title: Digital Genomic Footprinting assay of Moblized CD34 Primary Cells; DGF.DS12274

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS12274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7422
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1659
****************
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: GSM723022_UW.Mobilized_CD34_Primary_Cells.Digital_Genomic_Footprinting.RO_01535.DGF.DS12274.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS12274.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Mobilized CD34 Primary Cells, Donor RO 01535, Library DGF.DS12274 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.7630
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 242,028,273
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6629
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.6652
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6301
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM723022_UW.Mobilized_CD34_Primary_Cells.Digital_Genomic_Footprinting.RO_01535.DGF.DS12274.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS12274.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Mobilized CD34 Primary Cells, Donor RO 01535, Library DGF.DS12274 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.7635
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 4
BROWSER_TRACK_NAME: MCD34 DGF 35 74
BROWSER_TRACK_DESCRIPTION: UW CD34 Primary Cells Digital Genomic Footprinting Donor RO 01535 Library DGF.DS12274 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 242,028,273
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6629
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.6652
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6301
POISSON_PERCENTILE: 60

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

source_name: flow sorted CD34+ cells from cord blood; DGF.DS12274

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: Unknown


title: Digital Genomic Footprinting assay of Fetal Brain; DGF.DS11872

status: Public on May 12 2011

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS11872
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7450
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2448
****************
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: GSM723021_UW.Fetal_Brain.Digital_Genomic_Footprinting.H-22510.DGF.DS11872.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS11872.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Brain Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Brain, Donor H-22510, Library DGF.DS11872 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.7629
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 219,468,287
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6965
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6871
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9973
IROC_PERCENTILE: 40
POISSON_SCORE: 0.6608
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM723021_UW.Fetal_Brain.Digital_Genomic_Footprinting.H-22510.DGF.DS11872.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS11872.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Fetal Brain, Donor H-22510, Library DGF.DS11872 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.7634
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 4
BROWSER_TRACK_NAME: FB DGF 10 72
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain Digital Genomic Footprinting Donor H-22510 Library DGF.DS11872 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 219,468,287
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6965
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6871
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9973
IROC_PERCENTILE: 40
POISSON_SCORE: 0.6608
POISSON_PERCENTILE: 80

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Brain primary tissue, day 122; DGF.DS11872

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Brain

tag: molecule

value: genomic DNA

tag: disease

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

value: Primary Tissue

value: fetal brain

value: UW

value: fetal

value: 122 days

value: Male

value: Digital Genomic Footprinting

value: Qiagen minElut

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


title: Digital Genomic Footprinting assay of Fetal Heart; DGF.DS12531

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS12531
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7435
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2452
****************
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: GSM723023_UW.Fetal_Heart.Digital_Genomic_Footprinting.H-22662.DGF.DS12531.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS12531.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Heart Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Heart, Donor H-22662, Library DGF.DS12531 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.7627
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 282,391,646
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.5452
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.5269
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5695
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM723023_UW.Fetal_Heart.Digital_Genomic_Footprinting.H-22662.DGF.DS12531.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS12531.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Fetal Heart, Donor H-22662, Library DGF.DS12531 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.7632
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 4
BROWSER_TRACK_NAME: FH DGF 62 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart Digital Genomic Footprinting Donor H-22662 Library DGF.DS12531 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 282,391,646
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.5452
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.5269
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5695
POISSON_PERCENTILE: 40

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

source_name: Fetal Heart primary tissue, day 96; DGF.DS12531

value: Fetal Heart

value: fetal heart

value: 96 days


title: Seedling

status: Public on May 10 2011

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
Seedlings were ~ 7-10 cm in length.
polyA RNA

library_source: transcriptomic

data_processing:
Raw: Original unprocessed and unfiltered data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format.

Count: Raw sequence reads were initially filtered using the Illumina purity filter parameter.  Then, the remaining reads were mapped to a reference containing soybean ribosomal RNA (rRNA) sequences using Bowtie [Langmead et al., Genome Research, (2009)].  The final filtered reads have passed the Illumina purity filter and are devoid of rRNA sequences.  These sequences were used to map against the soybean reference genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net).  Only uniquely mapped reads (i.e. reads that map to one position within the genome) were used for subsequent analysis. Predicted gene models with at least one uniquely mapped read were considered transcriptionally active.  The total mapped read count for all predicted gene models (66,210 genes) were quantified from all sequencing runs combined.

molecule: total RNA

organism: Glycine max

source_name: Whole seedlings six days after imbibition

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., 2010). Seed stages were characterized by seed length as follows: globular stage (0.8-1.1 mm), heart stage (2-2.5 mm), cotyledon stage (3-3.9 mm), and early maturation stage (6-7 mm).  Dry seeds weighed approximately 200 mg.  Seedlings were isolated from seeds imbibed for six days.  Vegetative tissues (trifoliate leaves, roots, stems) were isolated from a mature plant 3-4 months old.  Floral buds consists of unopened buds with no signs of dehisced anthers.

extract_protocol:
Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to the manufacturerâs instructions. Isolated total RNA was treated with RNase-free DNase I (Ambion, Austin, TX) and was subjected to two rounds of poly-A+ RNA selection using oligo-d(T)25 magnetic beads (Dynabeads, Invitrogen, Carlsbad, CA).

Sequencing libraries were prepared using 100 nanograms of twice-selected polyA+ RNA following the Illumina mRNA-Seq Protocol (Part #1004898 Rev. D). Briefly, polyA+ RNA was fragmented and used as template for random-primed cDNA synthesis. Double-stranded cDNAs were treated with T4 and Klenow DNA Polymerases and T4 PNK to generate blunt-end cDNAs. An 'A' base was added to the 3â ends of the phosphorylated blunt-end cDNAs, followed by the ligation of Illumina adapters. Adapter-ligated cDNAs were size selected on an agarose gel for the desired size of ~ 200 bp. Purified cDNAs were amplified by PCR for 15 cycles. Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Amplified cDNA size was determined by agarose gel electrophoresis. Single-end 76-bp reads were generated for each library by the UCLA Genome Sequencing Center (http://gsc.ucla.edu/) using an Illumina Genome Analyzer IIx.

tag: cultivar

value: Williams 82

tag: tissue

value: whole seedlings

tag: developmental stage

value: 6 days after imbibition


title: Root

description:
Roots are devoid of nodules.
polyA RNA

source_name: Roots

value: roots


title: Globular-stage embryo proper region

description: The embryo proper region was captured from six-micron paraffin sections using the Leica AS LMD system.

source_name: Laser-captured embryo proper region from globular-stage embryo

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22Â°C.  For embryo proper and suspensor regions, seed pods with lengths between 0.5 and 1.2 cm containing seeds with globular-stage embryos were collected.  For early maturation seed coat parenchyma tissue, seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were harvested.

extract_protocol: Harvested seeds were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al., Plant Physiol.132. 27-35 (2003)).  The seed compartment was captured from six- to eight-micron sections using a Leica AS LMD System or a Leica LMD6000.  Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).  Three to five nanograms of total RNA was converted to complementary DNA (cDNAs) and amplified using the Nugen Ovation RNA-Seq kit.  Approximately 170 - 220 nanograms of cDNA was used as template for blunt end repairs, 3' A Tailing and adapter ligation following the Illumina mRNA-Seq protocol.  Adapter-ligated cDNAs were size selected on an agarose gel for the desired size of ~ 200 bp. Purified cDNAs were amplified by PCR for 15 cycles. Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Amplified cDNA size was determined by agarose gel electrophoresis. Single-end 76-bp reads were generated for each library by the UCLA Genome Sequencing Center (http://gsc.ucla.edu/) using an Illumina Genome Analyzer IIx.

value: Asgrow A3237

value: embryo proper

value: globular-stage embryo


title: Early-Maturation Stage Whole Seed

description:
Seed lengths ~ 6 â 7 mm.
polyA RNA

source_name: Soybean seeds containing early-maturation stage seeds

value: whole seeds

value: early maturation-stage embryo


title: Dry Whole Seed

description:
Dry seed weight ~ 200 mg.
polyA RNA

source_name: Dry seeds

value: dry


title: Cotyledon Stage Whole Seed

description:
Seed lengths ~ 3 â 3.9 mm.
polyA RNA

source_name: Soybean seeds containing cotyledon-stage embryos

value: cotyledon-stage embryo


title: Early maturation-stage seed coat parenchyma region

description: The seed coat parenchyma region was captured from eight-micron paraffin sections using the Leica LMD6000 system.

source_name: Laser-captured seed coat parenchyma region from early maturation-stage seed

value: seed coat parenchyma layer

value: early maturation-stage seed


title: Globular Stage Whole Seed

description:
Seed lengths ~ 0.8 â 1.1 mm.
polyA RNA

source_name: Soybean seeds containing globular-stage embryos


title: Globular-stage suspensor region

description: The suspensor region was captured from six-micron paraffin sections using the Leica AS LMD system.

source_name: Laser-captured suspensor region from globular-stage embryo

value: suspensor region


title: Cotyledons of seedlings

description:
polyA RNA
Seedlings six days after imbibition.

