description:
design description: H3K27me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS0997) using Illumina Genome Analyzer II
library name: HS0997
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 44 ug
SIZE_FRACTION: 60-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9733
CHIP_ANTIBODY_LOT: 1
****************
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: GSM428295_UCSF-UBC.H3K27me3.2.bam
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1523
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428295_UCSF-UBC.H3K27me3.1.bam
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1522
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428295_UCSF-UBC.H3K27me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K27me3 in the H1 cell line 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.1525
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM428295_UCSF-UBC.H1.H3K27me3.H1EScd1-me3K27-A.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0997-HS0997-1_305H8AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H1 Cell Line, Library H1EScd1-me3K27-A 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.4309
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: 0.2
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2469
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.301
POISSON_PERCENTILE: 2

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

ANALYSIS FILE NAME: GSM428295_UCSF-UBC.H1.H3K27me3.H1EScd1-me3K27-A.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0997-HS0997-1_305H8AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd1-me3K27-A 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.4358
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: H1 H3K27me3 A
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K27me3 Library H1EScd1-me3K27-A EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2469
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.301
POISSON_PERCENTILE: 2

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


title: Pupae_H3K27Me3_ChIPSeq_1

status: Public on Aug 13 2009

type: SRA

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

description: corresponding input record: GSM400665

library_source: genomic

data_processing: Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300Â bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Pupae

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of pupae at 1-2 days APF (after puparium formation), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Pupae are collected 2 days after the first pupa formed on the wall of the bottle. They are collected with a brush humidified with EWB and placed into an eppendorf tube. They are rinsed extensively with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.

treatment_protocol: No Treatment

tag: development point

value: Pupae

tag: antibody

tag: antibody manufacturer

value: Upstate

tag: antibody catalog number

tag: antibody lot number


status: Public on Aug 03 2009

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: H3K9me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS0998) using Illumina Genome Analyzer II
library name: HS0998
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 44 ug
SIZE_FRACTION: 60-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab8898
CHIP_ANTIBODY_LOT: 492774
****************
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: GSM428291_UCSF-UBC.H3K9me3.1.bam
ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1534
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.2.bam
ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1535
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.3.bam
ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1536
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.4.bam
ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1537
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9me3 in the H1 cell line 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.1538
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H1.H3K9me3.H1EScd1-me3K9-A.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0998-1_30WLLAAXX-HS0998-1_305Y8AAXX-HS0998-1_313MWAAXX-HS0998-1_3061PAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H1 Cell Line, Library H1EScd1-me3K9-A 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.4307
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: 0.2638
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2167
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9721
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4156
POISSON_PERCENTILE: 61

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

ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H1.H3K9me3.H1EScd1-me3K9-A.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0998-1_30WLLAAXX-HS0998-1_305Y8AAXX-HS0998-1_313MWAAXX-HS0998-1_3061PAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd1-me3K9-A 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.4356
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: H1 H3K9me3 A
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K9me3 Library H1EScd1-me3K9-A EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2638
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2167
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9721
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4156
POISSON_PERCENTILE: 61

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

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: cell line

tag: line

tag: Sex

value: male

tag: body site

value: Embryo ICM

tag: histological type

value: Embryonic stem cell

tag: is tumor

value: No


title: EOR-1 L3 replicate 1 GFP

status: Public on Jul 31 2009

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

description: Chromatin IP against anti-GFP

data_processing: Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200 bp.

organism: Caenorhabditis elegans

source_name: OP81, EOR-1:GFP:3xFLAG animals

growth_protocol: EOR-1:GFP:3xFLAG animals were grown on NGM plates to obtain gravity adults with embryos and then bleached to obtain embryos. Embryos were hatched overnight in M9 Buffer to obtain snychronized L1animals. L1 animals were then transfered into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grew at 20 oC in an incubator shaking at 230 rpm. Concentrated E. Coli were added as necessary during growth. When reached at L3 stage, animals were collected, washed, and cross-linked.

extract_protocol: Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody and purified using Qiangen PCR purification kit. The protocol for library preparation was adapted from the protocol "Preparing Samples for sequencing genomic DNA" by Illumina.

