title: ChIP-Seq analysis of H3K9me3 in human BM-MSC cells; Lib:MC:20100706:06--ChIP:MC:20100628:06:BM-MSC:H3K9Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:06--ChIP:MC:20100628:06:BM-MSC:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3766
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621426_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:06--ChIP:MC:20100628:06:BM-MSC:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4667
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0404
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.0841
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.7226
IROC_PERCENTILE: 22
POISSON_SCORE: 0.5203
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM621426_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:06--ChIP:MC:20100628:06:BM-MSC:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4941
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMDMSC H3K9me3 57
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 57 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0404
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.0841
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.7226
IROC_PERCENTILE: 22
POISSON_SCORE: 0.5203
POISSON_PERCENTILE: 88

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

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; Lib:MC:20100706:06--ChIP:MC:20100628:06:BM-MSC:H3K9Me3

value: genomic DNA

value: Primary Cell Culture

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in human BM-MSC cells; Lib:MC:20100706:02--ChIP:MC:20100628:02:BM-MSC:H3K4Me3

status: Public on Nov 12 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:02--ChIP:MC:20100628:02:BM-MSC:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3762
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM621422_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:02--ChIP:MC:20100628:02:BM-MSC:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4788
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.6564
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.6126
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9929
IROC_PERCENTILE: 15
POISSON_SCORE: 0.7285
POISSON_PERCENTILE: 89

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

ANALYSIS FILE NAME: GSM621422_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:02--ChIP:MC:20100628:02:BM-MSC:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.5062
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMDMSC H3K4me3 57
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 57 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.6564
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.6126
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9929
IROC_PERCENTILE: 15
POISSON_SCORE: 0.7285
POISSON_PERCENTILE: 89

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

molecule: genomic DNA

organism: Homo sapiens

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; Lib:MC:20100706:02--ChIP:MC:20100628:02:BM-MSC:H3K4Me3

extract_protocol: Library construction protocol: Single read - Illumina

value: healthy

tag: molecule

tag: disease

tag: markers

value: BM-MSC

value: Unknown

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in human BM-MSC cells; Lib:MC:20100706:03--ChIP:MC:20100628:03:BM-MSC:H3K36Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:03--ChIP:MC:20100628:03:BM-MSC:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3759
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621419_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:03--ChIP:MC:20100628:03:BM-MSC:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4610
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.5202
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.3677
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.998
IROC_PERCENTILE: 94
POISSON_SCORE: 0.7249
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM621419_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:03--ChIP:MC:20100628:03:BM-MSC:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4884
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMDMSC H3K36me3 57
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 57 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.5202
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.3677
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.998
IROC_PERCENTILE: 94
POISSON_SCORE: 0.7249
POISSON_PERCENTILE: 100

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

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; Lib:MC:20100706:03--ChIP:MC:20100628:03:BM-MSC:H3K36Me3

value: Abcam

value: Histone H3K36me3


title: T cell dependent immune responses: B cell activation and differentiation Group3 late germinal center B cell (GC2) Chip1

status: Public on Mar 29 2011

type: RNA

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of the second group (4 comparisons between two groups) and all chips were additionally compared within each group, (2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal Increase, MI; Decrease, D; Marginal Decrease, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset (accessible via public login without registration in the public data sets SGU of Bioretis) and compared successfully to Significance Analysis of Microarrays (SAM) and dChip in Menssen et al., 2009. Advantage of High Performance Chip Data Analysis (HPCDA) is amongst others the possibility to use always the same (default) parameters for all different datasets resulting in approx. 65 (Latin Square data set) up to 10,000 significant differentially regulated genes without parameter adjusting of the user.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: B cell subsets

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays.

growth_protocol: Follicular B cells (B220+CD21intCD231 +) and germinal center B cells (B220+PNAhigh) were sorted to high purity (>99%) using FACS Aria (BD Bioscience). Follicular B cells were sorted from the spleen of non-immunized BALB/c mice, germinal center B cells 7 days (early germinal center B cells) or 15 days (late germinal center B cells) after immunization with the T cell dependent antigen 2-phenyl Oxazolone coupled to the carrier chicken serum albumin.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: strain

value: BALB/c

tag: gender

value: female

tag: tissue

value: Spleen

tag: cell type

value: late germinal center B cell (GC2)


title: ChIP-Seq analysis of H3K27me3 in human ADMSC cells; Lib:XZ:20100107:03--ChIP:XZ:20100104:01:ADMSC:H3K27Me3

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:03--ChIP:XZ:20100104:01:ADMSC:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3760
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3889
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621420_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:03--ChIP:XZ:20100104:01:ADMSC:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.4780
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0149
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0934
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.7819
IROC_PERCENTILE: 13
POISSON_SCORE: 0.4595
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM621420_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:03--ChIP:XZ:20100104:01:ADMSC:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.5054
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ADMSC H3K27me3 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0149
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0934
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.7819
IROC_PERCENTILE: 13
POISSON_SCORE: 0.4595
POISSON_PERCENTILE: 54

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib:XZ:20100107:03--ChIP:XZ:20100104:01:ADMSC:H3K27Me3

value: genomic DNA

value: ADMSC

value: Female

value: Primary Cell Culture

value: Harvard University

value: Histone H3K27me3


title: genomic DNA from digynic placenta 3

status: Public on Jun 30 2011

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

description: digynic placental sample TP58

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Data in the table were processed by background normalization using GenomeStudio v1.0.5 that subtracts a background value derived by averaging the signals of built-in negative control bead types. Probes with detection p value less than 0.05 in at least one sample were eliminated

label: Cy5 and Cy3

source_name: digynic placenta

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using standard techniques and purified using Qiagen DNeasy Kit according to standard instructions

tag: sample type

value: placenta

tag: disease state

value: digyny


title: ChIP-Seq analysis of H3K4me1 in human BM-MSC cells; Lib:MC:20100706:01--ChIP:MC:20100628:01:BM-MSC:H3K4Me1

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:01--ChIP:MC:20100628:01:BM-MSC:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3742
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621402_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:01--ChIP:MC:20100628:01:BM-MSC:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4675
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.6649
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.6001
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9992
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7902
POISSON_PERCENTILE: 98

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

ANALYSIS FILE NAME: GSM621402_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:01--ChIP:MC:20100628:01:BM-MSC:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4949
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMDMSC H3K4me1 57
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 57 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.6649
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.6001
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9992
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7902
POISSON_PERCENTILE: 98