data_processing:
Raw: Original unprocessed and unfiltered data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format.
Count: Raw sequence reads were initially filtered using the Illumina purity filter parameter.  Then, the remaining reads were mapped to a reference containing soybean ribosomal RNA (rRNA) sequences using Bowtie [Langmead et al., Genome Research, (2009)].  The final filtered reads have passed the Illumina purity filter and are devoid of rRNA sequences.  These sequences were used to map against the soybean reference genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net).  Only uniquely mapped reads (i.e. reads that map to one position within the genome) were used for subsequent analysis. Predicted gene models with at least one uniquely mapped read were considered transcriptionally active.  The total mapped read count for all predicted gene models (66,210 genes) were quantified from all sequencing runs combined.

source_name: Cotyledons of seedlings six days after imbibition

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  Whole seeds were collected for mid-maturation (B1), late maturation (AA1), and dry stages.  For B1 and AA1 stage seeds, the embryo was dissected out of the seed coat, and the axis was manually separated from the cotyledons of the embryo.  The dry seed consists mostly of the cotyledon with a very small fraction contributed from the seed coat or the axis.  For cotyledons from seedlings, seeds were sown on soil and after six days after imbibition, the cotyledons were manually collected.

extract_protocol:
Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to the manufacturerâs instructions. Isolated total RNA was treated with RNase-free DNase I (Ambion, Austin, TX) and was subjected to two rounds of poly-A+ RNA selection using oligo-d(T)25 magnetic beads (Dynabeads, Invitrogen, Carlsbad, CA).
Sequencing libraries were prepared using 100 nanograms of twice-selected polyA+ RNA following the Illumina mRNA-Seq Protocol (Part #1004898 Rev. D). Briefly, polyA+ RNA was fragmented and used as template for random-primed cDNA synthesis. Double-stranded cDNAs were treated with T4 and Klenow DNA Polymerases and T4 PNK to generate blunt-end cDNAs. An "A" base was added to the 3âends of the phosphorylated blunt-end cDNAs, followed by the ligation of Illumina adapters. Adapter-ligated cDNAs were size selected on an agarose gel for the desired size of ~200 bp. Purified cDNAs were amplified by PCR for 15 cycles. Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Amplified cDNA size was determined by agarose gel electrophoresis. Single-end 76-bp reads were generated for each library by the UCLA Genome Sequencing Center (http://gsc.ucla.edu/) using an Illumina Genome Analyzer IIx.

value: cotyledons of seedlings


title: NAc_saline_smallRNA

status: Public on May 13 2011

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing: Sequences were extracted from image files using Firecrest and Bustard. The 3'adaptor sequences were trimmed from the reads, and reads 18-30 nt in length were aligned to all annotated mouse microRNAs from miRBase (www.mirbase.org; version 16) with Bowtie (bowtie-bio.sourceforge.net; version 0.12.7); only perfectly aligning reads were considered for miRNA expression level analysis. A custom Perl script was used to calculate the number of reads aligning to each specific miRNA gene.

organism: Mus musculus

source_name: Nucleus accumbens

growth_protocol: All mice were allowed to acclimate to the colony for at least one week before handling or injections. Mice were kept in the University of Connecticut Health Center animal facility on a 12 h light/dark cycle (lights on 7:00 am to 7:00 pm) and handled in accordance with University of Connecticut Health Center Institutional Animal Care and Use Committee guidelines. To reduce stress from handling during the injections, animals in all groups were handled for 1min/animal/day for 2-3 days prior to the start of injections. During injections, animals were brought into the behavior room to acclimate to the new environment for 45-60 minutes each day before the beginning of experiments.

extract_protocol: TRIzol; PSD sample buffers contained RNASecure

treatment_protocol: Mice were given a saline or cocaine injection and had their locomotor activity monitored for the subsequent 45 minutes. In the experiments in which RNA from NAc lysates was used for miRNA-Seq library preparation, animals were given injections of 20 mg/kg cocaine or saline (10 ml/kg) intraperitoneally each for 7 days. For all other experiments, animals received a lower dose of cocaine (10 mg/kg) on the first and last (7th) day, with the standard 20 mg/kg cocaine dose on days 2-6.

tag: strain

value: Brain

tag: treatment

value: Saline

tag: read length


title: Leaf

description:
Trifoliate young leaves.
polyA RNA

source_name: Trifoliate leaves

value: Williams 82

value: leaves


title: AA1 stage cotyledons

description:
polyA RNA
The two cotyledons weigh between 200 and 350 mg and are completely yellow.

source_name: Embryonic cotyledons from late-maturation (AA1) stage embryos

extract_protocol:
Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to the manufacturerâs instructions. Isolated total RNA was treated with RNase-free DNase I (Ambion, Austin, TX) and was subjected to two rounds of poly-A+ RNA selection using oligo-d(T)25 magnetic beads (Dynabeads, Invitrogen, Carlsbad, CA).

Sequencing libraries were prepared using 100 nanograms of twice-selected polyA+ RNA following the Illumina mRNA-Seq Protocol (Part #1004898 Rev. D). Briefly, polyA+ RNA was fragmented and used as template for random-primed cDNA synthesis. Double-stranded cDNAs were treated with T4 and Klenow DNA Polymerases and T4 PNK to generate blunt-end cDNAs. An "A" base was added to the 3âends of the phosphorylated blunt-end cDNAs, followed by the ligation of Illumina adapters. Adapter-ligated cDNAs were size selected on an agarose gel for the desired size of ~200 bp. Purified cDNAs were amplified by PCR for 15 cycles. Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Amplified cDNA size was determined by agarose gel electrophoresis. Single-end 76-bp reads were generated for each library by the UCLA Genome Sequencing Center (http://gsc.ucla.edu/) using an Illumina Genome Analyzer IIx.

value: embryonic cotyledon


title: B1 stage cotyledons

description:
polyA RNA
The two cotyledons weigh between 150 and 250 mg and are completely green.

source_name: Embryonic cotyledons of mid-maturation (B1) stage embryos


title: Stem

description:
Internodes only.
polyA RNA

source_name: Stems

value: stems


title: Floral Bud

description:
Unopened floral buds.
polyA RNA

source_name: Floral buds

value: floral buds


title: AGO1-associated sRNA_R2

city: Hsin-Chu

first: Wei-Chi

last: Wang

address: Room 112 Zhu-Ming Building, 75 Bo-Ai Street

country: Taiwan

institute: Institute of Bioinformatics and Systems Biology, NCTU

data_processing: We first clustered the same sequences to unique sequence and computed the sequence count. Then we selected the sequences which the first two nucleotides are "AG" in 5' end. Finally, trimmed the 3' adaptor sequences from the selected sequences. For AGO2-un library, it needs to be extracted 36 nts of sequence from 5' end before doing flow of processing raw data.

organism: Arabidopsis thaliana

source_name: Wild type Arabidopsis Col-0

growth_protocol: Arabidopsis plants were grown in a controlled growth room at 23°C ± 1°C with a 12/12 h (light/dark) photoperiod

extract_protocol: Four-week-old Arabidopsis were treated. Leaf tissue (3g) was ground into fine powder for either total RNA extraction (Col-0 WT and ago2), or co-immunoprecipitation (AGO1-IP and AGO2-IP). Total RNA was extracted using Trizol as described by manufacture (Invitrogen). Co-immunoprecipitation by AGO1 antibody or conjugated HA antibody for detecting HA-tagged AGO2 (3F10, Roche) was described by Montgomery et al. (2008). The small RNA libraries were constructed essentially as described by the manufacturer (miRCat® small RNA cloning kit; IDT). Briefly, 10µl of immunoprecipitated small RNAs were first ligated to a 3’-adaptor and were then ligated to a 5’-adaptor after gel purification. The adapted RNAs were reverse-transcribed into cDNA and amplified using a high-fidelity DNA polymerase (PrimeStar HS; Takara) for 22 cycles. The amplified fragments were gel purified and sequenced

treatment_protocol: Four-week-old Arabidopsis were inoculated with either mock (10 mM MgCl2) or Pst) expressing avrRpt2 (R2) at a concentration of 2 x 107 cfu/ml. Inoculated leaves were collected 14 hour after inoculation

tag: age

tag: ecotype

tag: antibody

tag: vendor

value: Dr. Yijun Qi (NIBS, Beijing, China)


title: AGO2-associated sRNA_R2

source_name: Arabidopsis (AGO2::HA:AGO2)

value: sc-805, santa cruz biotech, CA USA


title: AGO2-associated sRNA_mock


title: Heart Stage Whole Seed

description:
Seed lengths ~ 2 â 2.5 mm.
polyA RNA

source_name: Soybean seeds containing heart-stage embryos

value: whole seeds

value: heart-stage embryo


title: AGO1-associated sRNA_mock


title: PrEC_sr_rep2

status: Public on May 09 2011

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

data_processing: Reads were aligned to the human genome (hg18, downloaded from UCSC) using TopHat v0.1.3.  Only uniquely aligned reads were considered "-g 1". In cases where insert size was not available, we assumed an insert of 200bp.  We used a insert size standard deviation of 20bp for all lanes.  In addition to standard human chromosomes, adapter sequences and human ribosomal sequences were included in the initial reference in order to filter out the corresponding reads in subsequent processing steps.

