title: Chromatin accessibility assay of iPS DF 4.7 Cell line; DS15169

description:
sample_term_id: NTR_0001171
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15169
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5343
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5342
****************
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: GSM665803_UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15169.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of iPS DF 4.7 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the iPS DF 4.7 Cell Line, Library DS15169 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.6396
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2341
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.2838
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9886
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3696
POISSON_PERCENTILE: 18

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

ANALYSIS FILE NAME: GSM665803_UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15169.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 4.7 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the iPS DF 4.7 Cell Line, Library DS15169 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.6435
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iD4.7 DNase 69 69
BROWSER_TRACK_DESCRIPTION: UW iPS DF 4.7 Cell Line DNase Hypersensitivity Library DS15169 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2341
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.2838
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9886
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3696
POISSON_PERCENTILE: 18

source_name: iPS DF 4.7 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15169

value: iPS DF 4.7 Cell Line

tag: molecule

tag: disease

value: Unknown

value: Chromatin Accessibility


title: Chromatin accessibility assay of iPS DF 6.9 Cell line; DS15164

status: Public on Feb 02 2011

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15164
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5337
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5336
****************
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: GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15164.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the iPS DF 6.9 Cell Line, Library DS15164 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.6394
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2693
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.307
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9907
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3938
POISSON_PERCENTILE: 23

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

ANALYSIS FILE NAME: GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15164.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the iPS DF 6.9 Cell Line, Library DS15164 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.6433
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iD6.9 DNase 64 64
BROWSER_TRACK_DESCRIPTION: UW iPS DF 6.9 Cell Line DNase Hypersensitivity Library DS15164 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2693
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.307
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9907
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3938
POISSON_PERCENTILE: 23

molecule: genomic DNA

organism: Homo sapiens

source_name: iPS DF 6.9 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15164

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: iPS DF 6.9 Cell Line

value: genomic DNA

value: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison

value: Cell Line

tag: line

tag: lineage

value: Derived from newborn foreskin fibroblast:Cat# CRL-2097TM, ATCC

value: Induced pluripotent stem cell

tag: passage

tag: medium

tag: Sex

tag: batch

value: Qiagen minElut

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


title: Chromatin accessibility assay of Moblized CD34+ Primary cells; DS14040

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14040
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5316
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5315
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

source_name: flow sorted CD34+ Primary Cells, Mobilized, year 23; DS14040

value: Mobilized CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 23

value: Male

value: Caucasian


title: Chromatin accessibility assay of iPS DF 19.7 Cell line; DS15148

description:
sample_term_id: NTR_0001174
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15148
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5340
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5339
****************
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: GSM665800_UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15148.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of iPS DF 19.7 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the iPS DF 19.7 Cell Line, Library DS15148 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.6390
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2528
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.3004
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9933
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3539
POISSON_PERCENTILE: 13

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

ANALYSIS FILE NAME: GSM665800_UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15148.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.7 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the iPS DF 19.7 Cell Line, Library DS15148 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.6429
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iD19.7 DNase 48 48
BROWSER_TRACK_DESCRIPTION: UW iPS DF 19.7 Cell Line DNase Hypersensitivity Library DS15148 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2528
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.3004
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9933
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3539
POISSON_PERCENTILE: 13

source_name: iPS DF 19.7 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15148

value: iPS DF 19.7 Cell Line


title: Chromatin accessibility assay of CD8+ Primary cells; DS16012

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16012
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5349
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5348
****************
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: GSM665813_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01549.DS16012.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16012.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD8 Primary Cells, Donor RO 01549, Library DS16012 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.6399
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2532
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2432
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9927
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3042
POISSON_PERCENTILE: 3

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

ANALYSIS FILE NAME: GSM665813_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01549.DS16012.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16012.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD8 Primary Cells, Donor RO 01549, Library DS16012 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.6438
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CD8 DNase 70 12
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells DNase Hypersensitivity Donor RO 01549 Library DS16012 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2532
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2432
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9927
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3042
POISSON_PERCENTILE: 3

source_name: flow sorted CD8+ Cells,year 33; DS16012

value: CD8 Primary Cells

value: year 33

value: Female


title: HeLa_siSmB/B'

status: Public on Feb 01 2011

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

description: RNA-Seq performed on polyadenylated RNA (polyA+ RNA)

library_source: transcriptomic

data_processing: The sequence reads were aligned to exon-exon junctions in a database of cDNA/EST-mined cassette-type alternative splicing (AS) events as described [Pan et al. (2008) Nat Genet 40, 1413-1415]. The coordinates of the alternative exons and their upstream and downstream flanking constitutive exons (referred to as "C1-A-C2") are provided in the '.bed' processed file. For each sample, the number of counts mapping to the C1:A, A:C2, and C1:C2 exon-exon junctions are provided in the '.txt' processed file.  The .bed and .txt files are linked as supplementary files on the Series record.

molecule: total RNA

source_name: HeLa (cervical adenocarcinoma)

growth_protocol: HeLa cells were maintained in DMEM with 10% FBS and Pen/Strep prior to transfection.

extract_protocol: Illumina FastTrack mRNA-Seq library construction

treatment_protocol: HeLa cells were transfected with siRNAs at 100 nM using Dharmafect 1 (Dharmacon). Total RNA was isolated 3 days later using TRI reagent (Sigma).

tag: cell line

value: HeLa

tag: genotype/variation

value: SmB/B' knockdown


title: HeLa_siNT

value: control


title: H3_ChIPseq

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

description: Chromatin IP against H3

data_processing: Alignment: Sequence reads were obtained and mapped to the Arabidopsis thaliana (TAIR9, 2008) genomes using home-made perl script. All reads mapping with perfect mach and only once and longer than 40 nt were retained.

organism: Arabidopsis thaliana

source_name: Leaf tissue

growth_protocol: Plants were grown in vermiculite mixed with 30% soil in a growth chamber with growth conditions of 22°/18° C (day/night) and 16 hr of illumination per day.

extract_protocol: For immunoprecipitation, 2 ug H3-core (Ab1791; Abcam, Cambridge, MA), 4 ug H3K4me3 (Ab8580) or 3.6 ug H3K9ac (Ab10812) antibodies were added to 600 ul diluted chromatin and incubated overnight at 4oC with gentle rotation. Immunoprecipitated chromatin-DNA (IP-DNA) and 50 ul input chromatin-DNA (without IP) were subjected to reverse crosslink and purified for sequencing libraries preparation. ChIP-seq libraries were constructed according to protocols described in Illumina ChIP sequencing kit (Illumina Inc., San Diego, CA). Libraries with a range of 250-300-bp were excised and amplified for subsequent cluster generation and massively parallel sequencing.

tag: strain

value: Columbia 2x

tag: tissue

value: rosette leaf

tag: stage

value: Rosette leaves prior to bolting

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog #

tag: antibody lot #


title: H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3


title: H3K4me3_ChIP-seq

city: New York

first: Hao

last: Jiang

state: NY

address: 1230 York Ave

institute: Rockefeller University

description: Chromatin IP against H3K4me3

data_processing: For H3K4me3 ChIP-seq, Sequence reads (36 bases) from the ChIP experiment were compiled, post-processed and aligned to UCSC MM8 using NOVOALIGN. Aligned reads were used to estimate the number of end-sequenced ChIP fragments that overlap any given genomic position (at 25 bp resolution). For each position, we counted the number of reads that were oriented towards it and closer than the average length of a library fragment (∼300 bp). The result is a high-resolution density map that can be viewed through the UCSC Genome Browser and is used for downstream analyses. Conversion of TSS between mm9 (Dpy-30) and mm8 (H3K4me3) genome built was performed using the UCSC liftover tool.

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: E14 cells were cultured on 0.1% gelatinized tissue-culture plates in complete ESC growth medium supplemented with LIF

extract_protocol: Chromatin was sonicated nuclei and immunoprecipitated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: For Dpy-30 ChIP-seq, cells in monolayer culture were washed twice with 1 x PBS and fixed with 2 mM Disuccinimidyl glutarate (DSG) for 1 hour at room temperature. After removal of DSG and washing with PBS, cells were further fixed with 1.2% Formaldehyde in PBS/1 mM MgCl2 for 15 min at room temperature. For H3K4me3 ChIP-seq, cells were fixed with 1% Formaldehyde for 10 min at room temperature.