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

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; Lib:MC:20100706:01--ChIP:MC:20100628:01:BM-MSC:H3K4Me1

value: healthy

value: BM-MSC

value: Unknown

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me1 in human ADMSC cells; Lib:XZ:20100423:10--ChIP:XZ:20100331:10:ADMSC:H3K4Me1

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:10--ChIP:XZ:20100331:10:ADMSC:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3758
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3889
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621418_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:10--ChIP:XZ:20100331:10:ADMSC:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.4732
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.679
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6144
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7967
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM621418_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:10--ChIP:XZ:20100331:10:ADMSC:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.5006
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ADMSC H3K4me1 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.679
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6144
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7967
POISSON_PERCENTILE: 100

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib:XZ:20100423:10--ChIP:XZ:20100331:10:ADMSC:H3K4Me1

value: genomic DNA

value: Abcam

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in human ADMSC cells; Lib:XZ:20100107:07--ChIP:XZ:20100104:05:ADMSC:H3K9Me3

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:07--ChIP:XZ:20100104:05:ADMSC:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3738
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3889
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621398_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:07--ChIP:XZ:20100104:05:ADMSC:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.4670
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0187
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0606
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.7386
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3849
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM621398_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:07--ChIP:XZ:20100104:05:ADMSC:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.4944
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ADMSC H3K9me3 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0187
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0606
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.7386
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3849
POISSON_PERCENTILE: 54

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib:XZ:20100107:07--ChIP:XZ:20100104:05:ADMSC:H3K9Me3

value: ADMSC

value: Female

value: Primary Cell Culture

value: Histone H3K9me3


title: Bisulfite-Seq analysis of RRBS526 derived from human hiPS-20b cells; 42TWHAAXX100222-7-S

status: Public on Nov 11 2010

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-17950/Solexa-17937
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2321
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2304
****************
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: GSM621562_BI.iPS-20b.RRBS.RRBS526-527.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TWHAAXX100222-7-S-42TWHAAXX100222-8-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-20b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-20b Cell Line, Libraries RRBS526-527 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5245
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b RRBS 26
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line RRBS Libraries RRBS526-527 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.83

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

source_name: IPS cell line 20b; 42TWHAAXX100222-7-S

value: induced pluripotent stem cells 20b

value: Harvard University

value: Cell Line

tag: line

tag: lineage

value: induced pluripotent cells

value: undifferentiated

tag: passage

tag: medium

value: KSR

tag: Sex

value: Male

tag: batch

value: DNA Methylation

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: 20 ng

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: T4 Ligase (2,000U/ul) 16C o/n

value: 2x5hrs Epitect Kit

value: Pfu Turbo Cx hot start

value: Smith et al., Methods 48, 226-232

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Gel size selection


title: Bisulfite-Seq analysis of RRBS353 derived from human hiPS-20b cells; 30GRUAAXX090604-2-S

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-11961
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2311
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2298
****************
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: GSM621552_BI.iPS-20b.RRBS.RRBS353.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30GRUAAXX090604-2-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-20b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-20b Cell Line, Library RRBS353 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5247
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b RRBS 53
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line RRBS Library RRBS353 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.11

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

source_name: IPS cell line 20b; 30GRUAAXX090604-2-S

value: induced pluripotent stem cells 20b

value: genomic DNA


title: ChIP-Seq analysis of WCE in human ADMSC cells; Lib:XZ:20100107:02--ChIP:XZ:20091228:09:ADMSC:WCE

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:02--ChIP:XZ:20091228:09:ADMSC:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3783
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3889
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621443_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:02--ChIP:XZ:20091228:09:ADMSC:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.4820
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0093
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.957
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2856
POISSON_PERCENTILE: 73

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

ANALYSIS FILE NAME: GSM621443_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:02--ChIP:XZ:20091228:09:ADMSC:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 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.5094
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ADMSC Input 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0093
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.957
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2856
POISSON_PERCENTILE: 73

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib:XZ:20100107:02--ChIP:XZ:20091228:09:ADMSC:WCE

value: ADMSC

value: Female

value: Primary Cell Culture

value: Harvard University

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: genomic DNA from digynic placenta 2

description: digynic placental sample TP20

value: placenta

value: digyny


title: Bisulfite-Seq analysis of RRBS591 derived from human hiPS-20b cells; RRBS591

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS591/RRBS592
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3954
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3959
****************
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: GSM621735_BI.iPS-20b.RRBS.RRBS591-592.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS591-RRBS592.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-20b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-20b Cell Line, Libraries RRBS591-592 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5252
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b RRBS 91
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line RRBS Libraries RRBS591-592 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.29

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

source_name: IPS cell line 20b; RRBS591

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

value: induced pluripotent cells

value: KSR

value: Cell Line

value: undifferentiated

value: Male

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS548 derived from human HUES48 cells; RRBS548

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS548/RRBS549
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4023
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4040
****************
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: GSM621598_BI.HUES48.RRBS.RRBS548-549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS548-RRBS549.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES48 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES48 Cell Line, Libraries RRBS548-549 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5253
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: HUES48 RRBS 48
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line RRBS Libraries RRBS548-549 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.1

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

source_name: Harvard University Embryonic Stem Cells; RRBS548

value: HUES48 stem cells

value: embrionic stem cell

value: genomic DNA

value: Female

value: Harvard University

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Smith et al., Methods 48, 226-232

value: Gel size selection


title: T.8Nve.Sp.OT1#4

status: Public on Oct 08 2010

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: T.8Nve.Sp.OT1#4, spleen OT1 tg Naive CD8 replicate 4