molecule: polyA RNA

source_name: PrEC

growth_protocol: Human primary prostate epithelial cells were purchased from Lonza Inc. (Mapleton IL.), and the prostate cancer cell line LNCaP was obtained from ATCC (Manassas, VA). The PrEC and LNCaP cells were grown in PrEGM media (Lonza Inc. Mapleton IL) and RPMI 1640 containing 10% FBS (Invitrogen, Carlsbad, CA), respectively.

extract_protocol: Messenger RNA (1 microgram) was fragmented at 70 Â°C for 2 min in a fragmentation buffer (Ambion) and converted to single- stranded cDNA using SuperScript II reverse transcriptase (Invitrogen), followed by second-strand cDNA synthesis using Escherichia coli DNA polymerase I (Invitrogen). The double- stranded cDNA was further processed by Illumina mRNA- sequencing Prep kit. Briefly, double-stranded cDNA was end repaired by using T4 DNA polymerase and T4 polynucleotide kinase, monoadenylated using a Klenow DNA polymerase I (3' to 5' exonucleotide activity), and ligated with adaptor oligo mix (Illumina) using T4 DNA ligase. The adaptor-ligated cDNA library was then fractioned on a 4% agarose gel, and a smear corresponding to 300 nt was excised, purified, and PCR amplified (15 cycles) by Pfu polymerase (Stratagene). The PCR product was again size selected on a 4% agarose gel by cutting out the library smear at 300 base pairs. The library was then purified with the Qiaquick Minelute PCR Purification Kit (Qiagen) and quantified with the Agilent DNA 1000 kit on the Agilent 2100 Bioanalyzer following the manufacturerâs instruc- tions. Library (10 nM) was used to prepare flowcells with 100,000â130,000 clusters per lane for analysis on the Illumina Genome Analyzer II.

value: Prostate

tag: cell line

value: PrEC

tag: cell type

value: Normal Cell Line

tag: origin

value: Cell Line

tag: read type (single/paired-end)

tag: read length (bp)

tag: insert size (bp)

tag: insert size standard deviation (bp)


title: PrEC_sr_rep1


title: LNCaP_sr_rep6

source_name: LNCaP

value: LNCaP

value: Cancer Cell Line


title: LNCaP_sr_rep7


title: LNCaP_sr_rep5


title: LNCaP_sr_rep4


title: LNCaP_sr_rep2


title: LNCaP_sr_rep3


title: PrEC_pe_rep2


title: Dry seed

description:
polyA RNA
Whole dry seeds weigh between 100 to 250 mg.

source_name: Whole dry seeds

tag: cultivar

value: whole dry seed


title: PrEC_pe_rep1

tag: tissue


title: KpolDcr1-deltaC

status: Public on May 11 2011

city: San Francisco

first: David

middle: Eric

last: Weinberg

address: 600 16th Street, GH S572F

institute: University of California, San Francisco

description: Small RNA sequencing, 18-30 nt size selection.

data_processing: After removing the adaptor sequences, reads representing the small RNAs were collapsed to a non-redundant set, and 14-30 nt sequences were mapped to the appropriate template (i.e., Renilla luciferase or GFP), allowing no mismatches and recovering all hits.  The processed files are complete 36-nt reads (with adaptor sequences) collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.

organism: Vanderwaltozyma polyspora

source_name: In vitro processing with purified K. polysporus Dcr1-deltaC

extract_protocol: Total RNA was isolated from dicing reactions by phenol extraction and precipitation.  Small-RNA cDNA libraries were prepared as described in Grimson et al. (2008).

treatment_protocol: Standard single-turnover reactions were performed with the following modifications. 500 bp body-labeled dsRNA substrates contained 5'-monophosphate termini, and tRNA was omitted from dsRNA dilutions. For each enzyme, separate reactions were performed using dsRNA corresponding to fragments of the genes encoding Renilla luciferase and green fluorescent protein. Reactions were performed in a volume of 400 ul, with components at the same concentrations as in the standard reactions (protein at a final concentration of 30 nM and RNA at a final concentration of ~45 pg/ul). Reactions were incubated at room temperature for 90 s and quenched by addition to an equal volume of phenol supplemented with 1/10 volume 3 M NaCl and 1/74 volume 0.5 M EDTA, pooling reactions performed with the same enzyme but different dsRNA substrates.

tag: enzyme

value: K. polysporus Dcr1-deltaC


title: LNCaP-3

description: CpG enriched DNA library

data_processing: HPEAK: A Hidden Markov Model (HMM)-based algorithm previously used for Chip-Seq data analysis(http://www.sph.umich.edu/csg/qin/HPeak) was used to locate peaks from mapped reads obtained in each sequencing run.

growth_protocol: Human primary prostate epithelial cells were purchased from Lonza Inc. (Mapleton IL.), and the prostate cancer cell line LNCaP was obtained from ATCC (Manassas, VA).  The PrEC and LNCaP cells were grown in PrEGM media (Lonza Inc. Mapleton IL) and RPMI 1640 containing 10% FBS (Invitrogen, Carlsbad, CA), respectively.

extract_protocol: Methylplex library synthesis and GC-enrichment was obtained through a commercial service at Rubicon Genomics Inc. Ann Arbor, MI. Briefly, fifty nanograms of gDNA from tissues or cells were digested with a proprietary cocktail of methylation-sensitive restriction enzymes and then amplified by PCR with universal primers to create a MethylPlex library that is enriched for methylated DNA.  MethylPlex DNA was then subjected to additional enzymatic treatment to deplete all non-GC-rich DNA sequences, purified and amplified in a second round of PCR.  This created a highly enriched library of fully methylated GC-rich regions of the human genome, representing about 1% of total DNA.  After purification the amplification adaptors were removed by a restriction enzyme digestion.  One and five micrograms of the purified products from each cell line were directly incorporated into the genomic DNA sequencing sample preparation kit procedure of Illumina  (Illumina Inc, San Diego, CA) at the end repair step, skipping the nebulization process.  An adenine base was then added to the purified end repaired products using Klenow exo (3’ to 5’ exo minus) enzyme.  The reaction product was purified, ligated to illumina adaptors with DNA ligase and resolved on a 2% agarose gel.  For LnCaP and PrEC libraries gel pieces were excised at 200 and 400 base pair positions and the DNA was extracted using Qiagen gel extraction kit (Qiagen Inc, Valencia, CA).  Subsequently for all tissue samples 400bp gel cut was utilized.  One ul of this eluate was used as a template in a PCR amplification reaction with Phusion DNA polymerase (Finnzymes, INC., Woburn, MA) to enrich the adapter modified DNA fragments.  The PCR product was purified and analyzed by Bioanalyzer (Agilent Technologies, San Diego, CA) before using it for flow cell generation, where 10nM of library was used to prepare flowcells with approximately 30,000 clusters per lane.


title: LNCaP-1

description: CpG enriched DNA library


title: LNCaP-4

description: CpG enriched DNA library


title: LNCaP_sr_rep1


title: PrEC-4

description: CpG enriched DNA library


title: KpolDcr1-FullLength

source_name: In vitro processing with purified full-length K. polysporus Dcr1

value: K. polysporus Dcr1


title: PrEC-3

description: CpG enriched DNA library


title: PrEC-1

description: CpG enriched DNA library


title: LNCaP

description: CpG enriched DNA library


title: PrEC-2

description: CpG enriched DNA library


title: Sonicated_input_MT

status: Public on May 08 2011

city: New York

first: Brian

last: Dynlacht

address: 550 1st avenue

institute: NYU Langone Medical Center

description: This Sample represents multiple replicates.

data_processing:
Sequence reads within each individual replicate were filtered to remove identical sequence tags since those were likely generated by the LM-PCR amplification process, while identical sequences present after the merging of replicates were retained. The sequence reads were aligned against the mouse mm9 genome build using the Illumina Pipeline, and only tags locating to a single unique position were retained.

Peaks were identified using Qeseq, an algorithm developed in collaboration with Dr. Klugers' bioinformatics group. Setting for all MNase libraries: sigma=50 and cut-off=15. For sonicated libraries, the settings used were: sigma=100 and cut-off=12.

source_name: C2C12 myotubes differentiated for 96h

growth_protocol: C2C12 myoblasts were grown in DMEM containing 10% FBS and harvested at ~40% confluency for MB chromatin. For myotube differentiation, cells were allowed to grow to complete confluence, at which point differentiation was induced by changing the media to DMEM containing 2% horse serum. Induced cells were incubated for 4 days with one change of media (DMEM/2% horse serum) after two days, and myotubes were harvested after 4 days of differentiation.

extract_protocol: Libraries were generated from input chromatin or ChIP-enriched chromatin according to Illumina's standard protocol but using reagents from other companies: DNA end-repair was performed using the End-It DNA repair kit, Epicentre (cat:ER81050); 'A'-overhang generation was performed using Klenow from NED (cat: M0212); adapter ligation was performed using the LigaFast kit from Promega (cat:M8225); and LM-PCR was performed using the Phusion DNA pol master mix from NEB (cat:F-531S). Very stringent quality controls were applied to the libraries: [1] Enrichment of a given site had to be preserved in the libraries in a manner comparable to the original ChIP. 10-12 positive and negative sites were tested for library preparation, [2] The total yield of the LM-PCR had to be ~500 ng, and [3] The size distribution had to be centred around 250 bp for libraries generated from MNase chromatin and around 350 bp for sonicated chromatin with a variation no larger than +/- 75 bp. Libraries that did not pass these criteria were considered substandard and were not used for sequencing.