treatment_protocol: L3 animals were crossedliked in 2% formaldehyde solution for 30 minutes at room temperature, washed one time with 100 mM Tris pH 7.5 (to quench excess formaldehyde), 2 times with M9 Buffer, and once with FA buffer supplemented with protease inhibitors and then stored at -80 oC.

tag: strain

tag: growth stage

value: anti-GFP


title: EOR-1 L3 replicate 2 Input

description: No ChIP just input DNA from the same preparation


title: EOR-1 L3 replicate 2 GFP

description: Chromatin IP against anti-GFP


title: EOR-1 L3 replicate 1 Input


title: CEH-14 L2 replicate 2 GFP

description: Chromatin IP against anti-GFP

source_name: OP73, CEH-14:GFP:3xFLAG animals

growth_protocol: CEH-14:GFP:3xFLAG animals were grown on NGM plates to obtain gravity adults with embryos and then bleached to obtain embryos. Embryos were hatched overnight in M9 Buffer to obtain snychronized L1animals. L1 animals were then transfered into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grew at 20 oC in an incubator shaking at 230 rpm. Concentrated E. Coli were added as necessary during growth. When reached at L2 stage, animals were collected, washed, and cross-linked.

treatment_protocol: L2 animals were crossedliked in 2% formaldehyde solution for 30 minutes at room temperature, washed one time with 100 mM Tris pH 7.5 (to quench excess formaldehyde), 2 times with M9 Buffer, and once with FA buffer supplemented with protease inhibitors and then stored at -80 oC.


title: CEH-14 L2 replicate 1 GFP

description: Chromatin IP against anti-GFP


description:
design description: H3K9ac ChIP-Seq analysis of H1 embryonic stem cell line (HS0995) using Illumina Genome Analyzer II
library name: HS0995
EXPERIMENT_TYPE: Histone H3K9ac
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 44 ug
SIZE_FRACTION: 60-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K9ac
CHIP_ANTIBODY_PROVIDER: Millipore
CHIP_ANTIBODY_CATALOG: 07-352
CHIP_ANTIBODY_LOT: 24661
****************
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: GSM410807_UCSF-UBC.H3K9ac.bam
ANALYSIS TITLE: Mapping of H1 H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9ac in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1532
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM410807_UCSF-UBC.H3K9ac.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9ac in the H1 cell line 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.1533
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM410807_UCSF-UBC.H1.H3K9ac.H1EScd1-acK9-A.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0995.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the H1 Cell Line, Library H1EScd1-acK9-A 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.4319
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_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1388
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2077
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9946
IROC_PERCENTILE: 74
POISSON_SCORE: 0.2878
POISSON_PERCENTILE: 6

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

ANALYSIS FILE NAME: GSM410807_UCSF-UBC.H1.H3K9ac.H1EScd1-acK9-A.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0995.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd1-acK9-A 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.4368
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: H1 H3K9ac A
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K9ac Library H1EScd1-acK9-A EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1388
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2077
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9946
IROC_PERCENTILE: 74
POISSON_SCORE: 0.2878
POISSON_PERCENTILE: 6

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


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in hESC H1 (CDI-01) Cells; renlab.H3K36me3.CDI-01.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL220
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.890
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.891

****************
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: GSM409312_UCSD.H3K36me3.bam
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1514
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM409312_UCSD.H3K36me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in the H1 cell line 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.1515
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM409312_UCSD.H1.H3K36me3.LL220.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.CDI-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H1 Cell Line, Library LL220 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.4428
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: 0.2679
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3294
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9767
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4792
POISSON_PERCENTILE: 39

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

ANALYSIS FILE NAME: GSM409312_UCSD.H1.H3K36me3.LL220.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.CDI-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL220 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.4444
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: H1 H3K36me3 20
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K36me3 Library LL220 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2679
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3294
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9767
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4792
POISSON_PERCENTILE: 39