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: spleen

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: frosted microscope teasing

tag: age

value: 6 weeks

tag: exclusion markers

tag: genetic background

tag: phenotype markers

tag: separation method

value: dissection/trimming

value: male


title: T.8Nve.Sp.OT1#5

description: T.8Nve.Sp.OT1#5, spleen OT1 tg Naive CD8 replicate 5


title: T.8Mem.Sp.OT1.d45.LisOva#3

description: T.8Mem.Sp.OT1.d45.LisOva#3, spleen OT1 tg Memory CD8 day 45 VSV.OVA replicate 3


title: T.8Mem.Sp.OT1.d100.LisOva#4

description: T.8Mem.Sp.OT1.d100.LisOva#4, spleen OT1 tg Memory CD8 day 100 Lis.OVA repliacate 4


title: T.8Mem.Sp.OT1.d45.LisOva#1

description: T.8Mem.Sp.OT1.d45.LisOva#1, spleen OT1 tg Memory CD8 day 45 Listeria.OVA replicate 1


title: T.8Nve.Sp.OT1#3

description: T.8Nve.Sp.OT1#3, spleen OT1 tg Naive CD8 replicate 2


title: T.8Mem.Sp.OT1.d100.LisOva#1

description: T.8Mem.Sp.OT1.d100.LisOva#1, spleen OT1 tg Memory CD8 day 100 Listeria.OVA replicate 1


title: T.8Mem.Sp.OT1.d100.LisOva#3

description: T.8Mem.Sp.OT1.d100.LisOva#3, spleen OT1 tg Memory CD8 day 105 Lis.OVA repliacate 3


title: T.8Eff.Sp.OT1.d8.LisOva#2

description: T.8Eff.Sp.OT1.d8.LisOva#2, spleen OT1 tg effectors CD8 day 8 Listeria.OVA replicate 2


title: T.8Eff.Sp.OT1.d8.LisOva#3

description: T.8Eff.Sp.OT1.d8.LisOva#3, spleen OT1 tg effectors CD8 day 8 Listeria.OVA replicate 3


title: T.8Eff.Sp.OT1.d8.LisOva#1

description: T.8Eff.Sp.OT1.d8.LisOva#1, spleen OT1 tg effectors CD8 day 8 Listeria.OVA


title: T.8Eff.Sp.OT1.d6.LisOva#2

description: T.8Eff.Sp.OT1.d6.LisOva#2, spleen OT1 tg effectors CD8 day 6 Listeria.OVA replicate 2


title: T.8Eff.Sp.OT1.d6.LisOva#3

description: T.8Eff.Sp.OT1.d6.LisOva#3, spleen OT1 tg effectors CD8 day 6 Listeria.OVA replicate 3


title: T.8Eff.Sp.OT1.d15.LisOva#2

description: T.8Eff.Sp.OT1.d15.LisOva#2, spleen OT1 tg effectors CD8 day 15 Listeria.OVA replicate 2


title: T.8Eff.Sp.OT1.d15.LisOva#3

description: T.8Eff.Sp.OT1.d15.LisOva#3, spleen OT1 tg effectors CD8 day 15 Listeria.OVA replicate 3


title: T.8Eff.Sp.OT1.d15.LisOva#1

description: T.8Eff.Sp.OT1.d15.LisOva#1, spleen OT1 tg effectors CD8 day 15 Listeria.OVA


title: T.8Eff.Sp.OT1.d5.VSVOva#4

description: T.8Eff.Sp.OT1.d5.VSVOva#4, spleen OT1 tg effectors CD8 day 5 VSV.OVA replicate 4


title: T.8Eff.Sp.OT1.d6.LisOva#1

description: T.8Eff.Sp.OT1.d6.LisOva#1, spleen OT1 tg effectors CD8 day 6 Listeria.OVA


title: Mo.6C-IIint.Bl#3

description: Mo.6C-IIint.Bl#3, population 5 Ly6Clo MHCIIint

source_name: blood

extract_protocol: Disruption using syringe

value: CD115+ B220- CD43- Ly6C- MHCIIint


title: Mo.6C-IIint.Bl#4

description: Mo.6C-IIint.Bl#4, Nonclassical monocytes MHC II int


title: Mo.6C-IIint.Bl#5

description: Mo.6C-IIint.Bl#5, Nonclassical monocytes MHC II int


title: T.8Eff.Sp.OT1.d10.LisOva#3

description: T.8Eff.Sp.OT1.d10.LisOva#3, spleen OT1 tg effectors CD8 day 10 Listeria.OVA replicate 3


title: T.8Eff.Sp.OT1.d10.LisOva#2

description: T.8Eff.Sp.OT1.d10.LisOva#2, spleen OT1 tg effectors CD8 day 10 Listeria.OVA replicate 2


title: Mo.6C-IIint.Bl#1

description: Mo.6C-IIint.Bl#1, population 5 Ly6Clo MHCIIint


title: T.8Eff.Sp.OT1.d10.LisOva#1

description: T.8Eff.Sp.OT1.d10.LisOva#1, spleen OT1 tg effectors CD8 day 10 Listeria.OVA


title: T cell dependent immune responses: B cell activation and differentiation Group3 late germinal center B cell (GC2) Chip2

description: Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.

tag: strain

value: BALB/c

value: female

value: Spleen

value: late germinal center B cell (GC2)


title: MF.Thio5.II-480int.PC#2

source_name: Peritoneal Cavity

extract_protocol: Peritoneal Lavage

value: 8 weeks

value: CD115+ MHCII- F480int SiglecF- CD11c+


title: MF.Thio5.II-480int.PC#3


title: Mo.6C+II-.LN#3

description: Mo.6C+II-.LN#3, Classical monocytes MHC II-

source_name: Mesenteric LN

extract_protocol: Collagenase D, 30 min

value: F480+ Ly6c+ MHCII lo/+


title: MF.Thio5.II-480hi.PC#3

value: CD115+ MHC II- F480hi Siglec F-


title: Mo.6C-IIint.Bl#2

description: Mo.6C-IIint.Bl#2, population 5 Ly6Clo MHCIIint


title: Mo.6C+II-.LN#2

description: Mo.6C+II-.LN#2, Classical monocytes MHC II-


title: MF.Thio5.II-480hi.PC#2


title: MF.Thio5.II+480lo.PC#3

value: CD115+ MHC II+ F480lo SiglecF- CD11c+


title: MF.Thio5.II-480int.PC#1


title: Mo.6C+II-.LN#1

description: Mo.6C+II-.LN#1, Classical monocytes MHC II-


title: MF.Thio5.II-480hi.PC#1


title: MF.Thio5.II+480int.PC#2


title: MF.Thio5.II+480int.PC#1


title: MF.Thio5.II+480lo.PC#1


title: MF.Thio5.II+480lo.PC#2


title: MF.Thio5.II+480int.PC#3


title: DC.8-.Th#2

description: DC.8-.Th#2, thymus CD8- DCs

source_name: thymus

extract_protocol: gentle teasing using forceps, Liberase DL + DNAse I digestion, red blood cell lysis, depletion of NK1.1, GR1, CD19, CD3e, Ter119 positive cells using MACS system

value: Streptavidin-PECy7, propidium iodide

value: CD11b-FITC CD4-PE MHCII-APC CD11c-eFluor780 CD8-eFluor450


title: DC.8+.Th#3

description: DC.8+.Th#3, thymus CD8+ DCs


title: DC.8-4-11b-.Sp#4

description: DC.8-4-11b-.Sp#4, CD11c+, CD8a-, CD4-, CD11b- DCs (triple negative)