treatment_protocol: Isolated chromatin was either sonicated to an average size of 250 bp or digested with MNase to yield ~85% mono nucleososomal fragments.

value: myotubes

tag: chromatin preparation method

value: sonication

tag: chip antibody


title: MNAse_digested_input_MB

source_name: Growing C2C12 myoblasts

value: myoblasts

value: MNase digestion


title: MNAse_digested_input_MT


title: H4K12Ac_MT

tag: antibody vendor

value: Millipore

tag: antibody catalog number

tag: antibody lot number


title: H3K36me3_MT

value: Abcam


title: H3K18Ac_MB


title: H3K9Ac_MB


title: H3K18Ac_MT


title: H4K12Ac_MB


title: H3K9Ac_MT


title: H3K27me3_MT

description:
Only 12 cycles of LM-PCR.
This Sample represents multiple replicates.


title: H3K27me3_MB


title: H3K36me3_MB


title: H3K4me3_MT


title: LNCaP-2

description: CpG enriched DNA library


title: H3K4me3_MB


title: H3K4me2_MT


title: H3K4me2_MB


title: H3K4me1_MB


title: PolII_MB

value: Covance


title: H3K4me1_MT


title: PolII_MT


title: Myers_MCF-7_2_None_UW

status: Public on May 07 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:MCF-7_Crawford_protocol.pdf Yale_TFBS(Farnham):MCF-7_Farnham_protocol.pdf UW_Stam:Stam_15_protocols.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

tag: cell

tag: cell organism

value: Human

tag: cell description

value: mammary gland, adenocarcinoma

tag: cell karyotype

value: cancer

tag: cell sex

value: F

tag: replicate

tag: treatment

tag: obtainedby

value: UW


title: Myers_MCF-7_2_None_Stanford

value: Stanford


title: Myers_HEK293_2_None_Stanford

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: embryonic kidney

tag: cell lineage

value: endoderm

value: U


title: Myers_HEK293_1_None_Stanford


title: Sonicated_input_MB

tag: cell line

tag: cell type


title: Myers_MCF-7_1_None_Stanford


title: Myers_NT2-D1_1_None_Stanford

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NT2-D1_protocol.pdf

value: malignant pluripotent embryonal carcinoma (Ntera2)

value: The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line. - ATCC

value: M


title: GRO-seq_E2_160m_rep2

status: Public on May 06 2011

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
GRO-seq in MCF7 cells treated for 160 minutes with E2
molecule: nascent RNA
library strategy: GRO-Seq
library selection: bromo-UTP RNAs

data_processing:
Alignment: Short-reads were aligned to the human reference genome (hg18, NCBI36), including autosomes, X-chromosome, and one complete copy of an rDNA repeat (GenBank ID: U13369.1).  The SOAP2 software package (Li et al., 2009) was used to align reads with the following options: (1) all non-unique mappings were removed (-r 0), (2) three mismatches were allowed in each mapped read (-v 3), (3) low-quality reads with more than 10 ambiguous bases were removed (-N 10), and (4) for reads failing to align over the entire length of the read, the first 32 bp was used (-l 32).  SOAP2 output was processed using custom Perl scripts, and imported into R for most the analysis.

Detecting E2 Dependent Changes: We detected estrogen dependent changes in gene expression using a method that samples the variation between two biological replicates and identifies genes in the different treatment conditions that fall outside of this expected variation.  To determine E2-dependent changes in longer transcripts, we began by counting reads in the window between +1 kb and +13 kb relative to the TSS.  This window was chosen for the following three reasons: (1) it prevented the counting of reads originating from RNA polymerases engaged at the promoter, but that are not productively elongating (i.e. paused polymerases) (Core et al., 2008), (2) it captured the region whose transcripts will be up-regulated at 10 min. of E2 treatment, assuming that Pol II elongation rates may be as low as ~1.2-1.3 kb/min  (Ardehali and Lis, 2009), and (3) using this window over all points in the time course allowed the results to be compared between time points directly.  Next, regulation was determined using the edgeR package (v.1.4.1) (Robinson et al., 2010) for R/Bioconductor (Durinck et al., 2009; Kauffmann et al., 2009; Ritchie et al., 2009).  The edgeR package was designed to detect changes in gene expression using short-read "digital" data from a small number of biological replicates.  First, we used edgeR to fit the parameters of a negative binomial distribution to the variation in read counts between combinations of the two biological replicates.  Subsequently, this model was used in a negative binomial-based “exact test” (Robinson et al., 2010; Robinson and Smyth, 2008).  This “exact test” assigns a p-value to each gene which reflects the probability that the observed change in read counts (between two different biological conditions) will occur given the level of global variation observed between biological replicates (Robinson et al., 2010).  We used EdgeR to detect changes between the vehicle control and either the 10, 40, and 160 minute time points separately in annotated genes.  P-values returned by edgeR were adjusted for multiple hypotheses testing using the false discovery rate (FDR) correction in R (function p.adjust).  Transcripts with a FDR corrected q-value lower than 0.001 (approximate FDR under the model ~0.1%) were selected for further analysis.

The "GSE27463_RefSeq.all.tsv.gz" file (attached to the Series record) includes processed expression levels and FDR corrected q-values for all refseq genes (not just those that were found to be regulated using the statistical analysis reported in our paper).

growth_protocol: MCF-7 human breast adenocarcinoma cells were kindly provided by Dr. Benita Katzenellenbogen (University of Illinois, Urbana-Champaign).  The cells were maintained in minimal essential medium (MEM) with Hank’s salts (Sigma) supplemented with 5% calf serum (CS), sodium bicarbonate, penicillin/streptomycin and gentamicin.  Cells were plated for experiments in phenol red-free MEM (Sigma) supplemented with 5% charcoal-dextran treated calf serum (CDCS) prior to 17-b estradiol (E2) treatment.

extract_protocol: Nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of NTPs and 0.5% Sarkosyl in run-on buffer to allow a run-on of ~100 nucleotides.  The reaction was stopped by incubation with DNase I, followed by incubation with proteinase K.  Newly synthesized nascent RNAs were isolated by acid phenol-chloroform extraction, followed by ethanol precipitation.  After re-dissolving, the isolated RNAs were base-hydrolyzed with 0.2 N NaOH and the reaction was neutralized by the addition of 500 mM Tris×HCl, pH 6.8.  The base-hydrolyzed RNAs were subjected to BioRad P-30 chromatography for buffer exchange.  The isolated and base hydrolyzed RNAs were subjected to three bead binding steps where the bromo-UTP incorporated nascent RNAs (BrU-RNAs) were enriched using anti-bromo-deoxy-U antibody conjugated beads.  After each binding step, the BrU-RNAs were eluted, acid phenol-chloroform extracted, and precipitated.  Each of the three bead binding steps also contained additional manipulations.  After the first binding step, the BrU-RNAs were treated with tobacco acid pyrophosphatase to remove 5’-methyl guanosine caps, then with T4 polynucelotide kiase to remove 3’-phosphate group at low pH.  The BrU-RNAs were treated with T4 PNK again at high pH in the presence of ATP to add 5’-phosphate group.  5’-adaptors were added to the end-repaired BrU-RNAs by T4 RNA ligase.  After the addition of the 5’-adaptors, the BrU-RNAs were subjected to the second bead binding step to remove excessive adaptors and further enrich the BrU-RNAs.  After the second bead binding step, 3’ adaptors were ligated by T4 RNA ligase, followed by the third bead binding.  The affinity purified 5’- and 3’-adaptor-ligated BrU-RNAs were reverse transcribed into cDNAs usining annealed RT-oligo and Super Scripts III reverse transcriptase.  The RNAs were then degraded by incubation with RNase cocktail.  The cDNAs were then subjected to PCR-amplification using Phusion DNA Polymerase with small RNA PCR primers.  Samples of the amplified cDNAs were analyzed on a 2% agarose gel to assess yield and size.  The remaining samples were extracted by phenol:chloroform:isoamyl alcohol (25:24:1).  The purified cDNAs were run on a 6% native PAGE gel for further purification. The gel was stained with SYBRE gold and the cDNAs were visualized using a Dark Reader transilluminator.  The bands between size 100 bp to 250 bp were cut out and the cDNAs were eluted from the gel by incubating overnight in elution buffer.  The eluted cDNA were extracted again with phenol-chloroform, resuspended in water, and quantified using a Nanodrop.  The final libraries were then sequenced using an Illumina Genome Analyzer.

treatment_protocol: MCF-7 cells were plated at a density of 1 x 106 cells per 15 cm diameter dish in phenol-red free MEM + 5% CDCS, using one dish per experimental condition.  After three days, the cells were treated with 100 nM E2 as indicated and washed three times with ice cold PBS.