tag: cell type

value: E14 ES cells

tag: chip antibody

tag: antibody vender

value: Millipore

tag: antibody catalog number

tag: antibody lot number


title: input DNA

description: input DNA


title: P. putida 30°C

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

country: Germany

institute: Medical School Hannover

description: Supplementary processed data files include: gene expression from 30°C culture at mid-exp. Phase, aligned reads only map to intergenic regions, and aligned reads only map to open reading frames

data_processing:
Illumina Genome Analyzer GAII SR was used. Illumina Genome Analyzer Pipeline Version 0.2 software was used to qualify reads passing default signal quality filters (Klockgether et al., 2010). Each position in a sequence read is associated with a quality score Qsolexa reflecting the quality of the respective base call (depending on the measured signal during the sequencing process). For a base X, the relation of its probability value p(X) to the Qsolexa score is given by the formula   Qsolexa =  10 log ( p(X) / 1 – p(X) ). Therefore, a maximal Qsolexa value of 40 indicates a probability of 99.99 % for the called base, or an error probability of 0.01 %, respectively. Lower Qsolexa values typically appear at the end of reads. If no decisive base call could be made, the respective position in the sequence read was designated as ‘N’, (with Qsolexa set to –0.5 automatically). Sequence reads that passed the default signal quality filter and were not aligned by ELAND (Efficient Large-Scale Alignment of Nucleotide Databases; Illumina unpublished) to a reference of the P. putida rRNA genes were used for gene expression analysis. The reads were subsequently aligned to the P. putida genome (NC_002947) using the Bowtie software package (Langmead et al., 2009). Remaining reads mapped to rRNA were subsequently excluded with a custom PERL script. Four nucleotides were trimmed from the 3’ end of each read and a seed size of 28 bp was used, in which two mismatches were permitted. The quality mismatch sum was 100 and results were output in SAM format (command line: bowtie -t putida -l 28 -e 100 --best --sam -3 4 -n 2 -p 7).   A summary table was then generated with the integrative web analysis tool Galaxy (Giardine et al., 2005). The functions "coverage" and "join" were used respectively to summarize 1) coverage of each ORF from the P. putida NCBI annotation (version NC_002947.3) in terms of total bp and proportion covered by reads and 2) the number of reads mapped to each ORF. Reads mapped to ORFs had at least 1 bp overlap with the ORF. The two datasets for 30°C and 10°C differed in the absolute number of both total reads and reads that mapped to the genome. In addition, genes differ greatly in length, therefore reads were normalized as follows: The ORF length was standardized to 1000 bp and the number of reads to one million reads per experiment (RPKM, see Mortazavi et al., 2008). These analyses were then repeated in the same way for the intergenic regions. Coordinates of intergenic regions were gained using the Galaxy function "complement" on the ORF annotation in Galaxy's "interval" format. Mapped reads were then visualized with the Integrated Genome Browser (http://igb.bioviz.org/).
A summary table was then generated with the integrative web analysis tool Galaxy (Giardine et al., 2005). The functions "coverage" and "join" were used respectively to summarize 1) coverage of each ORF from the P. putida NCBI annotation (version NC_002947

organism: Pseudomonas putida KT2440

source_name: P. putida 30°C

growth_protocol: Bacterial cultures were inoculated from a frozen stock culture of P. putida wild type, and incubated at 30°C for 8 hours at 250 rpm in LB medium. An aliquot of 0.2 mL was added to 20 mL M9 medium (Na2HPO4 33.9 g/L, KH2PO4 15.0 g/L, NaCl 2.5 g/L, NH4Cl 5.0 g/L, MgSO4 2 mM, CaCl2 0.1 mM, FeSO4 x 7 H2O 0.01 mM, pH 6.8) supplemented with 15 mM succinate as sole carbon source in a 100 mL flask and incubated overnight at 30°C. For RNA extraction, the bacterial culture was inoculated in a 1.5 L batch culture (M9 + 15 mM succinate) using the BioFlo 110 Fermenter (New Brunswick Scientific Co., Edison, NJ) to ensure constant pH, aeration and agitation. When cultures reached mid-exponential phase (OD600 ~ 0.8) the temperature was decreased from 30°C to 10°C. Three samples, each for parallel RNA extraction, were subsequently taken immediately before temperature downshift (30°C) and two hours after the media had been cooled to 10°C.

extract_protocol: Total RNA extraction was performed according to the manufacturer's protocol provided by Qiagen for bacteria. Total cDNA was synthezised using reverse transcriptase SuperscriptII and random hexamers following the protocol provided by Invitrogen.

tag: growth condition


title: P. putida 10°C

description: Supplementary processed data files include: gene expression from 10°C culture after cold shock, aligned reads only map to intergenic regions, and aligned reads only map to open reading frames

source_name: P. putida 10°C


title: Dpy-30_ChIP-seq

description: Chromatin IP against Dpy-30

data_processing: For Dpy-30 ChIP-seq, the sequencing was performed on an Illumina Genome Analyzer IIx for 36 cycles. Image analysis and base calling were performed using Solexa pipeline V1.6 and short reads (pass quality filter) were aligned to mouse NCBI build 37 (UCSC MM9) using NOVOALIGN. Unique alignments were used for peak calling of the ChIP regions using MACS v1.3.7.1. Sequences were extended 296 bp, and then the whole genome was scanned by 300 bp windows. Statistically significant ChIP-seq enrichment regions (peaks) were identified by comparison to a Poissonian background model, using a p-value threshold of 10-5. Nearest TSSs (600 kb window) around calling peaks were then searched using the newest ENSEMBL database.

tag: antibody provider

value: unreleased product from Bethyl Laboratories, developed by Christina Hughes (David Allis lab, Rockefeller University) through Bethyl


title: Whole worm_Mixed stage_1

city: Salt Lake City

first: Michael

middle: Bryan

last: Warf

state: UT

address: 15 N Medical Dr East, room 4800

department: Biochemistry

institute: University of Utah

data_processing:
Sequence reads were obtained using the Illumina Genome Analyzer Pipeline version 1.6 (OLB 1.6, CASAVA 1.6.0)
Alingment: Sequnces were aligned to the genome (May 2008) using Novoalign, with an r-value of 0.2 and a q-value of 5. Sequences were filtered using the USeq software package component NovoalignParser, using a posterior probability of 0.1
1) chromosome
2) start position of read
3) end position of read
4) read sequence; quality information of alignment (generated by novoalign)
5) quality score of the alignment (generated by novoalign)
6) + vs - (where the read aligned to the Plus or Minus strand of the chromosome).

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were grown on OP50 lawn at 20 degrees Celsius

extract_protocol: Total RNA was isolating using TRIzol reagent (Invitrogen), small RNAs were isolated by gel purication and cDNA was prepared using the small RNA v1.5 illumina kit

treatment_protocol: no treatment

value: Wild-type (N2)

tag: developmental stage

value: mixed stage

value: Whole worm


title: HeLa_siSRSF1

tag: cell line

value: SRSF1 knockdown


title: H3K9ac_ChIPseq

description: Chromatin IP against H3K9ac


title: Treg-H3K4me3

status: Public on Jan 31 2011

city: Chongqing

first: Ni

last: Bing

address: PLA, Third Military Medical University

department: Institute of Immunology

country: China

institute: PLA, Third Military Medical University

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genome using the SOAP(Short Oligonucleotide Analysis Package). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Treg cells from PBMC, normal

extract_protocol: the expanded and sorted Treg and aTconv cells were used for ChIP analysis. For mapping enzyme target sites, 2×10e6 cells were crosslinked with formaldehyde and sonicated to obtain chromatin fragments of 200 to 300 bp. Sonicated chromatin was pre-cleared and incubated with 2mg of anti-H3K4me1(Abcam, United Kingdom), anti-H3K3me3 (Abcam) or anti-rabbit IgG (Upstate, USA) overnight at 4°C. The crosslinks were reversed, and The ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced with the Illumina 1G Genome Analyzer.

tag: gender

value: male

value: Treg cells

tag: chip antibody vendor


title: aTconv-H3K4me1

source_name: aTconv cells from PBMC, normal

value: aTconv cells


title: aTconv-H3K4me3


title: aTconv-IgG

value: IgG

value: Upstate


title: Treg-H3K4me1


title: pSmad2 input DNA Seq of ES cells treated for 18 hours in 1/5000 DMSO

city: Singapore

first: Yuriy

middle: L

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the Illumina Genome Analyzer II Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using processed data file. At each reatment condition (Activin, DMSO and SB) whole cell extracts (WCE) input DNA sequencing library was used as background for IP peak calling.

source_name: E14 TG2A mouse embryonic stem cells

growth_protocol: E14 TG2A mouse embryonic stem cells (ATCC) were propagated in ES media consisting of 20% ES cell qualified FBS in DMEM supplemented with 100μM non essential amino acids, 100U/ml penicillin, 100μg/ml streptomycin, 2mM GlutaMAX I (Invitrogen), 55μM β mercaptoethanol (Sigma) and 1X homemade Leukemia Inhibitory factor (LIF).

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with pSmad2 antibody.  Antibody is ABCAM ab16509, Rabbit polyclonal to Smad2 (phospho S465 + S467), ChIP Grade 100ug. (batch number 125959). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 200-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: For the establishment of Nodal/Activin signaling gradients in chemically defined conditions, KSR media containing 20% Knockout Serum Replacement (KSR, Invitrogen) in place of FBS and all other components of ES media excluding LIF were used. For acute (0 to 48 hours) signaling conditions, 25000 ES cells/cm2 were plated for 18 hours in ES media followed by pretreatment with 10μM SB 431542 (Tocris) in KSR media for 6 hours as previously described (Guzman-Ayala et al., 2009). High signaling was induced by treatment with KSR media containing 25ng/ml Activin (R&D Systems) or low signaling with 10μM SB and maintenance of endogenous signaling with control KSR media or 1/5000 dilution of DMSO vehicle as indicated.

value: E14 TG2A mouse embryonic stem cells

tag: fraction

value: Input DNA

tag: treatment


title: H3K27me3 ChIP-seq in HSPC

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
09232009_42WK9AAXX_B4
Chromatin IP against H3K27me3 in HSPC.

data_processing:
Image analysis and base calling were done using the Solexa pipeline.

For all samples, reads were aligned to the human genome build hg18 using Bowtie.