extract_protocol: Blendzyme liberase III + DNase digestion, CD3, CD19, NK1.1, GR1, Ter119 MACS depletion

value: Propidium iodide SA-PECy7

value: CD11b-FITC CD4-PE CD11c-eFluor780 CD8a-eFluor450 CD45-APC


title: DC.8-.Th#1

description: DC.8-.Th#1, thymus CD8- DCs

value: 6 weeks


title: DC.8-4-11b-.Sp#1

description: DC.8-4-11b-.Sp#1, triple negative: CD11c+, CD11b-, CD4-, CD8-

extract_protocol: digestion using Liberase III + DNase I, CD3, CD19, GR1, NK1.1, Ter-119

value: PI SA-PECy7

value: CD45-APC CD11b-FITC CD11c-eFluor780 CD4-PE CD8a-eFluor450

value: dissection/trimming


title: DC.8+.Th#2

description: DC.8+.Th#2, thymus CD8+ DCs

value: male


title: DC.8-4-11b-.Sp#2

description: DC.8-4-11b-.Sp#2, triple negative: CD11c+, CD11b-, CD4-, CD8-


title: NK.49H-.Sp#6

description: NK.49H-.Sp#6, Splenic NK cells lacking Ly49H receptor

extract_protocol: Glass slides, Ack lysis

value: dump, dead, Ly49H-


title: DC.8-4-11b-.MLN#1

description: DC.8-4-11b-.MLN#1, CD11c+, CD8a-, CD4-, CD11b-

source_name: mesenteric lymph node

value: CD11b-FITC CD4-PE CD11c-Alexa750 CD8a-PacificBlue CD45-APC


title: DC.8-4-11b-.MLN#6

description: DC.8-4-11b-.MLN#6, triple negative: CD11c+, CD11b-, CD4-, CD8-

source_name: mesenteric LNs

extract_protocol: digestion using Liberase III + DNase I, CD3, CD19, GR1, NK1.1, Ter-119 using MACS beads


title: NK.49H-.Sp#5

description: NK.49H-.Sp#5, Splenic NK cells lacking Ly49H receptor


title: NK.49H+.Sp#6

description: NK.49H+.Sp#6, Splenic NK cells expressing Ly49H receptor

extract_protocol: Glass slide, Ack lysis

value: dump, dead


title: NK.49H-.Sp#4

description: NK.49H-.Sp#4, Splenic NK cells lacking Ly49H receptor


title: Tgd.vg5-.IEL#4

description: Tgd.vg5-.IEL#4, small intestine

source_name: small intestine

extract_protocol: Mincing / Shaking / Percoll gradient, Flow Sorting

value: 5 weeks

value: CD8a+ CD8b- TCRgd+ Vg5- CD44lo


title: NK.49H+.Sp#5

description: NK.49H+.Sp#5, Splenic NK cells expressing Ly49H receptor


title: Tgd.vg5-.IEL#6

description: Tgd.vg5-.IEL#6, small intestine TCRd+ Vg5- CD44lo CD8aa+


title: Tgd.vg5-.act.IEL#2

description: Tgd.vg5-.act.IEL#2, small intestine TCRd+ Vg5- CD44+ CD8aa+

value: CD8a+ CD8b- TCRd+ Vg5- CD44hi


title: DC.8+.Th#1

description: DC.8+.Th#1, thymus CD8+ DCs (2 sorts pooled)


title: Tgd.vg5-.act.IEL#3

description: Tgd.vg5-.act.IEL#3, small intestine TCRd+ Vg5- CD44+ CD8aa+


title: DC.8-4-11b-.MLN#3

description: DC.8-4-11b-.MLN#3, CD11c+, CD8a-, CD4-, CD11b-


title: DC.8-.Th#3

description: DC.8-.Th#3, thymus CD8- DCs


title: Tgd.vg5-.act.IEL#1

description: Tgd.vg5-.act.IEL#1, small intestine TCRd+ Vg5- CD44+ CD8aa+


title: Tgd.vg5+.IEL#6

description: Tgd.vg5+.IEL#6, small intestine TCRd+ Vg5+ CD44lo CD8aa+

value: CD8a+ CD8b- TCRd+ Vg5+ CD44lo


title: Tgd.vg5+.IEL#5

description: Tgd.vg5+.IEL#5, small intestine TCRd+ Vg5+ CD44lo CD8aa+


title: Tgd.vg5+.IEL#4

description: Tgd.vg5+.IEL#4, small intestine TCRd+ Vg5+ CD44lo CD8aa+


title: Tgd.vg5+.act.IEL#4

description: Tgd.vg5+.act.IEL#4, small intestine TCRd+ Vg5+ CD44hi CD8aa+

value: CD8a+ CD8b- TCRd+ Vg5+ CD44hi


title: NK.49H+.Sp#4

description: NK.49H+.Sp#4, Splenic NK cells expressing Ly49H receptor


title: Tgd.vg2-.Sp.TCRbko#1

description: Tgd.vg2-.Sp.TCRbko#1, spleen TCRd+ Vg2- CD44-

extract_protocol: Glass TIssue Grinder, MACS depletion / Flow Sorting

value: TCRd+ Vg2- CD44-


title: Tgd.vg2-.Sp.TCRbko#3

description: Tgd.vg2-.Sp.TCRbko#3, spleen TCRd+ Vg2- CD44-

extract_protocol: Glass Tissue Grinder, MACS depletion / Flow Sorting


title: Tgd.vg2+.Sp.TCRbko#2

description: Tgd.vg2+.Sp.TCRbko#2, spleen TCRd+ Vg2+ CD44-

value: TCRd+ Vg2+ CD44-


title: Tgd.vg5+.act.IEL#1

description: Tgd.vg5+.act.IEL#1, small intestine TCRd+ Vg5+ CD44+ CD8aa+


title: Tgd.vg5-.IEL#5

description: Tgd.vg5-.IEL#5, small intestine TCRd+ Vg5- CD44lo CD8aa+


title: Tgd.vg2+.Sp.TCRbko#1

description: Tgd.vg2+.Sp.TCRbko#1, spleen TCRd+ Vg2+ CD44-


title: B.Fo.LN#1

status: Public on Aug 11 2011

description: B.Fo.LN#1, CD19+CD45R+CD23+CD21/35+

source_name: Subcutaneous LN

extract_protocol: single cell suspension using frosted glass slides, 1x flow sorting