tag: treatment time


title: GRO-seq_E2_160m_rep1


title: GRO-seq_E2_10m_rep1

description:
GRO-seq in MCF7 cells treated for 10 minutes with E2
molecule: nascent RNA
library strategy: GRO-Seq
library selection: bromo-UTP RNAs


title: GRO-seq_E2_40m_rep1

description:
GRO-seq in MCF7 cells treated for 40 minutes with E2
molecule: nascent RNA
library strategy: GRO-Seq
library selection: bromo-UTP RNAs


title: GRO-seq_E2_10m_rep2


title: GRO-seq_E2_40m_rep2


title: GRO-seq_Vehicle_rep1

description:
GRO-seq in untreated MCF7 cells
molecule: nascent RNA
library strategy: GRO-Seq
library selection: bromo-UTP RNAs


title: GRO-seq_Vehicle_rep2


title: seq-NA_N2_L3_1_N2.3PK-EGS [input DNA]

status: Public on May 02 2011

city: Chapel Hill

first: Tristan

last: De Buysscher

state: NC

address: CB# 3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description: input DNA

data_processing:
BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.
ChIP-Seq MACS Peak-calling:JL:1. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters: tagSize = 25 mfold = 10,30 genomeSize = 90000000 bandwidth = 300 pvalue = 1e-5
Processed data file build: ce6

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP. http://wiki.modencode.org/project/index.php/Worm_L3_extraction:JL:PK1

extract_protocol: Libraries were prepared according to Illumina's instructions for "Preparing Samples for ChIP Sequencing of DNA", with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase.  A's were then added to the 3' ends of the fragments using Kelow fragment (3'  5' exo minus). Paired-end adapters were then ligated onto the ends of the fragments.  DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA.

treatment_protocol: Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (20-30 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP. http://wiki.modencode.org/project/index.php/Worm_L3_Extraction_with_Dual_Crosslinking:JL:IL1

tag: tissue

value: whole body

tag: strain

tag: Stage


status: Public on May 04 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
ProteinG beads background precipitation BJ fibroblasts
wig file: density graphs of raw signal (150bp)

data_processing: Reads matching have been performed using Corona SOLiD matching tool versus hg18 reference genome allowing up to 6 mismatchs. Conversion to .BED files have been done with match2bedFile_converter.pl script from SOLiD ChIP-Seq_Util_1.0.0 tool. Density graphs of raw signal (.wig files) have been generated by computing the start position of the reads in 150bp  windows sliding by a 15bp step for uniquely placed reads, no more than 1 read per position for each strand, reads in both strands mixed, normalized to the total number of matched reads; printed if count >2. Peaks identification (.bed files) have been generated with SISSRs v1.4 software with .bed input uniquely aligned reads and parameters:  proteinG IP as background, pvalue 0.001 or 0.05, no more than 1 read per position (-a), fragment length 150bp.

source_name: Transformed BJ fibroblasts (SV40 largeT, hTERT, H-ras V12, according to Hahn et.al. Nature 1999)

growth_protocol: DMEM+10%SVF+Péni/Strepto, 37°C, 5%CO2, ambiant O2

extract_protocol:
ChIP protocol: 1% formaldehyde crosslink, DNA shearing by sonication in 1% SDS buffer, IP on proteinG sepharose beads in 0.1%SDS-1%Triton buffer, DNA purification by phenol-chloroforme extraction
ChIP_protocol_chromatin_amount: 175μg
ChIP_protocol_bead_type: Protein G Sepharose 4 Fast Flow, GE Healthcare
ChIP_protocol_bead_amount 0.25 mL
ChIP_protocol_antibody_amount25μg
Applied Biosystems SOLiD standard fragment library
barcoded fragment libraries were prepared with SOLiD™ Fragment Library Construction Kit using with SOLiD™ Fragment Library Barcoding Kit
Starting material 100 ng ChIP DNA
Libraries were size selected on agarose gels (150 to 200 nucleotides)

tag: culture

value: confluent, not synchronized cells

tag: chip antibody

tag: chip antibody provider

tag: chip antibody catalog


title: TRF2 polyclonal ChIP BJ fibroblasts

description:
TRF2 polyclonal ChIP BJ fibroblasts
bed files : SISSRs v1.4 peaks (pvalue=0.001 and 0.05) ;  wig file: density graphs of raw signal (150bp)

value: TRF2 polyclonal

value: Imgenex


title: seq-NA_N2_L3_1_N2.2PK-EGS [input DNA]

description: input DNA


title: seq-WA30534819_H3K4me3_N2_MXemb_2

description:
input control: GSM706160
Chromatin IP against H3K4me3. http://wiki.modencode.org/project/index.php/Worm_Chromatin_Immunoprecipitation:JL:5

growth_protocol: Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. http://wiki.modencode.org/project/index.php/Worm_embryo_growth_and_harvest:JL:5

treatment_protocol: Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. http://wiki.modencode.org/project/index.php/Worm_embryo_extraction:JL:2

tag: chip antibody supplier

value: Wako

tag: chip antibody catalog#


title: seq-WA30534819_H3K4me3_N2_MXemb_1

description:
input control: GSM706159
Chromatin IP against H3K4me3. http://wiki.modencode.org/project/index.php/Worm_Chromatin_Immunoprecipitation:JL:5


title: seq-SDQ0820_EPC1_N2_L3_2_EGS

description:
input control: GSM713235
Chromatin IP against EPC1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: SDQ0820 EPC1

value: SDI

tag: chip antibody lot#


title: seq-SDQ4663_RPC1_N2_MXemb_2_A_EE9_KI031

description:
input control: GSM706160
Chromatin IP against RPC1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:KI3


title: seq-SDQ4526_SFC1_N2_MXemb_1_A_EE8_KI034

description:
input control: GSM706160
Chromatin IP against SFC1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:KI3

value: SDQ4526 SFC1


title: seq-SDQ4663_RPC1_N2_MXemb_1_A_EE8


title: Myers_MCF-7_1_None_UW

tag: cell

tag: cell organism

value: Human

tag: cell description

value: mammary gland, adenocarcinoma

tag: cell karyotype

value: cancer

tag: cell sex

value: F

tag: replicate


title: seq-SDQ0820_EPC1_N2_L3_1_EGS

description:
input control: GSM713233
Chromatin IP against EPC1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-SDQ4526_SFC1_N2_MXemb_2_A_EE9_KI035


title: seq-WA30932379_H3K9ac_N2_L3_1

description:
input control: GSM706164
Chromatin IP against H3K9ac. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

growth_protocol: About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage. http://wiki.modencode.org/project/index.php/Worm_L3_growth_and_harvest:JL:PK1

treatment_protocol: Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP. http://wiki.modencode.org/project/index.php/Worm_L3_extraction:JL:PK1


title: seq-SDQ4470_TAG315_N2_MXemb_1_A_EE8_KI032

description:
input control: GSM706160
Chromatin IP against TAG315. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:KI3


title: TRF1 monoclonal ChIP BJ fibroblasts

description:
TRF1 monoclonal ChIP BJ fibroblasts
bed files : SISSRs v1.4 peaks (pvalue=0.001 and 0.05) ;  wig file: density graphs of raw signal (150bp)

value: TRF1 monoclonal

value: Abcam


title: TRF2 monoclonal ChIP BJ fibroblasts

description:
TRF2 monoclonal ChIP BJ fibroblasts
bed files : SISSRs v1.4 peaks (pvalue=0.001 and 0.05) ;  wig file: density graphs of raw signal (150bp)

value: TRF2 monoclonal


title: seq-SDQ4470_TAG315_N2_MXemb_2_A_EE9_KI033


title: seq-WA30534819_H3K4me3_N2_L3_1

description:
input control: GSM706164
Chromatin IP against H3K4me3. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-WA30534819_H3K4me3_N2_L3_2

description:
input control: GSM706167
Chromatin IP against H3K4me3. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-SDQ3599_DPL1_N2_L3_2

description:
input control: GSM706164
Chromatin IP against DPL1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: SDQ3599 DPL1


title: seq-SDQ3590_EFL1_N2_L3_1

description:
input control: GSM706161
Chromatin IP against EFL1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: SDQ3590 EFL1

value: G3048-110A01 Animal number SDQ3590


title: seq-SDQ3599_DPL1_N2_L3_1

description:
input control: GSM706161
Chromatin IP against DPL1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: whole body


title: seq-SDQ2370_LIN53_N2_L3_2

description:
input control: GSM706164
Chromatin IP against LIN53. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: SDQ2370 LIN53


title: seq-LPAR109_H4tetraac_109_N2_L3_2

description:
input control: GSM706167
Chromatin IP against H4tetraac. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: LPAR109 H4tetraac:109

value: Lake Placid Bio


title: seq-LPAR109_H4tetraac_109_N2_L3_1

description:
input control: GSM706164
Chromatin IP against H4tetraac. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-SDQ3590_EFL1_N2_L3_2

description:
input control: GSM706164
Chromatin IP against EFL1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-JL00002_SDC3_N2_L3_2

description:
input control: GSM706166
Chromatin IP against SDC3. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: Covance


title: seq-BK00001_HTZ1_N2_L3_1

description:
input control: GSM706162
Chromatin IP against HTZ1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: Bill Kelly


title: seq-JA00001_HTZ1_N2_L3_3

description:
input control: GSM706167
Chromatin IP against HTZ1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: Julie Ahringer


title: seq-WA30932379_H3K9ac_N2_L3_2

description:
input control: GSM706167
Chromatin IP against H3K9ac. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: Wako