For all samples, aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Hematopoietic Stem & Progenitor Cells, H3K27me3 ChIP

growth_protocol: Human CD133-positive Umbilical Cord Blood (UCB) cells were purchased from AllCells, Emeryville, CA. Cells were expanded for 10-11 days using Lodish conditions (Zhang et al. Blood 2008 (PMID: 18202223)) in StemSpan serum-free medium (StemCell Technologies,Vancouver, BC) supplemented with 10 µg/mL heparin (Sigma-Aldrich, St Louis, MO), 10 ng/mL mouse SCF, 20 ng/mL mouse TPO, 100 ng/mL human IGFBP2 (all from R&D Systems, Minneapolis, MN), and 10 ng/mL human FGF-1 (Invitrogen, Frederick, MD) and 500 ng/ul human Angptl5 (Abnova, Taipei City, Taiwan). At the end of culture, cells were positively selected for CD133 using an immunomagnetic MicroBead labeling system (StemCell Technologies). Cell purity was determined by FACS for CD34 and CD133 to be 75-90% double positive. For location analysis, cells were cross-linked with formaldehyde for 20 min.

extract_protocol:
Library prep protocol: YoungLab_MWG
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: CD133+ expanded umbilical cord blood (UCB) cells

tag: cell number

value: 1 million

tag: biological replicate


title: RNAP2 ChIP-Seq in HSPC, run 1

description:
09232009_42WK9AAXX_B2
Chromatin IP against RNAP2 in HSPC.

source_name: Hematopoietic Stem & Progenitor Cells, RNA Pol II ChIP

value: RNA Pol II

tag: antibody vendor

value: Covance


title: H3K79me2 ChIP-seq in HSPC

description:
09232009_42WK9AAXX_B3
Chromatin IP against H3K79me2 in HSPC.

source_name: Hematopoietic Stem & Progenitor Cells, H3K79me2 ChIP

extract_protocol:
Library prep protocol: YoungLab_MWG
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Abcam


title: pSmad2 input DNA Seq of ES cells treated for 18 hours in 25ng/ml Activin

value: 25ng/ml Activin


title: pSmad2 ChIPSeq of ES cells treated for 18 hours in 10uM SB

tag: antibody name

tag: antibody manufacturer

value: ABcam

tag: antibody batch number

value: ChIP DNA

value: 10uM SB


title: pSmad2 ChIPSeq of ES cells treated for 18 hours in 1/5000 DMSO

tag: cell type


title: RNAP2 ChIP-Seq in HSPC, run 2

description:
10272009_42YHBAAXX_B3
Chromatin IP against RNAP2 in HSPC.

tag: chip antibody

tag: antibody catalog number


title: pSmad2 input DNA Seq of ES cells treated for 18 hours in 10uM SB


title: hela_pAplus_1

status: Public on Jan 28 2011

city: Shanghai

first: Ling-Ling

last: Chen

address: 320 Yue-Yang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: RNAseq technical replicate 1

data_processing:
Alignment: Sequence reads were obtained and mapped to the human hg19 genomes by using bowtie with uniquely mapping and up to 2 mismatches
column description in the bedgraph files: Chromosome; start position; end position; height

source_name: HeLa cells

growth_protocol: HeLa cells were cultured under standard conditions.  hES H9 cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF).

extract_protocol: Isolated nonpolyadenylated or polyadenylated RNAs individually and libraries were prepared using the Illumina mRNA-Seq Sample Prep Kits (P/N 1004814) according to the manufacturer’s instructions.

value: HeLa

tag: chromosome

value: highly polyploid

tag: rna

value: polyAplus RNA


title: hela_pAplus_3

description: RNAseq technical replicate 3


title: hela_pAplus_2

description: RNAseq technical replicate 2


title: hela_pAminus_3

description: RNAseq technical replicate 3

value: polyAminus RNA


title: hela_pAminus_1

description: RNAseq technical replicate 1


title: hela_pAminus_2

description: RNAseq technical replicate 2


title: pSmad2 ChIPSeq of ES cells treated for 18 hours in 25ng/ml Activin


title: h9_pAplus_3

description: RNAseq technical replicate 3

source_name: hES h9 cells

value: human embryonic stem cell (hESC) H9

value: diploid

tag: passages


title: h9_pAminus_3

description: RNAseq technical replicate 3

tag: cell line


title: h9_pAplus_1

description: RNAseq technical replicate 1


title: h9_pAplus_2

description: RNAseq technical replicate 2


title: muscle2

status: Public on Jan 27 2011

city: Palo Alto

first: Weihong

last: Xu

state: CA

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

description: GG-H exon

data_processing: Alignment: sequence reads were obtained and mapped to GG-H exons using SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap). All reads mapping with two or fewer mismatches were retained for further analysis

source_name: Human Skeletal Muscle Total RNA (Ambion)

extract_protocol: Illumina (2009), mRNA Sequencing: Sample Preparation Guide Part # 1004898 Rev. D

tag: tissue

value: muscle


title: muscle3

description: GG-H exon


title: muscle4

description: GG-H exon


title: muscle1

description: GG-H exon


title: h9_pAminus_2

description: RNAseq technical replicate 2


title: MAC_CO RNA-Seq

first: Chengshu

last: Wang

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences, CAS

description: PolyA RNA from Metarhizium acridum infection of cockroach

data_processing: After base calling by transforming the raw image data into sequence data, the 3' adaptor was cleaned and the tags with “N” or the tags with only one copy were removed to generate clean tags. All clean tags were mapped onto either the Metarhizium anisopliae or M. acridum genome by allowing no more than 1nt mismatch. Clean tags mapped to reference genome from multiple places were filtered. The remaining clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).

organism: Metarhizium acridum

source_name: Fungal germlings

growth_protocol: The fungal spores of Metarhizium anisopliae and M. acridum were were inoculated on the hind wings of locust and cockroach, respectively and the RNA was extracted for RNA-Seq analysis 24 hrs post treatment from the infected wings.

extract_protocol: mRNA was purified from 6 µg of the total RNA from each sample using Oligo (dT) magnetic beads and reversely transcribed into cDNA. The generation of 5' CATG ends of tags was conducted using the endonuclease NlaIII and the Illumina adapter 1 was added to the 5' ends. The combination of the Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts the cDNA at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, the Illumina adapter 2 was introduced at the 3' ends of each tag to generate the tag libraries. After 15 cycles of linear PCR amplification, 85 base strips were purified by 6% TBE PAGE Gel electrophoresis and the single-chain molecules fixed onto the Solexa Sequencing Chip (flowcell) for sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 35bp.

tag: strain

tag: time

value: 24 hrs post inoculation of spores on host wings

tag: host

value: cockroach


title: liver3

description: GG-H exon

source_name: Human Liver Total RNA (Ambion)

value: liver


title: MAA_LO RNA-Seq

description: PolyA RNA from Metarhizium anisopliae infection of locust

organism: Metarhizium anisopliae

value: ARSEF 23

value: locust


title: MEIS1 ChIP-seq in HSPC, run 3

status: Public on Jan 26 2011

description: Chromatin IP against MEIS1 in HSPC.

source_name: Hematopoietic Stem & Progenitor Cells, MEIS1 ChIP

value: Abcam

tag: antibody lot number

value: CD133+ expanded umbilical cord blood (UCB) cells

tag: cell number

value: 3 million


title: Pu.1 ChIP-seq in HSPC, run 2

description: Chromatin IP against Pu.1 in HSPC.

source_name: Hematopoietic Stem & Progenitor Cells, Pu.1 ChIP

tag: antibody vendor

value: Santa Cruz

tag: biological replicate


title: MEIS1 ChIP-seq in HSPC, run 1

description: Chromatin IP against MEIS1 in HSPC.


title: Ikaros ChIP-seq in HSPC, run 1

description: Chromatin IP against Ikaros in HSPC.

source_name: Hematopoietic Stem & Progenitor Cells, Ikaros ChIP


title: TAL1 ChIP-seq in HSPC, run 2

description: Chromatin IP against TAL1 in HSPC.

source_name: Hematopoietic Stem & Progenitor Cells, TAL1 ChIP


title: Ikaros ChIP-seq in HSPC, run 2

description: Chromatin IP against Ikaros in HSPC.


title: liver2

description: GG-H exon


title: Pu.1 ChIP-seq in HSPC, run 1

description: Chromatin IP against Pu.1 in HSPC.


title: liver4

description: GG-H exon


title: liver1

description: GG-H exon


title: MAA_CO RNA-Seq

description: PolyA RNA from Metarhizium anisopliae infection of cockraoch


title: MEIS1 ChIP-seq in HSPC, run 2

description: Chromatin IP against MEIS1 in HSPC.


title: h9_pAminus_1

description: RNAseq technical replicate 1


title: Ngon_-O2_rep2

city: Rochester

first: Vincent

middle: M

last: Isabella

address: 601 Elmwood Ave

department: Microbilogy and Immunology

institute: University of Rochester

description: RNA-seq replicate 2, -O2

data_processing: BioScope (version 1.2, Applied Biosystems, CA) was used to map the color sequences of each bead to the annotated FA1090 reference genome obtained from the National Center for Biotechnology Information (NCBI). Sequences were counted if they matched a 25-color end of a reference sequence with no more than 2 mismatches (permitting some mismatches is necessary because of sequencing errors and actual variations from the reference sequence).  The length of the match was then determined by extending the alignment through the full 50-color sequence, allowing for more mismatches with increasing length. If a sequence read aligned to more than one genomic locus, the best alignment was selected. If a sequence read aligned equally well to a genomic locus, it was discarded.  Stringency was set so that any base in the gonococcal genome had to be counted at least 10 times in order to be considered mapped.  After mapping, colors were converted to bases.

organism: Neisseria gonorrhoeae F62

growth_protocol: Cells were grown on GCK agar plates either aerobically in a 37 degree incubator supplying 5% Carbon dioxide, or anaerobically in a Coy anaerobe chamber.  Plates grown anaerobically were supplemented with 5 mM nitrite

extract_protocol: mRNA enrichment were performed on total bacterial RNA using MICROBExpress Oligo MagBeads (Ambion, TX). The SOLiD™ 3 Plus system was used to read short (50 nt) RNA sequences, and all RNA processing procedures were performed using a SOLiD™ Total RNA-seq Kit as recommended by Applied Biosystems (SOLiD™ Total RNA-seq Kit Protocol, Applied Biosystems, CA). Briefly, RNA was fragmented with RNase III, directionally hybridized and ligated with flanking adapters containing sequences for priming PCR amplification and sequencing reactions. After reverse transcription of the ligated RNA, the cDNA molecules were size selected by PAGE, amplified by PCR (limiting the number of cycles to minimize PCR bias), quantified by real-time PCR, and diluted to a concentration optimal for monoclonal amplification by emulsion PCR, during which copies of template molecules were attached to beads. Beads were deposited on slides upon which the sequential reactions and washing steps were done automatically by the SOLiD™ 3 plus instrument. DNA attached to beads was sequenced with 50 rounds of oligonucleotide annealing and ligation (five different primers, 10 sequential ligations per primer). During each round, an oligonucleotide labeled with a fluorescent dye was annealed and ligated to the 3’ end of the primer or the oligo ligated in the previous round.  The next two unoccupied nucleotides of the strand attached to the bead determined which oligo (“color”) was ligated. Use of staggered primers permitted determination of the unique base sequences.