value: 8 weeks

value: CD3 TER119 GR1 Ly6c AA4.1 CD24 IgM CD43


title: Tgd.vg2+.Sp.TCRbko#3

description: Tgd.vg2+.Sp.TCRbko#3, spleen TCRd+ Vg2+ CD44-


title: Tgd.vg2-.Sp.TCRbko#2

description: Tgd.vg2-.Sp.TCRbko#2, spleen TCRd+ Vg2- CD44-


title: Tgd.vg2+.Sp#4

description: Tgd.vg2+.Sp#4, Spleen TCRgammadelta Vg2+ resting

extract_protocol: Glass Tissue Grinder, CD19 MACS Depletion, CD4 and CD8 Dynal Magnetic Bead Depletion


title: T.4FP3-.Sp#3

description: T.4FP3-.Sp#3, Spleen Na????ve CD4 FoxP3- 25-

extract_protocol: Glass Slide, Dynabeads/Flowsorting

value: 6 weeks


title: Tgd.vg2+.Sp#5

description: Tgd.vg2+.Sp#5, Spleen TCRgammadelta Vg2+ resting


title: Tgd.vg2+.Sp#6

description: Tgd.vg2+.Sp#6, Spleen TCRgammadelta Vg2+ resting


title: T.4FP3-.Sp#2

description: T.4FP3-.Sp#2, Spleen Na????ve CD4 FoxP3- 25-


title: Tgd.vg5+.act.IEL#3

description: Tgd.vg5+.act.IEL#3, small intestine TCRd+ Vg5+ CD44+ CD8aa+

extract_protocol: Mincing / Shaking / Percoll Gradient, Flow Sorting


title: T.4.PLN.BDC#2

description: T.4.PLN.BDC#2, Pancreatic LN CD4, BDC islet-reactive TCR Tg

source_name: Pancreatic LN

extract_protocol: Glass Slide Teasing


title: T.4.PLN.BDC#4

description: T.4.PLN.BDC#4, Pancreatic LN CD4, BDC islet-reactive TCR Tg


title: T.4.Pa.BDC#5

description: T.4.Pa.BDC#5, Pancreas-Infiltrating CD4, BDC islet-reactive TCR Tg

source_name: pancreas

extract_protocol: Collagenase Type IV / DNase digestion, Flow sorting


title: T.4.LN.BDC#3

description: T.4.LN.BDC#3, Subcutaneous LN CD4, BDC islet-reactive TCR Tg


title: T.4FP3-.Sp#1

description: T.4FP3-.Sp#1, Spleen Na????ve CD4 FoxP3- 25-


title: T.4.LN.BDC#2

description: T.4.LN.BDC#2, Subcutaneous LN CD4, BDC islet-reactive TCR Tg


title: T.4.LN.BDC#4

description: T.4.LN.BDC#4, Subcutaneous LN CD4, BDC islet-reactive TCR Tg


title: T.4.Pa.BDC#2

description: T.4.Pa.BDC#2, Pancreas-Infiltrating CD4, BDC islet-reactive TCR Tg


title: T.4.PLN.BDC#1

description: T.4.PLN.BDC#1, Pancreatic LN CD4, BDC islet-reactive TCR Tg


title: T.8Nve.PP#1

status: Public on Apr 29 2010

description: T.8Nve.PP#1, Peyers Patches Naive CD8

source_name: Peyer's patches

extract_protocol: Glass slide teasing,  FACS sorting

value: CD11b CD11c CD19 CD25 CD49b Ter119 Gr1

value: TCR+ CD8+ CD44low CD62Lhigh


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group3 ND2

status: Public on May 12 2010

description:
Gene expression profiles of FACSAria sorted (a) CD3- CD56bright CD62L+, (b) CD3- CD56dim CD62L+ and (c) CD3- CD56dim CD62L- NK cells from human peripheral blood of three donors were compared using Affymetrix GeneChip HG-U133_Plus_2 arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the three groups to the GeneChip arrays. Group1: CD62L+ CD56bright CD3-,. Group2: CD62L+ CD56dim CD3-,. Group3: CD62L- CD56dim CD3-.
CD56dim CD62L+ NK cells have an intermediate gene expression profile between CD56bright and CD56dim CD62L- NK cells.

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacterers instruction. Briefly, after total RNA extraction for three samples per group, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the 9 GeneChip arrays. The HG-U133_Plus_2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PMID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All three chips of one group were compared to any of the three chips of a second group (9 comparisons,between two groups) and all chips were additionally compared within each group,(6 comparisons within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 9 SLR values of group 1 vs group 2 and 6 plus 6 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or (b) more than 50% of non parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets (for up- and downregulated genes separately) of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009; PubMedID: 19265543.

label: biotin

source_name: CD62L+CD56brightCD3-, CD62L+CD56dimCD3- and CD62L-CD56dimCD3- NK cells from human peripheral blood

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll Hypaque density gradient centrifugation from leukocyte concentrates obtained from healthy donors (DRK, Berlin, Germany). NK cell subsets were separated by MACS to enrich CD56+ cells (Miltenyi Biotech) and CD3- CD56bright CD62L+, CD3- CD56dim CD62L+ and CD3- CD56dim CD62L- NK cells were sorted using a FACSAria (BD Biosciences).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Quiagen) according to the munufacterers instruction. The amount, purity, and integrity of RNA was assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

value: CD3- CD56dim CD62L- NK cells


title: T.8Nve.PP#4

description: T.8Nve.PP#4, Peyers Patches Naive CD8

extract_protocol: glass slide teasing  double sort on ARIA

value: PI CD4 CD11b CD11c CD19 CD25 CD49b Gr-1 Ter119

value: TCRb+ CD8+ CD44low CD62Lhigh

value: dissection/trimming

value: male


title: T.8Nve.MLN#4

description: T.8Nve.MLN#4, Mesenteric LN Naive CD8

extract_protocol: Glass Slide  Flow Sorting


title: T.8Nve.LN#3

description: T.8Nve.LN#3, Subcutaneous LN Naive CD8

source_name: Subcutaneous LNs


title: T.8Nve.LN#2

description: T.8Nve.LN#2, Subcutaneous LN Naive CD8


title: Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group1 Hopx-/- Chip4

status: Public on Sep 30 2010

description: Gene expression profiles of (a) Hopx-/-, (b) Hopx+/-, and (c) Hopx+/+ Th1 cells generated from TcR-transgenic OT2 mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+.