title: seq-JA00001_HTZ1_N2_L3_2

description:
input control: GSM706166
Chromatin IP against HTZ1. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-JA00011_LIN35_N2_L3_4

description:
input control: GSM706164
Chromatin IP against LIN35. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-BH00003_LIN37_N2_L3_1

description:
input control: GSM706161
Chromatin IP against LIN37. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: Bob Horvitz


title: seq-BH00005_LIN9_N2_L3_1

description:
input control: GSM706161
Chromatin IP against LIN9. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-BH00005_LIN9_N2_L3_2

description:
input control: GSM706164
Chromatin IP against LIN9. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-JA00011_LIN35_N2_L3_2

description:
input control: GSM706161
Chromatin IP against LIN35. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-BH00001_LIN52_N2_L3_1

description:
input control: GSM706161
Chromatin IP against LIN52. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-BH00001_LIN52_N2_L3_2

description:
input control: GSM706164
Chromatin IP against LIN52. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-BH00004_LIN54_N2_L3_2

description:
input control: GSM706164
Chromatin IP against LIN54. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-BH00004_LIN54_N2_L3_1

description:
input control: GSM706161
Chromatin IP against LIN54. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-AR0144_H3_144_N2_L3_2

description:
input control: GSM706165
Chromatin IP against H3:144. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-BH00003_LIN37_N2_L3_2

description:
input control: GSM706164
Chromatin IP against LIN37. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-SDQ2370_LIN53_N2_L3_1

description:
input control: GSM706161
Chromatin IP against LIN53. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

value: SDI


title: seq-AR0144_H3_144_N2_L3_1

description:
input control: GSM706161
Chromatin IP against H3:144. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-JL00002_SDC3_N2_L3_3

description:
input control: GSM706163
Chromatin IP against SDC3. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-AB1791_H3_N2_L3_7

description:
input control: GSM706166
Chromatin IP against H3. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2


title: seq-NA_N2_L3_IL-1 [input DNA]

description:
C. elegans N2 L3 input control.

Input lanes for ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus.

Contributors: Julie Ahringer, Isabel Latorre.

data_processing:
BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.
Processed data file build: ce6

source_name: Control sample from L3 stage N2 worms, whole body

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

treatment_protocol: Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.


title: seq-NA_N2_L3_1_mE1 [input DNA]


title: seq-NA_N2_L3_IL-2 [input DNA]


title: seq-NA_N2_L3_1_mE5 [input DNA]


title: normal_N23

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

description: ds cDNA from polyA selected mRNA

data_processing: Alignment: Sequence reads were obtained and mapped to the hg18 (March, 2006) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained

source_name: Prostate matched normal of C23

extract_protocol:
Total RNA was extracted using Trizol and mRNA enriched using oligo(dT) capture and ds cDNA was prepared. The ds cDNA was fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors. Average insert size is 150 bp (median = 152 bp), standard deviation is 38 bp.
Illumina mRNA-seq protocol

treatment_protocol: Tissue was extracted from patients before treatment

value: Normal prostate tissue

tag: tumor stage

tag: sequencing protocol

value: paired-end, 36-mer sequencing


title: seq-NA_N2_L3_3 [input DNA]

tag: tissue

tag: strain


title: normal_N19

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C19


title: normal_N11

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C11


title: seq-AB1791_H3_N2_L3_2

description:
input control: GSM706165
Chromatin IP against H3. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

tag: Stage

value: Abcam


title: normal_N09

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C09


title: normal_N13

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C13


title: seq-NA_N2_L3_1_mE6 [input DNA]


title: normal_N03

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C03


title: normal_N06

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C06


title: carcinoma_C39

description: ds cDNA from polyA selected mRNA

source_name: Prostate adenocarcinoma

value: Prostate cancer tissue

value: Gleason score 7


title: carcinoma_C40

description: ds cDNA from polyA selected mRNA

value: Gleason score 6


title: normal_N02

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C02


title: seq-AB1791_H3_N2_L3_1

description:
input control: GSM706161
Chromatin IP against H3. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

tag: chip antibody


title: seq-NA_N2_L3_2 [input DNA]


title: carcinoma_C33

description: ds cDNA from polyA selected mRNA


title: carcinoma_C29

description: ds cDNA from polyA selected mRNA


title: carcinoma_C23

description: ds cDNA from polyA selected mRNA

value: Gleason score 8


title: carcinoma_C18

description: ds cDNA from polyA selected mRNA


title: seq-NA_N2_MXemb_6_EE8 [input DNA]

description:
C. elegans N2 L3 input control.

Input lanes for ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus.

Contributors: Jason Lieb, Morten Jensen.

source_name: Control sample from mixed embryo N2 worms, whole body

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

treatment_protocol: Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

value: whole body

value: mixed stages


title: carcinoma_C27

description: ds cDNA from polyA selected mRNA


title: carcinoma_C37

description: ds cDNA from polyA selected mRNA


title: normal_N15

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C15


title: carcinoma_C15

description: ds cDNA from polyA selected mRNA


title: carcinoma_C13

description: ds cDNA from polyA selected mRNA


title: carcinoma_C09

description: ds cDNA from polyA selected mRNA


title: carcinoma_C08

description: ds cDNA from polyA selected mRNA


title: carcinoma_C16

description: ds cDNA from polyA selected mRNA


title: carcinoma_C11

description: ds cDNA from polyA selected mRNA


title: normal_N08

description: ds cDNA from polyA selected mRNA

source_name: Prostate matched normal of C08


title: carcinoma_C03

description: ds cDNA from polyA selected mRNA


title: carcinoma_C05

description: ds cDNA from polyA selected mRNA


title: carcinoma_C02

description: ds cDNA from polyA selected mRNA


title: carcinoma_C06

description: ds cDNA from polyA selected mRNA


title: M2-p300

status: Public on Apr 30 2011

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

description: p300 binding in mutant liver

data_processing: We obtained approximately 124 millions reads of 36 nt uniquely aligning to mouse genome (mm8, UCSC genome database). Then, we extended 36 nt reads to 120 bp based on the average size of nucleosomal DNA fragments. Nucleosome positions were defined as genomic regions containing at least four extended reads, based on the average reads at each sequencing locus with 20% FDR. ChIP-Seq binding regions were identified with an input-directed algorithm GLITR.

source_name: Mutant liver

extract_protocol: Native chromatin without cross-linking was released from nuclei by incubation in the buffer containing 0.1 N CaCl2, and then digested with MNase for 15 min (partial digestion) and 30 min (full digestion). Mononucleosomal DNA was collected and pooled from both partial and full digestion of four mouse livers. Mononucleosomal and undigested genomic DNA were purified with the Qiagen PCR purification kit after the digestion with protease K. For DNA sequencing, nucleosomal DNA was further modified following the Illumina sequencing protocol and sequenced with an Illumina Genome Analyzer. For ChIP-Seq, after crosslinking, chromatin was sonicated to reduce the size of DNA to 100~1,000 bp, which was further modified for Illumina sequencing as described above.

value: liver


title: C1-CBP

description: CBP binding in control liver

source_name: Control liver

value: CBP


title: hp1-f

description: hp1 binding in mutant liver


title: hp1

description: hp1 binding in control liver


title: M21-CBP

description: CBP binding in mutant liver


title: carcinoma_C19

description: ds cDNA from polyA selected mRNA

value: Gleason score 9


title: C1-p300

description: p300 binding in control liver


title: FoxA2 Liver4

description: FoxA2 Liver4


title: Female Bur-0 x Male Col-0 RNA

city: Vienna

first: Marc

last: Rehmsmeier

address: Dr. Bohr-Gasse 3

country: Austria

institute: GMI - Gregor Mendel Institute of Molecular Plant Biology GmbH

description: Total RNA from F1 seeds

data_processing:
SNP windows: TAIR8 chromosome sequences were downloaded from TAIR   (ftp.arabidopsis.org/home/tair/Genes/TAIR8_genome_release/tair8.at.chromosomes.fas,   chromosomes 1 to5), together with the TAIR8 genome annotation   (ftp.arabidopsis.org/home/tair/Genes/TAIR8_genome_release/TAIR8_gff3/TAIR8_GFF3_ge   nes.gff). Bur-0 SNPs [Ossowski et al. Genome Res. 2008], 569,859 SNPs in total for chromosomes 1 to 5, were downloaded   from the 1001 genomes website    (http://1001genomes.org/data/MPI/MPIOssowski2008/releases/2008_06_05/strains/Bur-   0/Bur-0_homozygous_snp_080605.txt). For each of the 569,859 Col-0/Bur-0 SNPs, we   extracted a 71nt genomic window around the SNP (SNP position plus/minus 35nt) from the   Col-0 reference sequence and annotated it as a Col-0 window. The nucleotide in the SNP was   then replaced by the Bur-0 variant and the resulting sequence annotated as a Bur-0 window.
Mapping: A suffix array was constructed from the union of Col-0 and Bur-0 windows with the mkvtree   program (http://www.vmatch.de/) [Abouelhoda et al. Journal of Discrete Algorithms 2004]. RNAseq reads were mapped with the vmatch program   (http://www.vmatch.de/) in both forward and reverse complementary orientation (options -d   and -p), allowing up to two mismatches (option -h 2), requiring the whole read to map (option   -l 36), and generating maximal substring matches that are unique in the Col-0/Bur-0 window   dataset (option -mum cand). This procedure resulted in 8,576,779 matches for Bur-x-Col   reads (out of 102,705,076 total reads) and 6,773,239 matches for Col-x-Bur reads (out of   122,367,092 total reads).