treatment_protocol: For harvesting, cells were scraped from plates into GCP broth and immediately centrifuged and flash frozen.  RNA was isolated following standard protocols, and mRNA was enriched with MICROBExpress kit to remove ribosomal RNA

tag: genotype

value: wild-type

tag: condition


title: MAC_LO RNA-Seq

description: PolyA RNA from Metarhizium acridum infection of locust


title: Ngon_-O2_rep1

description: RNA-seq replicate 1, -O2


title: TAL1 ChIP-seq in HSPC, run 1

description: Chromatin IP against TAL1 in HSPC.

tag: cell type


title: Ngon_+O2_rep2

description: RNA-seq replicate 2, +O2


title: WCE_HSPC

description: HSPC chromatin input control.

source_name: Hematopoietic Stem & Progenitor Cells, input

tag: chip antibody


title: SGIV-infected GP cells

status: Public on Jan 29 2011

city: Guangzhou

first: Yang

last: Yan

address: West Xingang Road

institute: South China Sea Institute of Oceanology Chinese Academy of Sciences

description: total RNAs extracted from a pool of SGIV-infected GP cells

data_processing: Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequence were trimed by our Perl scripts.

organism: Epinephelus tauvina

source_name: SGIV-infected GP cells

growth_protocol: Grouper embryonic cells (GP) were grown in Eagle’s minimum essential medium (EMEM) containing 10% fetal bovine serum (Invitrogen, USA) at 25 ℃

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, USA) and digested with TURBO DNase™ ( Ambion, USA) to discard the DNA contaminant. Then the total RNA was electrophoresed on 15% polyacrylamide-8 M urea gel, and small RNAs with less than 30-nt size were extracted from the gel and purified. Sequentially, a pair of Solexa proprietary adaptors was ligated to their 5’ and 3’ ends, following by reverse transcription and amplification by PCR using a pair of primers complementary to the linker sequences.

treatment_protocol: After allowing the cells to adhere for 18 h to 80% confluence, GP cells were infected with SGIV at an MOI of 0.1. At 6 h, 24 h, 48 h post infection (p.i.), SGIV infected cell cultures were harvested and pooled for total RNA extraction.

value: grouper embryo-derived cells

tag: virus strain

value: SGIV (strain A3/12/98)


title: Ngon_+O2_rep1

description: RNA-seq replicate 1, +O2


title: FOXA1 sequencing in estradiol (E2) treated T47D cells

status: Public on Jan 25 2011

first: Guoliang

last: Li

address: 60 Biopolis Street, #02-01, Genome

department: Computational and Systems Biology

description: Chromatin IP against FOXA1

data_processing: Alignment: Sequence reads were obtained and mapped to the human (hg18) genome using the Illumina Genome Analyzer II Pipeline. ELAND program provided with the 1G analyzer software package and in-house (Genome Institute of Singapore) computational tools for mapping the sequence tags to the reference genome hg18 and clustering short sequences. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.

source_name: T47D breast cancer cells

growth_protocol: MCF-7 cancer cells were grown to 70-80% confluence in D-MEM (Invitrogen/Gibco) supplemented with 10% FBS (Hyclone) in 150 mm dishes. In preparation for the 17 beta-estradiol (“estrogen/E2”, Sigma) treatment, cells were then split into 1:3 into serum starving medium [phenol red-free D-MEM/F-12 medium (Invitrogen/Gibco) supplemented with 5% charcoal-dextran stripped FBS (Hyclone)] and cultured for 72 hours to 70-80% confluence. T47D cancer cells were grown to 70-80% confluence in RPMI (Invitrogen/Gibco) supplemented with 10% FBS (Hyclone) in 150 mm dishes. In preparation for the 17 beta-estradiol (“estrogen/E2”, Sigma) treatment, cells were then split into 1:3 into serum starving medium [phenol red-free RPMI medium (Invitrogen/Gibco) supplemented with 5% charcoal-dextran stripped FBS (Hyclone)] and cultured for 72 hours to 70-80% confluence.

extract_protocol: All DNA samples were processed as per the Illumina Solexa ChIP-seq sample processing methods. 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An A base was added to the polished DNA fragments followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to Solexa sequencing according to the manufacturer’s instruction.

treatment_protocol: Hormone-depleted cells were treated with E2 to a final concentration of 10 nM for 45 minutes to 3 hours before the ChIP/FAIRE procedure. The control cells were treated with an equal volume and concentration of vehicle, DMSO (Merck), for 45 minutes-3 hours. For the ChIP experiment, we routinely used approximately 1 x 108 cells from 5-6, 150 mm diameter cell culture plates. For isolating the open chromatin regions in the genome we performed Formaldehyde assisted isolation of regulatory elements (FOXA1) as described previously (Giresi et al, 2007).

value: T47D breast cancer cells, E2 treated

value: FOXA1 - Cat# AB4124, Chemicon


title: H3K4me1 sequencing in non-treated (DMSO as vehicle) T47D cells

description: Chromatin IP against H3K4me1

value: T47D breast cancer cells, non-treated

value: H3K4me1 - Cat# ab8895, Abcam


title: FOXA1 sequencing in non-treated (DMSO as vehicle) T47D cells

description: Chromatin IP against FOXA1


title: cJun sequencing in non-treated (DMSO as vehicle) MCF-7 cells

description: Chromatin IP against cJun

source_name: MCF-7 breast cancer cells

value: MCF-7 breast cancer cells, non-treated

value: cJun - Cat# sc-45, Santa Cruz


title: FAIRE sequencing in estradiol (E2) treated T47D cells

description: FAIRE


title: FAIRE sequencing in non-treated (DMSO as vehicle) T47D cells

description: FAIRE


title: H3K4me1 sequencing in estradiol (E2) treated T47D cells

description: Chromatin IP against H3K4me1


title: FOXA1 sequencing in non-treated (DMSO as vehicle) MCF-7 cells

description: FOXA1 sequencing


title: cJun sequencing in estradiol (E2) treated MCF-7 cells

description: Chromatin IP against cJun

value: MCF-7 breast cancer cells, E2 treated


title: cFos sequencing in non-treated (DMSO as vehicle) MCF-7 cells

description: Chromatin IP against cFos

value: cFos - Cat# sc-7202, Santa Cruz


title: FOXA1 sequencing in estradiol (E2) treated MCF-7 cells

description: FOXA1 sequencing, after E2 treatment


title: hESC_Input_XL_ChIP-Seq

first: Matthew

last: Trotter

address: West Forvie Building, Forvie Site, Robinson Way

department: Department of Surgery

country: United Kingdom

institute: University of Cambridge

description:
Input control for ChIP-Seq: DNA cross linked with formaldehyde plus extra chemical linkers.
One rep: Control_s_1

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Reads were filtered for overlap with UCSC hg18 RepeatMasker.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) as described in (Teo et al. Genes Dev, 2010, In Press).

source_name: Input DNA: H9 human embryonic stem cell (hESC)

growth_protocol: H9 hESCs (WiCell, Madison, WI) were cultured in CDM with 10 ng/ml Activin A and 12 ng/ml FGF2 as described previously (Brons et al., Nature, 2007, 448(7150):191-5). hESCs were induced to differentiate into endoderm using CDM-PVA + 100 ng/ml Activin + 10 ng/ml BMP4 + 20 ng/ml FGF2 + 10 uM LY294002 (Promega) (Touboul et al., Hepatology, 2010, 51(5):1754-65).

extract_protocol: Libraries were prepared using the Solexa ChIP-seq DNA sample prep kit (IP102-1001). After amplification, DNA fragments of between 180 to 400bp were gel extracted and the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following manufacturer's protocols.

value: H9 hESC

tag: developmental stage

value: embryonic stem cell


title: hESC_48h-endodiff_EOMES_XL_ChIP-Seq_reps1and2

description:
Chromatin IP for EOMES: DNA cross linked with formaldehyde plus extra chemical linkers.
Two reps: EOMES_rep1_s_3 and EOMES_rep2_s_5.

source_name: EOMES ChIP fraction: early endoderm (hESC differentiated towards endodermal fate 48h)

value: early endoderm 48h

value: EOMES

tag: chip antibody vendor

value: Abcam (Cambridge, UK)

tag: chip antibody catalog#


title: cFos sequencing in estradiol (E2) treated MCF-7 cells

description: Chromatin IP against cFos


title: Heat shock partial digestion, rep2

status: Public on Jan 24 2011

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

description:
HS.partial_rep2
DNA fragment size selection ~150 bp.

data_processing: Alignment: Sequence reads were obtained and mapped to the yeast (October, 2003; sacCer1) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

organism: Saccharomyces cerevisiae

source_name: yeast culture, heat shock, partial digestion

growth_protocol: 3ml pre-culture of Saccharomyces cerevisiae strain JKM139 in YE media was diluted to 500ml of YE media. For the optimal growth samples, the culture was grown to OD600= 0.7-0.8 at 28oC. For the heat-stressed samples, an ensuing step of 36oC incubation (water bath) for 20 minutes was applied.