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction for two samples per group, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

data_processing:
Data processing
Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of a second group (4 comparisons between two groups) and all chips were additionally compared within each group,(2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset and compared to Significance Analysis of Microarrays (SAM) and dChip as shown in Menssen et al., 2009; PubMedID: 19265543.

source_name: Hopx-/- Th1 cells in comparison to Hopx-expressing (Hopx+/- and Hopx+/+) Th cells

growth_protocol: Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: genotype/variation

value: Hopx-/-

tag: gender

value: Male

value: spleen

value: Th1 effector memory cells


title: T.8Nve.LN#1

description: T.8Nve.LN#1, Subcutaneous LN Naive CD8


title: proB.FrBC.BM#4

description: proB.FrBC.BM#4, Fr. B/C (pro-B)

source_name: Bone marrow

extract_protocol: 1ml syringe disruption  Flow sorting

value: CD3 Ter119 Ly6c Cd11b Gr-1

value: CD19+ IgM- CD45R+ CD43+ HSA+


title: Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group3 Hopx+/+ Chip3

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction for two samples per group, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

treatment_protocol: Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.

value: Hopx+/+

tag: tissue

tag: cell type


title: Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group1 Hopx-/- Chip3


title: T.8Nve.MLN#1

description: T.8Nve.MLN#1, Mesenteric LN Naive CD8

extract_protocol: Glass Slide Disruption  Flow Sorting


title: T.8Nve.MLN#3

description: T.8Nve.MLN#3, Mesenteric LN Naive CD8


title: Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group2 Hopx+/- Chip3

value: Hopx+/-


title: T.8Mem.Sp.OT1.d45.VSVOva#3

description: T.8Mem.Sp.OT1.d45.VSVOva#3, spleen OT1 tg Memory CD8 day 45 VSV.OVA replicate 3

extract_protocol: frosted microscope teasing  FACSaria


title: Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group2 Hopx+/- Chip4


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group3 ND1

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacterers instruction. Briefly, after total RNA extraction for three samples per group, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the 9 GeneChip arrays. The HG-U133_Plus_2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll Hypaque density gradient centrifugation from leukocyte concentrates obtained from healthy donors (DRK, Berlin, Germany). NK cell subsets were separated by MACS to enrich CD56+ cells (Miltenyi Biotech) and CD3- CD56bright CD62L+, CD3- CD56dim CD62L+ and CD3- CD56dim CD62L- NK cells were sorted using a FACSAria (BD Biosciences).


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group2 ND3

value: CD3- CD56dim CD62L+ NK cells


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group3 ND3

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All three chips of one group were compared to any of the three chips of a second group (9 comparisons,between two groups) and all chips were additionally compared within each group,(6 comparisons within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 9 SLR values of group 1 vs group 2 and 6 plus 6 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or (b) more than 50% of non parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets (for up- and downregulated genes separately) of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009; PubMedID: 19265543.


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group2 ND2

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Quiagene) according to the munufacterers instruction. The amount, purity, and integrity of RNA was assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group1 ND2

value: CD3- CD56bright CD62L+ NK cells


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group2 ND1


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group1 ND3


title: T.8Nve.PP#2

description: T.8Nve.PP#2, Peyers Patches Naive CD8

extract_protocol: glass slide teasing  sorting on ARIA

value: 6 weeks

value: CD11b CD11c CD19 CD25 CD49b Ter119 Gr1

value: TCRb+ CD8+ CD44low CD62L high


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells Group1 ND1


title: Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group3 Hopx+/+ Chip4


title: T.8Mem.Sp.OT1.d45.VSVOva#2

description: T.8Mem.Sp.OT1.d45.VSVOva#2, spleen OT1 tg Memory CD8 day 45 VSV.OVA replicate 2

extract_protocol: frosted microscope teasing  FACsaria


title: T.8Mem.Sp.OT1.d45.VSVOva#1

description: T.8Mem.Sp.OT1.d45.VSVOva#1, spleen OT1 tg Memory CD8 day 45 VSV.OVA replicate 1


title: T.8Mem.Sp#3

description: T.8Mem.Sp#3, Spleen Memory-Phenotype CD8


title: T.8Mem.Sp#1

description: T.8Mem.Sp#1, Spleen Memory-Phenotype CD8


title: T.8Mem.Sp.OT1.d106.VSVOva#2

description: T.8Mem.Sp.OT1.d106.VSVOva#2, spleen OT1 tg Memory CD8 day 106 VSV.OVA replicate 2


title: T.8Mem.LN#1

description: T.8Mem.LN#1, Subcutaneous LN Memory-Phenotype CD8

extract_protocol: Glass slide teasing, ACK lysis  Two round sort on ARIA

value: PI CD4 CD11b CD11c CD19 CD25 CD49b Gr-1 Ter119

value: CD8 TCRb CD44high CD122high


title: T.8Eff.Sp.OT1.d8.VSVOva#4

description: T.8Eff.Sp.OT1.d8.VSVOva#4, spleen OT1 tg effectors CD8 day 8 VSV.OVA replicate 4

value: dissection/trimming


title: T.8Mem.LN#3

description: T.8Mem.LN#3, Subcutaneous LN Memory-Phenotype CD8

value: male


title: T.8Mem.Sp.OT1.d106.VSVOva#3

description: T.8Mem.Sp.OT1.d106.VSVOva#3, spleen OT1 tg Memory CD8 day 106 VSV.OVA replicate 3


title: T.8Eff.Sp.OT1.d8.VSVOva#2

description: T.8Eff.Sp.OT1.d8.VSVOva#2, spleen OT1 tg effectors CD8 day 8 VSV.OVA replicate 2


title: T.8Mem.LN#2

description: T.8Mem.LN#2, Subcutaneous LN Memory-Phenotype CD8


title: T.8Eff.Sp.OT1.d6.VSVOva#4

description: T.8Eff.Sp.OT1.d6.VSVOva#4, spleen OT1 tg effectors CD8 day 6 VSV.OVA replicate 4


title: T.8Eff.Sp.OT1.d8.VSVOva#3

description: T.8Eff.Sp.OT1.d8.VSVOva#3, spleen OT1 tg effectors CD8 day 8 VSV.OVA replicate 3


title: T.8Eff.Sp.OT1.d6.VSVOva#1

description: T.8Eff.Sp.OT1.d6.VSVOva#1, spleen OT1 tg effectors CD8 day 6 VSV.OVA replicate 1