source_name: 4 DAP F1 seed

growth_protocol: Plants were grown in a growth cabinet under long day photoperiods (16 h light and 8 h dark) at 22°C. After 10 days, seedlings were transferred to soil and plants were grown in a growth chamber at 60 % humidity and daily cycles of 16 h light at 22°C and 8 h darkness at 18°C.

extract_protocol: Sequencing libraries were prepared with the Illumina mRNA-Seq Sample Prep Kit (Illumina, San Diego, USA) according to the manufacturer’s instructions. After adapter ligation library fragments of ~250 bp were isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 15 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Genome Analyzer IIx following the manufacturer's protocols. 4 lanes per sample were sequenced, at a read length of 36 basepairs.

treatment_protocol: For reciprocal crosses, designated female partners were emasculated, and the pistils hand-pollinated two days after emasculation.

tag: parents

value: Male Col-0, Female Bur-0

tag: generation

value: seeds

tag: age

value: 4 DAP


title: FoxA2 Liver5

description: FoxA2 Liver5


title: Female Col-0 x Male Bur-0 RNA

description: Total RNA from F1 seeds

value: Female Col-0, Male Bur-0


title: carcinoma_C07

description: ds cDNA from polyA selected mRNA


title: Nucleosomal DNA_Mnase-Seq

description: 3WT Nuc Map


title: 24hrs_0μM_IPTG_2mM_3-AT_plates

status: Public on Apr 28 2011

city: Worcester

first: Scot

last: Wolfe

state: MA

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

library_source: synthetic

data_processing: The sequences from each B1H experiment were labeled using a 3bp barcode.  The raw reads were parsed and assigned to the appropriate data set, based on the barcode sequence.  Furthermore, only reads that matched the expected constant region, TGTACCGCNNNNNNATTTTTNNNNTGGCCAGCT, (N's indicate randomized positions) , except for up to two mismatches at non-randomized positions, were assigned to the appropriate data sets.  All of the reads that did not meet these criteria were placed in the 'unassigned' set.  Reads with randomized regions that included an 'N' character were also placed in the 'unassigned' set.  The *.uniqSeq_2_counts.tsv files indicate the number of times each unique  6bp long randomized binding site was observed.  The single liquid media experiment, 4hrs_50μM_IPTG_5mM_3-AT_liquid, was sequenced in a different lane together with other multiplexed experiments.  It's barcode was GAT.  The 6bp upstream of the constant region ATTTTT were parsed out and used to generate the corresponding *.uniqSeq_2_counts.tsv file.

molecule: other

organism: synthetic construct

source_name: B1H selection

extract_protocol: After each selection, all of the cells were scraped off the plate.  The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR.  The PCR products from different experiments were digested with different restriction enzymes  in the first step of uniquely encoding sequences from different experiments.  The restriction enzyme fragments were then barcoded, pooled and sequenced using a Illumina Genome Analyzer IIx machine.  See the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289 for a more detailed description of the experimental protocol employed for each selection.

tag: 3-at concentration (mm)

tag: duration of experiment (hours)

tag: media

value: agarose gel


title: 24hrs_0μM_IPTG_0.5mM_3-AT_plates


title: 24hrs_10μM_IPTG_0.5mM_3-AT_plates

tag: iptg concentration (μm)


title: 24hrs_0μM_IPTG_1mM_3-AT_plates


title: 24hrs_10μM_IPTG_1mM_3-AT_plates


title: 12hrs_50μM_IPTG_2mM_3-AT_plates


title: 18hrs_50μM_IPTG_2mM_3-AT_plates


title: 18hrs_0μM_IPTG_0.5mM_3-AT_plates


title: 18hrs_0μM_IPTG_1mM_3-AT_plates


title: 18hrs_10μM_IPTG_0.5mM_3-AT_plates


title: 12hrs_50μM_IPTG_1mM_3-AT_plates


title: 18hrs_0μM_IPTG_2mM_3-AT_plates


title: 18hrs_50μM_IPTG_0.5mM_3-AT_plates


title: 12hrs_50μM_IPTG_0.5mM_3-AT_plates


title: 18hrs_10μM_IPTG_2mM_3-AT_plates


title: 12hrs_10μM_IPTG_2mM_3-AT_plates


title: 18hrs_50μM_IPTG_1mM_3-AT_plates


title: 12hrs_0μM_IPTG_1mM_3-AT_plates


title: 12hrs_10μM_IPTG_0.5mM_3-AT_plates


title: 12hrs_0μM_IPTG_2mM_3-AT_plates


title: 18hrs_10μM_IPTG_1mM_3-AT_plates


title: 8hrs_50μM_IPTG_2mM_3-AT_plates


title: 12hrs_0μM_IPTG_0.5mM_3-AT_plates


title: 8hrs_50μM_IPTG_0.5mM_3-AT_plates


title: 8hrs_10μM_IPTG_2mM_3-AT_plates


title: 12hrs_10μM_IPTG_1mM_3-AT_plates


title: 8hrs_10μM_IPTG_1mM_3-AT_plates


title: 8hrs_10μM_IPTG_0.5mM_3-AT_plates


title: 8hrs_0μM_IPTG_2mM_3-AT_plates


title: 8hrs_50μM_IPTG_1mM_3-AT_plates


title: 8hrs_0μM_IPTG_1mM_3-AT_plates


title: 4hrs_50μM_IPTG_2mM_3-AT_plates


title: 4hrs_10μM_IPTG_2mM_3-AT_plates


title: 4hrs_50μM_IPTG_0.5mM_3-AT_plates


title: 4hrs_50μM_IPTG_1mM_3-AT_plates


title: 24hrs_10μM_IPTG_2mM_3-AT_plates


title: 4hrs_50μM_IPTG_5mM_3-AT_liquid

description: The liquid media selection was performed by the Stormo lab, all other selections were performed by the Wolfe lab

source_name: B1H randomized library

value: liquid media


title: 4hrs_0μM_IPTG_2mM_3-AT_plates


title: 4hrs_10μM_IPTG_1mM_3-AT_plates


title: 4hrs_10μM_IPTG_0.5mM_3-AT_plates


title: 4hrs_0μM_IPTG_0.5mM_3-AT_plates


title: 24hrs_50μM_IPTG_1mM_3-AT_plates


title: 4hrs_0μM_IPTG_1mM_3-AT_plates


title: HeLa_hCAGE_standard_rep2

city: Yokohama

first: Hideya

last: Kawaji

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Omics Science Center

country: Japan

institute: RIKEN

description: HeLa.Std.5000ng.2nd_20100614.Riken2.fc1.ch9

data_processing: After the filtering with filterSMS in HeliSphere package, the obtained reads are aligned to the human genome (hg18) with indexDPgenomic and only the alignments with the best alignment score in unique location are selected. Gene expression counts (Matrix hCAGE_non-normalized) represent calcurated from the read counts in the +/- 500bp region from RefSeq. The expression counts are normalized as tpm (tags per million), where expression counts are divided by the total number of mapped reads and multiplied by one million (hCAGE_normalized.txt).

source_name: HeLa cell line

growth_protocol: THP-1 cells were cultured in RPMI1640 (Invitrogen) supplemented with 10% FBS, Penicillin/Streptomycin (Invitrogen), 10 mM HEPES (Invitrogen), 1 mM sodium pyruvate and 50 ÂµM 2-mercaptoethanol.   HeLa cells were cultured in Eagleâs MEM (Invitrogen) supplemented with 10% FBS, 1% NEAA (Invitrogen) and Penicillin/Streptomycin.

extract_protocol: First strand cDNA is generated from total RNA using an excess of random primer. 5’ end complete first strand cDNAs are captured for capped RNAs. First strand cDNA is polyA tailed and blocked and then loaded directly onto the HeliScope flow cell for sequencing. MPG beads are used in cap-trapping step for the standard protocol (for starting from 5ug or more total RNA), and DYNAL M270 streptavidin magnetic beads (Life Technologies) are used for low quantity version (less than 1ug). Further details are written in the manuscript.

tag: starting total rna

value: 5Âµg

tag: cell line

value: HeLa


title: 8hrs_0μM_IPTG_0.5mM_3-AT_plates


title: 24hrs_50μM_IPTG_2mM_3-AT_plates


title: HeLa_hCAGE_standard_rep3

description: HeLa.Std.5000ng.3rd_20100614.Riken2.fc2.ch7


title: THP1_hCAGE_standard_rep3

description: THP1.Std.5000ng.3rd_20100614.Riken2.fc2.ch22

source_name: THP-1 cell line


title: N6_initial_library

description: The reads obtained by sequencing the entire library of randomized sites before selection.  The Illumina Bustard base calling software was only run on the cycles expected to correspond to the randomized portion of each read in order to yield more reads.  The first 4 bp of these reads correspond to the key region, the last 6bp correspond to the randomized binding site region.