extract_protocol: The cell pellet was subjected to zymolase treatment and MNase digestion. After MNase digestion, supernatant was collected by centrifugation and used as affinity purification material. DNA was extracted and subjected to electrophoresis. Mono-nucleosomal DNA bands (~150bp) were recovered and subjected to Illumina massive sequencing.

treatment_protocol: For crosslinking chromatin prior to MNase digestion, cells were incubated with 1% formaldehyde for 15min and quenched with 0.125M glycine prior to cell harvesting.

tag: mnase digestion time

value: 5 min

tag: growth temperature


title: Cross-linking partial digestion

description:
CL.partial
DNA fragment size selection ~150 bp.

source_name: yeast culture, cross-linking, partial digestion

tag: strain

tag: treatment

value: formaldehyde cross-linking


title: Heat shock complete digestion, rep2

description:
HS.complete_rep2
DNA fragment size selection ~150 bp.

source_name: yeast culture, heat shock, complete digestion

value: 25 min


title: Cross-linking complete digestion

description:
CL.complete
DNA fragment size selection ~150 bp.

source_name: yeast culture, cross-linking, complete digestion


title: Wild type complete digestion, rep2

description:
WT.complete_rep2
DNA fragment size selection ~150 bp.

source_name: yeast culture, complete digestion


title: Heat shock partial digestion, rep1

description:
HS.partial_rep1
DNA fragment size selection ~150 bp.


title: Tcruzi_epi_J1_ko_SLT

status: Public on Jan 21 2011

city: Bern

first: Daniel

last: Nilsson

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

description:
GDG-41
instrument model: GA-Iix

data_processing:
The demultiplexing is handled by the standard Illumina tools (by reading extra bases off a barcode after the ordinary cycles finish), and hence no barcode or adaptor sequences are found in the raw output files.
Base calling was performed using the Genome Analyzer Pipeline (Illumina), RTA SCS.2.6, CASAVA 1.6. Linker sequences were removed while separating reads according to identified barcodes. Only sequence reads of inserts with a length of at least 24 nt were retained. A pipeline was set up using languages with open source interpreters (bash, perl and R) to automate the following analysis. The reads were mapped to the genome sequence of T. cruzi CL Brener using maq (http://maq.sourceforge.net) with n=3. Single mapping reads were separated from multi mapping reads by an alignment quality threshold of 30. Tags ending in the same position were joined together, and their counts were added (using bioperl). Tag counts were normalized to the library size and scaled linearly to reflect counts of tags per million (TPM). Mapped tags were assigned to the downstream annotated protein coding gene. Tags mapping internally to a coding sequence (CDS) were assigned to it as internal splice sites.

molecule: polyA RNA

organism: Trypanosoma cruzi

source_name: Trypanosoma cruzi cell culture

growth_protocol: Y strain T. cruzi epimastigotes were grown in liver infusion Tryptose media as previously described (Camargo, 1964). Cultures were harvested at mid log phase by centrifugation. Metacyclics were obtained from epimastigotes by axenic induction as described previously (Contreras et al., 1994). Briefly, epimastigotes were transferred to Grace’s insect media supplemented with 10% fetal bovine serum and grown for 10-14 days at 37C. Differentiated metacyclic stages were purified using TAAUAG media and was confirmed by their morphology. These metacyclics were then used to infect irradiated vero and myoblast cells as previously described (da Silva et al., 2009). Trypomastigotes were then grown in monolayers of Vero cells/myoblasts in Modified Eagle’s Media containing 20% fetal bovine serum. Emergent trypomastigotes were harvested daily and examined by light microscopy. Preparations containing >95% of trypomastigotes were used in the subsequent assays.

extract_protocol: SLT_protocol_1.2: RNA was extracted using TriPure (Roche, Switzerland) according to the manufacturer. PolyA mRNA was purified from 7.5 μg total RNA using Dynabeads oligo-(dT) beads according to the manufacturer (Invitrogen, USA). First strand cDNA was synthesized from polyA RNA using random hexamers and Superscript II reverse transcriptase (Invitrogen, USA) in a final volume of 20 μl for 1 hour at 42ºC. Half of the first strand mix was used for second strand synthesis (10 μl 1st strand mix, 1 μl RNaseH, 15 minutes at 37ºC). Second strand synthesis was done using 2 μl 10x Thermopol buffer (New England BioLabs), 1 μl dNTPs 10mM, 1 μl 2nd strand primer 10μM ([BIOT]5'- AATGATACGGCGACCACCGAGATCTACAGTTTCTGTACTATATTG -3'), 2 units Taq polymerase (New England BioLabs, USA) and 4.5 μl H2O by incubation for 5 minutes at 50ºC and then 5 minutes at 72ºC. The cDNA was purified on a Qiagen MinElute column (Qiagen, USA) and eluted in 10ul TE buffer. Adapter ligation to the purified dsDNA was done using (10.0 μl DNA, 2.5 μl 10X Ligase Buffer (New England BioLabs), 10.0 μl H2O, 1.0 μl Fasteris customized bar-coded paired-end Illumina adapter, 600 units T4 DNA Ligase (New England BioLabs, USA) for 1hour at room temperature. The ligation mix was purified from unligated linker with Streptavidin beads (Dynabeads). After incubation at room temperature for 15 minutes beads were separated on a magnetic stand, and washed twice and then resuspended in 20 μl 10mM Tris buffer. 5 μl was used for PCR amplification with primers including an indexing sequence, and otherwise following the standard Illumina mRNA-SEQ library amplification protocol. Fragments in the range 150-400 bp were separated on a 2% agarose-TBE gel and subsequently purifieda on Qiagen Gel Extraction MinElute columns (Qiagen, USA). Quality control for insert size was performed by TOPO cloning and subsequent ABI sequencing.

tag: life cycle stage

value: Epimastigote


title: Tcruzi_epi_wt_SLT

description:
GDG-40
instrument model: GA-Iix

value: Y (wt)


title: Tcruzi_trypo_wt_SLT

description:
GDG-42
instrument model: GA-Iix

value: Trypomastigote


title: Tcruzi_trypo_J1_ko_SLT

description:
GDG-43
instrument model: GA-Iix


title: Tcruzi_meta_J1_ko_SLT

description:
GDG-39
instrument model: GA-Iix

value: Metacyclic


title: Tcruzi_ama_J1_ko_SLT

description:
GDG-37
instrument model: GA-Iix

value: Amastigote


title: Tcruzi_meta_wt_SLT

description:
GDG-38
instrument model: GA-Iix


title: RNA_whole_worm_mixed_stages [kourosh]

first: Kristin

middle: C

last: Gunsalus

department: Biology

institute: NYU Center for Genomics and Systems Biology

data_processing: The rawdata .sff file was generated by the 454 GS FLX System Software version 2.3.  The GS De Novo Assembler (Newbler) was used to align the untrimmed reads to the WS190 genome assembly.   77% of the reads aligned to WS190, resulting in an assembly of 4818 contigs.  The assembled contigs and quality data output by Newbler are in .fna and .qual files respectively.  The Galaxy tool was used to convert contig coordinates to a .bed file for visualization on a genome browser. The Newbler aligner settings are recorded in 454MappingProject.xml.

source_name: N2 wildtype

growth_protocol: Mixed stage worms were grown on 10 cm2 NGM plates seeded with OP50.

extract_protocol:
RNA extraction was performed following the vendor’s protocol with the following modification: 3 times freeze/thaw/vortex and disruption with pellet pestle was included to increase worm lysis efficiency.
Total RNA was incubated at 55°C for one hour in presence of Superscript III Reverse Transcriptase (Invitrogen) and a universal VN poly-dT reverse primer, according the manufacture specifications. 3'UTR amplification were performed in 96-well plates format using transcript-specific forward primers and the universal reverse primer in presence of RNA prepared in the first strand reaction, using the following PCR parameters: denaturing 94°C 30 sec, annealing 60°C 30 sec, extension 72°C for 3 minutes. 3'UTRs were recombined into pDONR P2R-P3 entry vector using the BP Clonase II Enzyme Mix kit (Invitrogen) following the manufacturer's specifications and transformed into MultiShot Stripwell TOP 10 plates (Invitrogen). The transformed bacteria were grown overnight at 37°C under kanamycin selection.   1ul of each overnight bacteria growth was used as template for 6,432 PCR amplifications using the following primers:   forward: GTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA   Reverse: TAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  The PCR amplicons were then pooled, gel purified and prepared for 454 sequencing using manufacture instructions.

value: mixed stages


title: IntestineEpi_APOBEC1

status: Public on Jan 23 2011

first: Brad

last: Rosenberg

address: 1 Gustave L Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
RNA-Seq on polyA RNA - aligned only uniquely-mappable reads
Paired-end library: The insert size is approximately 80 bp and the standard deviation is approximately 35 bp (same for both samples).

data_processing: Prior to alignment, sequences were trimmed by removing the first 2-nt of each read.  Reads were mapped to the C57/BL6 reference mouse genome (NCBI37/mm9) using the Tuxedo Tools software packages, Bowtie (v0.11.2.0) and TopHat (v1.0.12).  For mapping, up to 2 mismatches were permitted in the seed region (first 28 nt) of each read, and only reads mapping to unique sites in the genome were analyzed - all alignments to multiple sites or ambiguous positions were suppressed.