title: T.8Eff.Sp.OT1.d5.VSVOva#2

description: T.8Eff.Sp.OT1.d5.VSVOva#2, spleen OT1 tg effectors CD8 day 5 VSV.OVA replicate 2


title: T.4Nve.PP#2

description: T.4Nve.PP#2, Peyers Patches Naive CD4

value: TCR+ CD4+ CD44low CD62Lhigh


title: T.8Eff.Sp.OT1.d15.VSVOva#4

description: T.8Eff.Sp.OT1.d15.VSVOva#4, spleen OT1 tg effectors CD8 day 15 VSV.OVA replicate 4


title: T.4Nve.PP#1

description: T.4Nve.PP#1, Peyers Patches Naive CD4


title: T.8Eff.Sp.OT1.d5.VSVOva#1

description: T.8Eff.Sp.OT1.d5.VSVOva#1, spleen OT1 tg effectors CD8 day 5 VSV.OVA replicate 1


title: T.4Nve.MLN#3

description: T.4Nve.MLN#3, Mesenteric LN Naive CD4


title: T.4Nve.LN#3

description: T.4Nve.LN#3, Subcutaneous LN Naive CD4


title: T.4Nve.MLN#2

description: T.4Nve.MLN#2, Mesenteric LN Naive CD4


title: T.8Mem.Sp#4

description: T.8Mem.Sp#4, Spleen Memory-Phenotype CD8


title: T.4Nve.LN#2

description: T.4Nve.LN#2, Subcutaneous LN Naive CD4


title: T.8Eff.Sp.OT1.d15.VSVOva#3

description: T.8Eff.Sp.OT1.d15.VSVOva#3, spleen OT1 tg effectors CD8 day 15 VSV.OVA replicate 3


title: T.4Nve.LN#1

description: T.4Nve.LN#1, Subcutaneous LN Naive CD4


title: T.4Nve.MLN#1

description: T.4Nve.MLN#1, Mesenteric LN Naive CD4


title: T.4Mem44h62l.Sp#3

description: T.4Mem44h62l.Sp#3, Spleen Memory-Phenotype CD4 cells from GFP-Foxp3-CD45.1-B6 mice

value: PI CD8 CD11b CD11c CD19 CD49b Gr-1 Ter119 Foxp3

value: CD4 TCRb CD44hi CD62Llo


title: T.8Eff.Sp.OT1.d6.VSVOva#3

description: T.8Eff.Sp.OT1.d6.VSVOva#3, spleen OT1 tg effectors CD8 day 6 VSV.OVA replicate 3


title: T.4Mem44h62l.Sp#2

description: T.4Mem44h62l.Sp#2, Spleen Memory-Phenotype CD4 cells from GFP-Foxp3-CD45.1-B6 mice


title: T.4Mem44h62l.Sp#1

description: T.4Mem44h62l.Sp#1, Spleen Memory-Phenotype CD4 cells from GFP-Foxp3-CD45.1-B6 mice


title: T.4Mem44h62l.LN#2

description: T.4Mem44h62l.LN#2, Subcutaneous LN Memory-Phenotype CD4 cells from GFP-Foxp3-CD45.1-B6 mice


title: T.4Mem44h62l.LN#1

description: T.4Mem44h62l.LN#1, Subcutaneous LN Memory-Phenotype CD4 cells from GFP-Foxp3-CD45.1-B6 mice


title: T.4Mem44h62l.LN#3

description: T.4Mem44h62l.LN#3, Subcutaneous LN Memory-Phenotype CD4 cells from GFP-Foxp3-CD45.1-B6 mice


title: T.4Mem.Sp#5

description: T.4Mem.Sp#5, Spleen Memory-Phenotype CD4


title: T.4Mem.Sp#4

description: T.4Mem.Sp#4, Spleen Memory-Phenotype CD4


title: T.4Mem.LN#1

description: T.4Mem.LN#1, Memory T4 from LNs

value: PI CD8 CD11b CD11c CD19 CD25 CD49b Gr-1 Ter119

value: TCRb CD44high CD122lo CD4


title: ChIP-Seq analysis of H3K27me3 in human BM-MSC cells; Lib:MC:20100706:04--ChIP:MC:20100628:04:BM-MSC:H3K27Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:04--ChIP:MC:20100628:04:BM-MSC:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3794
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621454_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:04--ChIP:MC:20100628:04:BM-MSC:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.4818
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1232
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.1741
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9356
IROC_PERCENTILE: 62
POISSON_SCORE: 0.6273
POISSON_PERCENTILE: 94

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

ANALYSIS FILE NAME: GSM621454_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:04--ChIP:MC:20100628:04:BM-MSC:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.5092
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMDMSC H3K27me3 57
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 57 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1232
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.1741
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9356
IROC_PERCENTILE: 62
POISSON_SCORE: 0.6273
POISSON_PERCENTILE: 94

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

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; Lib:MC:20100706:04--ChIP:MC:20100628:04:BM-MSC:H3K27Me3

extract_protocol: Library construction protocol: Single read - Illumina

value: healthy

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: T.4Mem.LN#2

description: T.4Mem.LN#2, Memory T4 from LNs

value: 6 weeks

value: dissection/trimming

value: male


title: proB.FrA.FL#3

description: proB.FrA.FL#3, Fr. A (pre-pro-B)

source_name: Fetal Liver

extract_protocol: ground between 2 glass slides, ACK lysis of RBCs  1x flow sorting

value: 15 days

value: Ly6c Ter119 CD3 CD11b Gr-1

value: CD19- IgM- CD43+ CD24intermediate CD45R+ AA4.1+ CD117+ IL7R+

value: both (pooled)


title: T.4Mem.LN#3

description: T.4Mem.LN#3, Memory T4 from LNs

value: PI CD8 CD11b CD11c CD19 CD25 CD49b Gr-1 Ter119

value: TCRb CD44high CD122lo CD4


title: proB.FrA.FL#2

description: proB.FrA.FL#2, Fr. A (pre-pro-B)

value: Ly6c Ter119 CD3 Gr-1 CD11b

value: CD19- IgM- CD43+ CD24intermediate AA4.1+ CD45R+ CD117+ IL7R+


title: proB.FrA.BM#8

description: proB.FrA.BM#8, Fr. A (pre-pro-B)

extract_protocol: disruption using 1ml syringe, ACL lysis of RBCs  1x sorting

value: 10 weeks

value: Ter119 Ly6c CD3 CD11b Gr-1


title: proB.FrA.FL#1

description: proB.FrA.FL#1, Fr. A (pre-pro-B)