title: 28bp_48hrs_10μmM_IPTG_5mM_3-AT_plates

description: This selection was performed by the Stormo lab

library_source: other

data_processing: The sequences from each B1H experiment were labeled using a barcode.  The raw reads were parsed and assigned to the appropriate data set, based on the barcode sequence.  Only reads that matched the expected constant region, or 'barcode' exactly were considered.  N's correspond to randomized positions.  In the case of samples bp_48hrs_10μM_IPTG_0mM_3-AT_plates and 28bp_48hrs_10μM_IPTG_5mM_3-AT_plates, mismatches were allowed at the second position only, which was expected to be a ligated 'T'.  In the case of the N28_initial_library, the last two positions of the expected sequence ('GC'), or 'barcode,' were allowed allowed to be mismatches.

extract_protocol: A prey library containing a 28bp long randomized region was used for this selection.  A prey library containing a 6bp long randomized region immediately adjacent to the consensus site for finger 1 was used for most of the other selections.  After each selection, all of the cells were scraped off the plate.  The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR.  The PCR products from different experiments were digested with different restriction enzymes  in the first step of uniquely encoding sequences from different experiments.  The restriction enzyme fragments were then barcoded, pooled and sequenced using a Illumina Genome Analyzer IIx machine.  See the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289 for a more detailed description of the experimental protocol employed for each selection.


title: 28bp_36hrs_10μmM_IPTG_5mM_3-AT_plates

description: This selection was performed by the Woolf lab


title: HeLa_hCAGE_standard_rep1

description: HeLa.Std.5000ng.1st_20100614.Riken2.fc1.ch8


title: 28bp_36hrs_10μmM_IPTG_2mM_3-AT_plates


title: 24hrs_50μM_IPTG_0.5mM_3-AT_plates


title: unassigned_plates

description: all the reads that did not match the one of the expected sequences sufficiently well were grouped together


title: 28bp_48hrs_10μmM_IPTG_0mM_3-AT_plates


title: THP1_hCAGE_standard_rep1

description: THP1.Std.5000ng.1st_20100614.Riken2.fc1.ch23


title: THP1_hCAGE_low_quantity_200ng_rep2

description: THP1.LqDynal.200ng.2nd_20100527.Riken4.fc1.ch15


title: THP1_hCAGE_standard_rep2

description: THP1.Std.5000ng.2nd_20100614.Riken2.fc1.ch24


title: THP1_hCAGE_low_quantity_500ng_rep1

description: THP1.LqDynal.500ng.1st_20100527.Riken4.fc1.ch2


title: THP1_hCAGE_low_quantity_500ng_rep2

description: THP1.LqDynal.500ng.2nd_20100527.Riken4.fc1.ch24


title: THP1_hCAGE_low_quantity_100ng_rep1

description: THP1.LqDynal.100ng.1st_20100527.Riken4.fc1.ch9


title: THP1_hCAGE_low_quantity_1000ng_rep2

description: THP1.LqDynal.1000ng.2nd_20100527.Riken4.fc1.ch5


title: THP1_hCAGE_low_quantity_200ng_rep1

description: THP1.LqDynal.200ng.1st_20100527.Riken4.fc1.ch18


title: THP1_hCAGE_low_quantity_1000ng_rep1

description: THP1.LqDynal.1000ng.1st_20100527.Riken4.fc1.ch8


title: Gingeras_K562_1k (SOLiD)

status: Public on Apr 27 2011

description: SPECIAL NOTE: The combined BAM file for Samples GSM714693 and GSM714694 is on Sample record GSM714693.

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisDnaPet

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisDnaPet

tag: lab

value: GIS

tag: lab description

value: Ruan - Genome Institute of Singapore

tag: datatype

value: DnaPet

tag: datatype description

value: DNA Paired-End Tags

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell lineage

value: mesoderm

tag: fragsize

tag: fragsize description

value: 1 kb DNA fragments


title: Gingeras_GM12878_1k

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/GM12878_protocol.pdf

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

tag: cell karyotype

value: normal


title: Gingeras_GM12878_5k

value: 5 kb DNA fragments


title: Gingeras_K562_10k (SOLiD)

description: SPECIAL NOTE: The combined BAM file for Samples GSM714698 and GSM714699 is on Sample record GSM714698.

value: 10 kb DNA fragments


title: Gingeras_GM12878_10k


title: Gingeras_K562_10k (Illumina)


title: Gingeras_K562_20k

value: 20 kb DNA fragments


title: Gingeras_K562_1k (Illumina)


title: STAT5B_IL2_ChIPSeq (mouse)

status: Public on Apr 24 2011

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Chromatin IP against STAT5B

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) and the mouse (Febrary, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

source_name: T cell

growth_protocol: CD4+ cells were preactivated by anti-CD3/anti-CD28 for 48 hrs

extract_protocol: Th1 cells or preactivated cells were cross-linking with formaldehyde. Formaldehyde-treated nuclear lysates were subjected to immunoprecipitation with antibodies specific for STAT1 (Santa Cruz),STAT4  (R&D Systems), STAT5A (R&D Systems), STAT5b (R&D Systems) or normal rabbit serum at 4°C overnight. After deproteination and reversal of cross-links, amounts of selected DNA sequences were assessed by CHIP-Seq

treatment_protocol: cells were rest o/n, and stimulated with IL-2 for 1 hrs

tag: strain

tag: cell type

value: T cell

tag: antibody

tag: treatment


title: STAT5B_control_ChIPSeq (mouse)

description: Chromatin IP against STAT5B

treatment_protocol: cells were rest o/n, and non-treated for 1 hrs

value: control


title: Control

status: Public on Apr 25 2011

city: Shenzhen

first: Bosheng

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

description: sRNA

data_processing: Sequencing reads were first aligned against the P. trichocarpa genome (JGI P. trichocarpa genome V 1.1) by SOAP software (Li et al., 2008). Sequences with perfect match were retained for further analysis. By comparing the existing sRNA database, all small RNAs were annotated in the order of the following categories: 1. rRNAetc: rRNA, tRNA, snRNA, scRNA and snoRNA deposited at Genebank (http://www.ncbi.nih.gov/Genbank/); Rfam (http://rfam.sanger.ac.uk/) database. In this category, RNA sequences based on structural conservation were also considered. GtRNAdb (http://lowelab.ucsc.edu/GtRNAdb/Ptric/popTri2-tRNAs.fa), a highly confidential Populus tRNA database predicted by tRNAscan based on structure (Schattner et al., 2005), was also used for excluding tRNA. 2. known miRNA: previously discovered miRNAs in miRBase13.0; 3. exon_sense/antisense: genomic exon sequences in sense/antisense direction; 4. intron_sense/antisense: genomic intron sequences in sense/antisense direction. Both of the exon_sense/antisense and intron_sense/antisense were classified by the Populus genome data from P. trichocarpa genome V 1.1 (http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html). 5. unknown sRNA.

organism: Populus euphratica

source_name: normal growth condition

growth_protocol: One year-old seedlings of P. euphratica, obtained from the Xinjiang Uygur Autonomous Region of China, were planted in individual pots (15 L) containing loam soil and placed in a greenhouse at Beijing Forestry University. Each pot contained three individuals. Potted plants were well irrigated according to evaporation demand and watered with 1 L full-strength Hoagland nutrient solution every 2 weeks for two months before drought stress treatment. The temperature in the greenhouse was 20 ℃ to 25 ℃ with a 16 hour photoperiod (4 AM-8 PM).

extract_protocol: For material harvest, mature leaves from the same position of eight different plants in each treatment were mixed and ground immediately in liquid nitrogen. Total RNA was extracted from mixed leave tissues by standard CTAB method for plants (Chang, 1993). Then the total RNA was used for high through-put sequencing and microarray profiling.

treatment_protocol: In the drought stress treatment, P. euphratica plants were submitted to soil water deficiency in four RSMC levels for two months according to previous research (Hasio, 1973). They were Group A with RSMC 70-75%; Group B with RSMC 50-55%; Group C with RSMC 35-40% and Group D with RSMC 15-20%. Soil with sufficient irrigations everyday kept RSMC at 70-75% because of transpiration, so Group A was used as control sample. Leaf water potential was measured by PsyPro water potential data logger (WescorTM). Net photosynthetic rate and transpiration rate were measured by Li-6400 Photosynthesis System (LI-COR TM). All data were statistically analyzed by one-way ANOVA using SPSS (SPSS statistical package 10.1, Chicago, IL, USA).

tag: tissue

value: leaves


title: Group C

description: sRNA

source_name: drought treatment samples


title: STAT5A_control_ChIPSeq (mouse)

description: Chromatin IP against STAT5A


title: STAT5A_ChIPSeq (mouse)

description: Chromatin IP against STAT5A

source_name: Th1 cell

growth_protocol: naïve CD4+ cells cells were cultured under Th1 condition

treatment_protocol: 2 rounds priming (2ug/ml of anti-CD3, 1ug/ml of anti-Cd28,10 ng/ml IL-12 + 10 μg/ml anti-IL-4) was performed

value: Balb/C

value: Th1 cell

value: 2 rounds priming


title: STAT4_ChIPSeq (mouse)

description: Chromatin IP against STAT4


title: Input DNA (mouse)

description: Chromatin IP against IgG

value: IgG


title: STAT5B_ChIPSeq (mouse)

description: Chromatin IP against STAT5B