050711

source_name: Generated in vitro from CD34+ above

value: Healthy donor cells


title: RRBS hematopoietic progenitor cells Promyelocte_060611


title: ChiP-Seq SUZ12 APL blast


title: RRBS remission bone marrow APL_11624


title: RRBS hematopoietic progenitor cells Promyelocyte_240511


title: RRBS lin- pMIGR transduced 10

source_name: lin- mouse bone marrow

value: pMIGR transduced lin- BM cells day 10

value: 12-week old