source_name: Small Intestine Epithelium

growth_protocol: Mouse small intestines were removed and washed in Hanks Buffered Saline Solution (HBSS) with Ca2+ and Mg2+. Jejunum segments were dissected, everted and cut into ~5 cm pieces. Enterocytes were isolated with a protocol adapted from Xie Y, et al. Am J Physiol Gastrointest Liver Physiol 285, G735-46 (2003). Briefly, jejunum segments were washed 5 times in HBSS (with Ca2+ and Mg2+) containing 1% (v/v) fetal bovine serum (FBS) and then washed once in HBSS (without Ca2+ and Mg2+) containing 2% (w/v) glucose and 2% bovine serum albumin (BSA). Jejunum segements were transferred to enterocyte isolation buffer (HBSS without Ca2+ and Mg2+, 1.5 mM EDTA, 0.5 mM DTT) and incubated at 37°C with agitation for 30 minutes. Enterocyte suspensions were collected, washed and resuspended in TRI Reagent (Ambion) for RNA preparation.

extract_protocol: Enterocyte total RNA was prepared by TRI Reagent (Ambion) extraction and treated with TURBO DNase (Ambion). Isolation of poly-A+ mRNA from total RNA was performed on polyT resin (MicroPoly(A)Purist Kit, Ambion). Poly-A+ mRNA was fragmented in fragmentation buffer (40 mM Tris acetate pH 8.2, 100 mM potassium acetate, 30 mM magnesium acetate) at 94°C for exactly 4 minutes 30 seconds. Fragmented RNA was reverse transcribed (Superscript III, Invitrogen) and cDNA was prepared with the Double-stranded cDNA Synthesis Kit (Invitrogen). Sequencing adapter oligonucleotides (Illumina) were added with T4 DNA Ligase (Quick Ligation Kit, New England Biolabs). ds-cDNA libraries were size-separated by agarose gel electrophoresis and fragments ranging from approximately 175nt - 225nt were excised and PCR amplified with linker specific primers (Illumina). Integrity and quality of RNA and cDNA were monitored throughout on the Agilent Bioanalyzer 2100.

tag: genotype/variation

value: Small Intestine Epithelium

value: Adult


title: IntestineEpi_WT

value: wild-type


title: Wild type partial digestion, rep2

description:
WT.partial_rep2
DNA fragment size selection ~150 bp.

source_name: yeast culture, partial digestion


title: Tcruzi_ama_wt_SLT

description:
GDG-36
instrument model: GA-Iix


title: Wild type complete digestion, rep1

description:
WT.complete_rep1
DNA fragment size selection ~150 bp.


title: Ring1b ChIP-Seq in mES cells

status: Public on Jan 19 2011

description:
05142008_209LAAAXX_B6
Chromatin IP against Ring1b in mES cells.

data_processing:
Images analysis and base calling were done using the Solexa pipeline.

For all samples, reads were aligned to mouse genome build mm8 using Bowtie.

For all samples, aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embryonic stem cells, Ring1b ChIP

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: V6.5 embryonic stem cells


title: s5_ago104 Ovaries

city: Montpellier

last: Grimanelli

address: 911 Av Agropolis

country: France

institute: IRD

data_processing: Alignment: 17pb tags were were extracted from the raw data and mapped to the maize (March, 2010) B73 reference genome using BOWTIE. All reads mapping with 0-1 mismatches were retained.

organism: Zea mays

growth_protocol: Ovaries collected from immature ears grown in screen-house conditions, temperature 20 (night) -25 (days) with 14 hours of light/day.

extract_protocol: RNAs isolated using TRIZOL.  Illumina libraries were constructed for the wild type and mutant samples following Illumina/Solexa's standard protocol for Digital Gene Expression Tag Profiling library preparation. Adapter was as follows: 5′-CAAGCAGAAGACGGCATACGATCTAACGATGTACGCA GCAG-3’, corresponding to DpnII-derived tags.

tag: cultivar

value: ago104 KO

value: Immature ovaries


title: WT_NET-seq

city: San Francisco

first: L. Stirling

middle: Stirling

last: Churchman

address: 1700 Fourth St. Byers Hall - Room 404

institute: University of California-San Francisco

description: IP against 3xFLAG affinity label

data_processing: Image data obtained by the Illumina Genome Analyzer 2 was analyzed using the GAPipeline to extract raw sequences. Matrix and phasing parameters were estimated from a φX control lane. Raw sequences 40 bases long were composed of the cDNA of the fragmented RNA sequence. For RNA fragments smaller than 40 bases, the sequence is followed by part of the 5’ Illumina linker sequence which was removed in silico. Alignments to the yeast genome was performed by the alignment program, Bowtie 0.12.0 (http://bowtie-bio.sourceforge.net/). Bowtie settings were chosen so that three mismatches were allowed and alignments were required to be unique. The shortest sequenced fragments were approximately 18 nucleotides due to the RNA size selection step after ligation and random fragmentation. Alignments were first performed against tRNA and rRNA sequences to remove them. The remaining sequences were aligned against a recent version of the yeast genome downloaded from the Saccharomyces Genome Database (SGD, http://www.yeastgenome.org/) on October 11, 2009

source_name: yeast BY4741, mid-exponential phase

growth_protocol: Yeast strains were grown in YEPD at 30°C with shaking from an initial OD of 0.1 to mid-log phase with an OD of 0.6-0.8.

extract_protocol: Frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). An preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~10 cycles) by band extraction from a polyacrylamide gel that had not reached saturation. DNA was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.

tag: library strategy

value: NET-Seq

tag: molecule

value: nascent RNA

tag: ip

value: IP against 3xFLAG affinity label


title: Total RNA Pol2 ChIP-seq in mES cells with shSpt4 with flavopiridol

description:
04172009_313AFAAXX_B1
Chromatin IP against Total RNA Pol2 mES+shSpt4+flavopiridol.

source_name: Embryonic stem cells, Spt4 knockdown, total RNA pol2 ChIP

treatment_protocol: The Spt4 subunit of the DSIF Complex was knocked down using an shRNA specific to Spt4. It was knocked down for approximately 4 days prior to crosslinking. Cells were treated with 1uM flavopiridol for 1 hour prior to crosslinking. This was done in collaboration with Ryan Flynn from the Sharp lab.

tag: strain/background

value: RNA Pol II (Rpb1 N-terminus)

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number

tag: knockdown

tag: drug treatment

value: flavopiridol

tag: treatment duration

value: 1 hr


title: Total RNA Pol2 ChIP-seq in mES cells with shSpt5 with flavopiridol

description:
04172009_313AFAAXX_B2
Chromatin IP against Total RNA Pol2 mES+shSpt5+flavopiridol.

source_name: Embryonic stem cells, Spt5 knockdown, total RNA pol2 ChIP

treatment_protocol: The Spt5 subunit of the DSIF Complex was knocked down using an shRNA specific to Spt5. It was knocked down for approximately 4 days prior to crosslinking. Cells were treated with 1uM flavopiridol for 1 hour prior to crosslinking. This was done in collaboration with Ryan Flynn from the Sharp lab.

tag: cell type

tag: chip antibody


title: RCO1D_NET-seq

description: IP against 3xFLAG affinity label

value: RPB3-3xFLAG::NAT rco1D::URA3


title: DST1D_NET-seq

description: IP against 3xFLAG affinity label

value: RPB3-3xFLAG::NAT dst1D::URA3


title: SET2D_NET-seq

description: IP against 3xFLAG affinity label

value: RPB3-3xFLAG::NAT set2D::URA3


title: EAF3D_NET-seq

description: IP against 3xFLAG affinity label

value: RPB3-3xFLAG::NAT eaf3D::URA3


title: WT_mRNA-seq

extract_protocol:
Total RNA purification from clarified lysate was done by the hot acid phenol method. Polyadenylated mRNA was purified from 50 µg total RNA using magnetic oligo-dT DynaBeads (Invitrogen).
Purified RNA was fragmented by alkaline hydrolysis and size selected by electrophoresis on a polyacrylamide gel to yield lightly fragmented RNA of size distribution similar to that of nascent RNA. Fragmented mRNA was dephosphorylated by T4 polynucleotide kinase (NEB). An preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~10 cycles) by band extraction from a polyacrylamide gel that had not reached saturation. DNA was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.

value: mRNA


title: Total RNA Pol2 ChIP-seq in mES cells with shNelfE with flavopiridol

description:
04172009_313AFAAXX_B3
Chromatin IP against Total RNA Pol2 mES+shNelfE+flavopiridol.

source_name: Embryonic stem cells, NelfE knockdown, total RNA pol2 ChIP

treatment_protocol: The NelfE subunit of the NELF Complex was knocked down using an shRNA specific to NelfE. It was knocked down for approximately 4 days prior to crosslinking. Cells were treated with 1uM flavopiridol for 1 hour prior to crosslinking. This was done in collaboration with Ryan Flynn from the Sharp lab.

value: NelfE


title: REST ChIP-Seq in mES cells

description:
11112008_30FFUAAXX_B8
Chromatin IP against REST in mES cells.

source_name: Embryonic stem cells, REST ChIP

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: REST

value: Upstate

tag: antibody lot number


title: MCAF1 ChIP-Seq in mES cells

description:
10022009_42TM0AAXX_B1
Chromatin IP against MCAF1 in mES cells.

source_name: Embryonic stem cells, MCAF1 ChIP

tag: strain

value: V6.5 embryonic stem cells

value: Bethyl


title: Total RNA Pol2 ChIP-seq in mES cells with shControl with flavopiridol

description:
04242009_42759AAXX_B8
Chromatin IP against Total RNA Pol2 mES+shControl+flavopiridol.

source_name: Embryonic stem cells, control knockdown, total RNA pol2 ChIP

treatment_protocol: A control shRNA was used for this analysis in parallel with shSpt5, shSpt4 and shNelfE. Control shRNA was infected approximately 4 days prior to crosslinking. Cells were treated with 1uM flavopiridol for 1 hour prior to crosslinking. This was done in collaboration with Ryan Flynn from the Sharp lab.