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

source_name: CDI-01; renlab.H3K36me3.CDI-01.01

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

tag: molecule

value: genomic DNA

tag: disease

value: Cellular Dynamics International

value: Cell Line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 30 and 50

tag: medium

value: mTeSER

value: Male

value: Histone H3K36me3

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in hESC H1 (CDI-01) Cells; renlab.H3K4me1.CDI-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL228
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.890
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.875

****************
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: GSM409307_UCSD.H3K4me1.bam
ANALYSIS TITLE: Mapping of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me1 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1516
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM409307_UCSD.H3K4me1.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me1 in the H1 cell line 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.1517
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM409307_UCSD.H1.H3K4me1.LL228.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.CDI-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H1 Cell Line, Library LL228 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.4415
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: 0.0458
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1997
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.7639
IROC_PERCENTILE: 5
POISSON_SCORE: 0.4372
POISSON_PERCENTILE: 9

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

ANALYSIS FILE NAME: GSM409307_UCSD.H1.H3K4me1.LL228.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.CDI-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Cell Line, Library LL228 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.4548
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: H1 H3K4me1 28
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me1 Library LL228 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0458
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1997
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.7639
IROC_PERCENTILE: 5
POISSON_SCORE: 0.4372
POISSON_PERCENTILE: 9

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

source_name: CDI-01; renlab.H3K4me1.CDI-01.01

value: Histone H3K4me1


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in hESC H1 (CDI-01) Cells; renlab.H3K4me3.CDI-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL227
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.890
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.879

****************
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: GSM409308_UCSD.H3K4me3.bam
ANALYSIS TITLE: Mapping of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1547
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM409308_UCSD.H3K4me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me3 in the H1 cell line 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.1548
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM409308_UCSD.H1.H3K4me3.LL227.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.CDI-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library LL227 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.4436
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: 0.6745
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.6545
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6993
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM409308_UCSD.H1.H3K4me3.LL227.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.CDI-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL227 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.4489
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: H1 H3K4me3 27
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me3 Library LL227 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.6745
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.6545
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6993
POISSON_PERCENTILE: 85

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

source_name: CDI-01; renlab.H3K4me3.CDI-01.01

value: Histone H3K4me3

value: Millipore


title: HLH-8 L3 replicate 2 Input

source_name: OP74, HLH-8:GFP:3xFLAG animals

growth_protocol: HLH-8:GFP:3xFLAG animals were grown on NGM plates to obtain gravity adults with embryos and then bleached to obtain embryos. Embryos were hatched overnight in M9 Buffer to obtain snychronized L1animals. L1 animals were then transfered into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grew at 20 oC in an incubator shaking at 230 rpm. Concentrated E. Coli were added as necessary during growth. When reached at L3 stage, animals were collected, washed, and cross-linked.

tag: antibody


title: ChIP-Seq analysis of H3K9ac in human H1 cells, 30H81AAXX090613-6-S

status: Public on Aug 05 2009

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-12526
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.950
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.951

****************
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: GSM433171_BI.H3K9ac.bam
ANALYSIS TITLE: Mapping of H1 H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9ac in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1508
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM433171_BI.H3K9ac.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9ac in the H1 cell line 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.1509
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM433171_BI.H1.H3K9ac.Solexa-12526.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the H1 Cell Line, Library Solexa-12526 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.4724
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_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1358
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2242
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8583
IROC_PERCENTILE: 9
POISSON_SCORE: 0.3263
POISSON_PERCENTILE: 29

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

ANALYSIS FILE NAME: GSM433171_BI.H1.H3K9ac.Solexa-12526.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-12526 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.4998
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: H1 H3K9ac 26
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K9ac Library Solexa-12526 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1358
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2242
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8583
IROC_PERCENTILE: 9
POISSON_SCORE: 0.3263
POISSON_PERCENTILE: 29