value: Ter119 Ly6c CD11b Gr-1 CD3


title: proB.FrA.BM#1

description: proB.FrA.BM#1, Fr. A (pre-pro-B)

extract_protocol: Needle/Syringe  Flow sorting


title: proB.FrA.BM#4

description: proB.FrA.BM#4, Fr. A (pre-pro-B)

extract_protocol: disruption using 1ml syringe, ACK lysis of RBCs  1x flow sorting

value: 11 weeks


title: proB.CLP.FL#3

description: proB.CLP.FL#3, Common Lymphoid Progenitor

extract_protocol: ground between 2 glass slides, ACL lysis of RBCs  1x flow sorting

value: CD19- IgM- CD43+ CD24intermediate CD45R- AA4.1+ CD117+ IL7R+


title: proB.FrA.BM#5

description: proB.FrA.BM#5, Fr. A (pre-pro-B)


title: proB.CLP.FL#1

description: proB.CLP.FL#1, Common Lymphoid Progenitor

value: CD19- IgM- CD43+ CD24intermediate AA4.1+ CD45R- CD117+ IL7R+


title: proB.CLP.BM#6

description: proB.CLP.BM#6, Common Lymphoid Progenitor


title: preB.FrD.FL#3

description: preB.FrD.FL#3, Fr D (pre-B)

extract_protocol: Ground between 2 glass slides, ACK lysis of RBCs

value: 18 days

value: CD3 Ly6c Ter119 Gr-1 CD11b


title: proB.CLP.BM#1

description: proB.CLP.BM#1, Common Lymphoid Progenitor

value: 6 weeks

value: dissection/trimming

value: male


title: T.4Mem.Sp#1

description: T.4Mem.Sp#1, Spleen Memory-Phenotype CD4

source_name: spleen


title: preB.FrD.FL#1

description: preB.FrD.FL#1, Fr D (pre-B)

extract_protocol: ground between 2 glass slides, ACK lysis of RBCs  2x flow sorting


title: NKT.44+NK1.1-.Th#3

description: NKT.44+NK1.1-.Th#3, Developing iNKT cells from thymus, stage 2

extract_protocol: homogenize, stain  MACS enrichment, double sort FACS Aria

value: CD8a Ter119 CD19 CD11c CD11b Ly6/Gr-1 CD8a PI NK1.1

value: aGC CD1d tet CD3 CD44


title: preB.FrD.FL#2

description: preB.FrD.FL#2, Fr D (pre-B)

value: both (pooled)


title: NKT.44-NK1.1-.Th#1

description: NKT.44-NK1.1-.Th#1, Thymic iNKT cell precursors, stage 1

extract_protocol: homogenize, stain  MACS, double sort

value: Ter119 CD19 CD11c CD11b Ly6/Gr-1 CD8a PI CD8a CD44 NK1.1

value: aGC CD1d tet CD3e


title: NKT.4-.Lv#4

description: NKT.4-.Lv#4, CD4- iNKT cells from Liver

source_name: liver

extract_protocol: homogenize, ficoll, stain  double sort on FACS Aria

value: PI B220 CD4

value: CD45 TCRb aGalCer-loaded CD1d tet


title: NKT.4-.Sp#1

description: NKT.4-.Sp#1, CD4- iNKT cells from Spleen

extract_protocol: homogenize, ACK lyse, Stain  MACS enrichment, Double sort on FACS Aria

value: PI CD19 B220 CD11b Ter119 CD4

value: TCRbeta+ aGalCer tet+ CD4-


title: NKT.44+NK1.1-.Th#2

description: NKT.44+NK1.1-.Th#2, Developing thymic iNKT cells, stage 2

extract_protocol: homogenize, stain  MACS enrichment, double sort (FACS Aria)


title: proB.CLP.FL#2

description: proB.CLP.FL#2, Common Lymphoid Progenitor

value: 15 days

value: Ly6c Ter119 CD3 Gr-1 CD11b


title: NKT.4-.Lv#3

description: NKT.4-.Lv#3, CD4- iNKT cells from Liver


title: NKT.4-.Lv#1

description: NKT.4-.Lv#1, CD4- iNKT cells from Liver


title: NKT.4-.Sp#3

description: NKT.4-.Sp#3, CD4- iNKT cells from spleen

extract_protocol: Homogenize, ACK lyse, stain  MACS enrichment, double sort on FACS Aria


title: NKT.4+.Sp#3

description: NKT.4+.Sp#3, CD4+ iNKT cells from Spleen

extract_protocol: homogenized, ACK lyszed, stained  MACS enrichement, double sort on FACS Aria

value: CD19 B220 CD11b Ter119 PI

value: TCRb aGalCer-loaded CD1d-tetramer CD4


title: proB.CLP.BM#8

description: proB.CLP.BM#8, Common Lymphoid Progenitor

extract_protocol: disruption using 1ml syringe, ACK lysis of RBCs  1x sorting

value: 10 weeks

value: Ter119 Ly6c CD3 CD11b Gr-1


title: NKT.4-.Lv#2

description: NKT.4-.Lv#2, CD4- iNKT cells from Liver

value: 6 weeks

value: dissection/trimming


title: NKT.4+.Lv#4

description: NKT.4+.Lv#4, CD4+ iNKT cells from Liver

value: PI B220

value: CD45 TCRb aGalCer-loaded CD1d tet CD4

value: male


title: NKT.4+.Lv#1

description: NKT.4+.Lv#1, CD4 + iNKT cells from Liver

extract_protocol: Homogenization, Ficoll, stain  double sort on FACS Aria


title: NKT.44-NK1.1-.Th#2

description: NKT.44-NK1.1-.Th#2, Thymic iNKT cell precursors, stage 1

extract_protocol: homogenize, stain  MACS, double sort (Aria

value: Ter119 CD19 CD11c CD11b Ly6/Gr-1 CD8a PI CD8a CD44 NK1.1


title: NK.H+.MCMV7.Sp#3

description: NK.H+.MCMV7.Sp#3, Splenic Ly49H+ NK cells from B6 mice 7 days following MCMV infection

extract_protocol: Glass slide teasing,  FACS sorting

value: CD3 CD4 CD5 CD8 CD19 Gr-1 Ter119

value: NK1.1+ TCRb- Ly49H+


title: NKT.4+.Lv#2

description: NKT.4+.Lv#2, CD4+ iNKT cells from Liver

extract_protocol: homogenization, ficol, stain  double sort on FACS Aria