value: control


title: ChIP-Seq for H3K4me3 in MEF

description:
07092009_42F6GAAXX_B2
Chromatin IP against H3K4me3.

source_name: Mouse embryonic fibroblasts, H3K4me3 ChIP

growth_protocol: Mouse embryonic fibroblasts were grown in DMEM with 10% FBS.

value: mouse embryronic fibroblast (MEF)

value: Abcam


title: ChIP-Seq for H3K9me3 in 2nd MEF

description:
06122009_42B4HAAXX_B5
Chromatin IP against H3K9me3.

source_name: Mouse embryonic fibroblasts with Dox-inducible Klf4, Sox2 and Oct4 (KSO), H3K9me3 ChIP

growth_protocol: Oct4/Klf4/Sox2-inducible iPS cells with Oct4-selectable cassette were derived in the presence of Wnt3a-conditioned medium and were injected into BDF2 blastocysts. Secondary fibroblasts were harvested from the resulting chimeric embryos at 13.5dpc. Fibroblasts derived from the injected iPS cells were selected for with 2µg/ml puromycin for 48 hours. Cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% cosmic calf serum, β-mercaptoethanol, nonessential amino acids, L glutamine and penicillin/streptomycin.

value: secondary mouse embryronic fibroblast (MEF)


title: H4K20me3 ChIP-Seq in mES cells

description:
06122009_42B4HAAXX_B7
Chromatin IP against H4K20me3 in mES cells.

source_name: Embryonic stem cells, H4K20me3 ChIP


title: s3_WildType Ovaries

source_name: wild-type

value: wild-type

value: Immature ovaries


title: ChIP-Seq for H3K9me3 in MEF

description:
07092009_42F6GAAXX_B3
Chromatin IP against H3K9me3.

source_name: Mouse embryonic fibroblasts, H3K9me3 ChIP


title: ChIP-Seq for H3K27me3 in MEF

description:
07092009_42F6GAAXX_B4
Chromatin IP against H3K27me3.

source_name: Mouse embryonic fibroblasts, H3K27me3 ChIP


title: Nucleus accumbens DNA input 2

status: Public on Jan 18 2011

first: Li

last: Shen

address: 1425 Madison Ave

department: Neuroscience

description: Replicate 2

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Filtering: BED files were converted from ELAND sorted.txt files using a custom PERL script. The ELAND sorted.txt files contain short reads that pass the default Illumina pipeline's quality filtering and can be uniquely aligned to the reference genome.

Chromosome name<TAB>Start<TAB>End<TAB>Name(always "U0")<TAB>Score(always "0")<TAB>Strand

source_name: Mouse nucleus accumbens 24 hr

extract_protocol: 24 hours after the last dose, chromatin immunoprecipitation was performed utilizing previously validated methods. Each experimental condition was performed in either duplicate or triplicate (2 cocaine, 3 saline). Briefly, for each ChIP, bilateral 14-gauge NAc punches (anterior and posterior) were pooled from 5 mice (20 punches). Tissue was lightly fixed to cross-link DNA with associated proteins and the material was further sheared and immunoprecipitated using sheep anti-rabbit magnetic beads conjugated to an antibody that specifically recognizes H3K9me3. Resulting immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-sequencing using an Illumina kit according to manufacturer’s instructions. 20 ng of starting material, as determined by PicoGreen concentrations, was used in each case.  Briefly, each sample underwent end repair followed by addition of an A base to the 3’ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 3% agarose gel. The range of excision was 175-225 bp. Following DNA clean up, samples were amplified with 21 cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. 5 pM concentrations were used to generate clusters for sequencing analysis.

treatment_protocol: Animals received daily i.p. injections of either 'saline' (7 treatments of saline) or 'repeated' cocaine (7 treatments of 20 mg/kg cocaine).

tag: age

value: 8-week old male

tag: tissue

value: Bilateral, anterior/posterior 1mm-thick, 14-gauge punches, pooled together from 5 animals

tag: fraction

value: Input DNA


title: Nucleus accumbens DNA input 4

description: Replicate 4


title: Nucleus accumbens DNA input 3

description: Replicate 3


title: Nucleus accumbens DNA input 1

description: Replicate 1


title: Nucleus accumbens repeated cocaine 24 hr 2

description: Replicate 2

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Filtering: BED files were converted from ELAND sorted.txt files using a custom PERL script. The ELAND sorted.txt files contain short reads that pass the default Illumina pipeline's quality filtering and can be uniquely aligned to the reference genome (mm9).
Included are stardard six field BED files:

Chromosome name<TAB>Start<TAB>End<TAB>Name(always "U0")<TAB>Score(always "0")<TAB>Strand

value: 8-week old

tag: gender

value: male

tag: treatment

value: 7 treatments of 20 mg/kg cocaine

tag: antibody

value: Upstate Millipore

tag: antibody catalog#

tag: antibody lot#

value: ChIP DNA


title: Nucleus accumbens DNA input 5

description: Replicate 5


title: Nucleus accumbens DNA input 6

description: Replicate 6


title: Nucleus accumbens Saline 24 hr 3

description: Replicate 3

value: 7 treatments of saline

tag: antibody vendor


title: Lin28 IP_seq

description:
Lin28  immunoprecipitated RNAs
RNAseq
total reads: 11524253
uniquely mapped reads with up to 2 mismatches: 6074622

data_processing:
Alignment: Sequence reads were obtained and mapped to the human hg18 (March, 2006) genomes by using bowtie with uniquely mapping and up to 2 mismatches
Column description in the bedgraph files: Chromosome; start position; end position; height

source_name: hES h1 cells, IP

growth_protocol: H1 hESCs were cultured in Matrigel-coated plates in mouse embryonic fibroblast conditioned medium supplemented with 8 ng/mL bFGF

extract_protocol: Lin28 immunoprecipitated or preimmune RNAs were individually extracted and libraries were prepared using the Illumina mRNA-Seq Sample Prep Kits (P/N 1004814) according to the manufacturer’s instructions

value: H1 human embryonic stem cells

tag: chromosome

value: diploid

tag: passages

tag: sample type

value: Lin28 immunoprecipitated fractioni

value: anti-Lin28 antibody

tag: antibody batch/lot#


title: preimmune_seq

description:
preimmune RNA
RNAseq
total reads: 9496883
uniquely mapped reads with up to 2 mismatches: 4746125

source_name: hES h1 cells, preimmune

tag: cell type


title: Nucleus accumbens repeated cocaine 24 hr 1

description: Replicate 1


title: sperm cytosine methylation caloric restriction diet B43.1

status: Public on Jan 14 2011

city: Jerusalem

first: naomi

last: habib

address: Givat-Ram

department: Computer Scince

country: Israel

institute: Hebrew University

description: immunoprecipitation using antibodies against 5me-C followed by deep sequencing

data_processing: Mapped the first 30 nt of sequencing reads to the mouse genome (mm9) using Bowtie, allowing 1 mismatch. We only retained reads that map to one location in the genome for further analysis. We extended every read by 400 bp (the average size of cloned DNA fragment) in the 3' end direction.

source_name: Sperm cells

growth_protocol: Sperm were isolated from caudal epididymus tissue in mice at ~12 weeks of age

extract_protocol: Methyl-DNA immunoprecipitation protocol : 4 μg of purified genomic DNA was fragmented to a mean size of 300bp using a Covaris machine. The sonicated DNA was denatured, then incubated with 5mC antibody (Eurogentec) in IP buffer for 2 hours at 4 C. Pre-washed M-280 Dynabeads (Invitrogen) were added to the IP, and incubated for 2 hours. The MeDIP samples were washed 4X in IP buffer. DNA was purified from IPs.

treatment_protocol: Mice males were raised on diet (control or low-protein) until 9-12 weeks of age.

tag: diet

value: Caloric Restriction


title: sperm cytosine methylation control diet B43.2

value: Control


title: sperm cytosine methylation control diet B87.1


title: Ler x C24 F1 hybrid - Whole 2-week old seedlings Rep1

status: Public on Jan 12 2011

city: Acton

first: Michael

last: Groszmann

state: ACT

address: Clunies Ross St

department: Agriculture

country: Australia

institute: CSIRO

description: small RNA

data_processing: RNA-seq reads were mapped to Arabidopsis genome (Tair 8) using Novoalign version 2.10 from NovoCraft Technologies (www.novocraft.com) with '-a' (adaptor stripping) invoked.

source_name: Whole 2-week old seedlings

growth_protocol: All plants were grown at 23C under a 16-hour light/8-hour dark cycle.

extract_protocol: 14 to 15 day old seedlings were collected, pooled and RNA extracted using trizol (Ambion). RNA underwent 1 chloroform step before being precipitated in isopropanol over night at minus 20 degrees.  Total RNA was washed once in 75% ethanol before being resuspended in DEPC treated water. Total RNA was stored at -80oC before being sent to Geneworks (Adeliade, Australia) where the RNA underwent standard illumina small RNA preparation and sequencing.

tag: ecotype

value: Ler x C24 F1 hybrid

value: whole seedlings

value: 2-weeks old


title: sperm cytosine methylation low protein diet B87.2

value: Low Protein

tag: strain


title: C24 x Ler F1 hybrid - Whole 2-week old seedlings - Rep1

description: small RNA

value: C24 x Ler F1 hybrid

tag: age


title: Nucleus accumbens Saline 24 hr 2

description: Replicate 2

value: 8-week old

tag: tissue

value: Bilateral, anterior/posterior 1mm-thick, 14-gauge punches, pooled together from 5 animals


title: Ler - Whole 2-week old seedlings - Rep1

description: small RNA

value: Landsberg erecta (Ler)


title: Nucleus accumbens Saline 24 hr 1

description: Replicate 1

value: male

value: Upstate Millipore

tag: fraction


title: mut-16(mg461), adult

city: Boston

first: Taiowa

last: Montgomery

address: 185 Cambridge Street, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing: Sequences were parsed and mapped to the C. elegans genome (Wormbase release WS203) using CASHX (version 2.0).  R, Microsoft Excel, custom perl scripts and programs included in the CASHX software package were used for subsequent data analyses.

source_name: whole worms

growth_protocol: C. elegans were grown at 20˚C on OP50.

extract_protocol: Total RNA was isolated from synchronized worms and small RNAs were size selected, tobacco acid pyrophosphatase (TAP) treated to remove 5’ di- and triphosphate groups, ligated to 5’ and 3’ adapters and subjected to RT-PCR.

tag: developmental stage

value: adult


title: C24 - Whole 2-week old seedlings - Rep1

description: small RNA


title: mut-16(pk710), adult


title: wild type, adult


title: wild type, embryo

source_name: embryos

value: embryo


title: 2268 LD, mRNA

city: Nanchang

first: Lusheng

last: Huang

state: Jiangxi Province

address: No. 1101, Zhimin Avenue

institute: Jiangxi Agricultural University

description:
Leaf fat weight: 2842.5 g
Veil fat weight: 1347.5 g
Abdominal fat weight: 1480 g
Body weight at day: 97.6 kg
Shoulder fat thickness: 3.982 mm
Waist fat thickness: 2.706 mm

Understanding the complexity of the pig transcriptome.

data_processing:
Sequence reads were obtained and filtered using the Illumina Genome Analyzer Pipeline. The following reads were filtered: those with more than half of the base's qualities <5, those containing >5 Ns, and those containing adapters.

Reads were mapped to the reference genome (Sscrofa9.2) by SOAP2 (Li et al. 2009) to analyze their expression and distribution on the genome.

organism: Sus scrofa

source_name: longissimus dorsi muscle

growth_protocol: All animals were housed in the same environmental conditions and had a good body condition. The room temperatures were uncontrolled with natural lighting. Animals were floor fed three times a day.

extract_protocol:
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions. Remaining DNA was removed with RNase-free DNase I (New England Biolabs) for 30 min at 37oC. The quality of total RNA was assessed by the 2100 Bioanalyzer (Agilent) and agarose gel electrophoresis. We isolated poly (A) mRNA from the total RNA samples with oligo (dT) magnetic beads (Invitrogen). Purified mRNA was first fragmented by the RNA fragmentation kit (Ambion). The first-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase (Invitrogen), and the second-strand cDNA was synthesized using RNase H (Invitrogen) and DNA polymerase (New England Biolabs).
The cDNA libraries were prepared using the Illumina Genomic DNA Sample Prep kit (Illumina) in accordance with the manufacturer’s protocol and loaded onto flow cell channels of the Illumina HiSeq 2000 platform for paired-end 90 bp × 2 sequencing. The average insert size for the paired-end libraries was 200 bp (from 180 to 220 bp).

treatment_protocol: All samples were put into liquid nitrogen within 30 min after slaughtering, and then conserved in a -80oC ultra freezer until RNA extraction.

tag: breed

value: White Duroc × Erhualian

tag: generation

tag: gender

value: female

value: 240 days

value: longissimus dorsi muscle

tag: sib


title: 2270 LI, mRNA

description:
Leaf fat weight: 977.5 g
Veil fat weight: 830 g
Abdominal fat weight: 980 g
Body weight at day: 68.7 kg
Shoulder fat thickness: 3.06 mm
Waist fat thickness: 1.882 mm

Understanding the complexity of the pig transcriptome.

source_name: liver

value: liver


title: TR

status: Public on Jan 10 2011

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

description: Dicer wild-type mESC short-RNA library.

data_processing: Raw reads were processed to remove traces of 3' linker and summarized by identical sequences (observations).

source_name: mESC

extract_protocol: 10E7 cells were plated and 48 hours later irradiated once with 4000 mJ/cm2. For immunoprecipitation, anti-mouse Ago2 mAb (lot# PEM0820 Wako 2x100ul 018-22021) was used, followed by deep-sequencing of RNA tags (CLIP-seq). One short RNA library was prepared for cloning and sequencing from total RNA extracted from Dicer WT mESCs.  Libraries were cloned and sequenced using standard Illumina protocol.

value: mouse embryonic stem cells

tag: genotype

value: wild type

tag: genetic background

value: mixed 129/B6


title: 2270 LD, mRNA


title: 2270 AF, mRNA

source_name: abdominal fat

value: abdominal fat


title: 2268 LI, mRNA


title: KO2

description: Dicer-null mESC CLIP library; Performed photo-crosslinking immunoprecipitation using antibodies against Ago2, followed by deep-sequencing of RNA tags (CLIP-seq) in mouse embryonic stem cells (mESCs).

tag: antibody

tag: antibody manufacturer

value: Wako

tag: antibody catalog #

tag: antibody lot #

value: Dicer null


title: KO1

tag: cell type


title: 2268 AF, mRNA


title: WT2

description: Dicer wild-type mESC CLIP library; Performed photo-crosslinking immunoprecipitation using antibodies against Ago2, followed by deep-sequencing of RNA tags (CLIP-seq) in mouse embryonic stem cells (mESCs).


title: WT1A


title: mut-16(pk710), embryo


title: K562-TPA-H3K27ME3

city: Rechovot

first: Ram

last: Jaschek

address: P.O Box 26

institute: Weizmann Institute of Science

description:
Chromatin IP against H3K27me3
instrument model: Illumina Genome Analyzer IIx.

data_processing: CASAVA_1.6 -  K562-TPA-Gata1.txt,K562-TPA-Gata12.txt  GAPipeline-1.4.0 -  K562-TPA-Fos2.txt, K562-TPA-FosB2.txt,  K562-TPA-Fos.txt,  K562-TPA-FosB.txt,   K562-TPA-K27.txt,  CMK-  GAPipeline-1.3.2 -  K562-TPA-NIS2.txt, K562-TPA-Runx12.txt, K562-NIS2.txt, K562-Runx12.txt, K562-NIS.txt, K562-Runx1.txt     GAPipeline-1.0 - CMK-NIS.txt, CMK-Runx1.txt, K562-TPA-NIS.txt,  K562-TPA-Runx1.txt

source_name: K562 Cells, 24 hours following induction with TPA

growth_protocol: Culture in RPMI

extract_protocol: ChIP samples were prepared using 5*10 7 cells per condition. Chromatin was prepared as described in Ainbinder et. Al Mol Cell Biol. 2002.  ChIP libraries were created following illumina sample preparation protocol from 10ng of DNA. Following end-repair and A-base addition, primers were ligated and samples were size selected on a 2% agarose gel. Fragments of 200bp were excised and purified using Qiagen gel-extraction kit with gel melting at room temperature. Enrichment was carried out using 18 cycles of amplification. Library yield was quantified using Qubit (Invitrogen) while final fragment sizes were determined using Agilent BioAnalyzer. The ChIP-seq libraries were run on an Illumina GAIIx (K562-TPA-FOS, K562-TPA-FOSB, K562-TPA-GATA1) / GAII (All other tracks) at the Department of Biological Services at WIS, using illumina cluster generation kits and sequencing reagents.

treatment_protocol: cross-linked chromatin from ~108 K562 cells, before or 24h after treatment with TPA (40nM) or from ~108 cells CMK or 107 mature FL derived megakaryocytes, was prepared and fragmented to an average size of ~200bp by 40 cycles of sonications (30sec each) in 15ml tubes using the Bioruprtor UCD-200 sonicator (Diagenode, US). For immunoprecipitation, the following antibodies were added to 12ml of diluted, fragmented chromatin: 30ul of home-made anti-RUNX12 raised against the protein C-terminal fragment; anti-monomethyl-Histone H3(Lys4) and anti trimethyl-Histone H3(Lys27) (Millipore, US); anti C-FOS (Santa Cruz) and anti GATA1 (Abcam, US). Rabbit pre-immune serum was used as control. DNA was purified using QIAquick spin columns (QIAGEN, US).     Antibodies description:  NIS – non immune serum was taken from our rabbits   RUNX1- our home made antibody, described in Aziz-Aloya RB, Levanon D, Karn H, et al. Expression of AML1-d, a short human AML1 isoform, in embryonic stem cells suppresses in vivo tumor growth and differentiation. Cell Death Differ. 1998;5(9):765-773.  GATA1 – abcam, rabbit polyclonal – ChIP grade (ab11963) - 886538  FOS – Santa cruz, rabbit polyclonal – c-fos (4):sc-52, lot - #L1609  FosB: Cell Signaling, Rabbit monoclonal. FosB (5G4) lot:2  Ref: 12/2009   H3K4me1 – Milipore, rabbit polyclonal – Cat. #07-436 , Lot. #DAM1400139  H3K4me3 - Milipore, rabbit polyclonal – Cat. #17-622, Lot. #DAM1571267

tag: cell line

tag: treatment group

value: 24 hours following induction with TPA

tag: chip antibody


title: K562-TPA-H3K4ME1

description:
Chromatin IP against H3K4me1
instrument model: Illumina Genome Analyzer IIx.


title: K562_TPA-FOSB

description:
Chromatin IP against FOS
instrument model: Illumina Genome Analyzer IIx.

value: FOS


title: K562-TPA-NIS

description:
Non-immune Serum
instrument model: Illumina Genome Analyzer IIx.


title: K562-TPA-RUNX1

description:
Chromatin IP against RUNX1
instrument model: Illumina Genome Analyzer IIx.


title: K562-NIS

source_name: K562 Cells

value: untreated


title: K562-RUNX1


title: CMK-K4ME1

source_name: CMK Cells

value: CMK


title: CMK-RUNX1


title: CMK-NIS