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

extract_protocol: Library construction protocol: Single read - Illumina

value: Cellular Dynamics

value: undifferentiated

value: TESR

tag: sex

value: Unknown

value: Histone H3K9ac

value: SDS lysis

value: Bioruptor

value: standard


title: HLH-8 L3 replicate 1 Input


title: HLH-8 L3 replicate 1 GFP

description:
Chromatin IP against anti-GFP
library_strategy: ChIP-seq

value: anti-GFP


title: lacZ knockdown

city: Cold Spring Harbor

first: Benjamin

last: Czech

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: small RNA sequencing

library_source: transcriptomic

data_processing: The 36-nt long Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were mapped to the Release 5 genome excluding the Uextra portion. Non-mapping sequences were mapped to the lacZ sequence, and to the genomes of Drosophila C virus, Flock house virus, and Cricket paralysis virus. Only reads perfectly matching to the fly genome or lacZ sequence and reads matching the virus genomes with up to three mismatches were used for further analysis. For annotation, we used Flybase for protein coding genes, UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. For endo-siRNAs from structured loci we used custom annotations. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs. SEQ = the sequence of the small RNA. MAPNUM = the number of times the small RNA matches the respective genome sequence. TYPE = annotation category of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

molecule: total RNA

source_name: S2-NP cells

growth_protocol: 25°C in Schneider's medium (Invitrogen) supplemented with 10% FBS and 1% pen-strep (Invitrogen)

extract_protocol: Trizol (Invirogen) extraction

treatment_protocol: ~3X10^6 S2-NP cells were soaked in 1.5 mL serum-free Schneider’s medium containing 10 µg dsRNAs in 6-well plates, and 3 mL serum-containing medium was added 45 minutes later. After 4 days of initial dsRNA treatment, cells were treated with dsRNAs for a second round and harvested another 4 days later.

tag: cell line


title: r2d2 knockdown

description: small RNA sequencing


title: HLH-8 L3 replicate 2 GFP

description: Chromatin IP against anti-GFP


title: dcr-2 knockdown

description: small RNA sequencing


title: dcr-1 knockdown

description: small RNA sequencing


title: loqs-ORF knockdown

description: small RNA sequencing


title: HeLa

status: Public on Aug 25 2009

first: Christine

last: Mayr

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing: Reads containing linker matches were mapped (after removing linkers) to predicted pre-miRNAs (MirBase version 12.0)

source_name: cell line

growth_protocol: RNA was harvested from exponentially growing cells

extract_protocol: Total RNA extracted using standard Trizol extraction. Total RNA fractionated on 15% polyacrylamide gel and 3' and 5' adaptors sequentially ligated requiring a 3' hydroxyl group and 5' phosphate

value: HeLa


title: Pupae_INPUT_PolII

status: Public on Jul 30 2009

tag: development point

value: Pupae

tag: reference

value: input


title: L3_INPUT_PolII

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of third instar larvae (L3), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 48 hours. 3. L3 larvae are collected at 8.45 am using a filter mesh and a brush. L3 larvae are the larvae not going through the first mesh. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: L1_INPUT_PolII

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of first instar larvae, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. 3. L1 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: MCF7


title: E12-16_INPUT

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 12-16 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.


title: E8-12_PolII_ChIPSeq_1

description:
PolII_ChIPSeq_1
corresponding input record: GSM432636

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 8-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 8 pm and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8 am in 1.8% formaldehyde at room temperature for 15 min.

value: PolII

tag: antibody manufacturer

value: Covance

tag: antibody catalog number

tag: antibody lot number


title: E8-12_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM432636

value: Abcam


title: untreated (mock)

description: small RNA sequencing


title: L1_PolII_ChIPSeq_1

description:
PolII_ChIPSeq_1
corresponding input record: GSM432637


title: L3_PolII_ChIPSeq_1

description:
PolII_ChIPSeq_1
corresponding input record: GSM432638


title: L1_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400663


title: E16-20_PolII_ChIPSeq_1

description:
PolII_ChIPSeq_1
corresponding input record: GSM400659

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 16-20 hours egg laying, new plates are added after a 2hours pre-egglaying at 1 pm and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 8.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: CEH-14 L2 replicate 2 Input


title: Pupae_PolII_ChIPSeq_1

description:
PolII_ChIPSeq_1
corresponding input record: GSM432639


title: E12-16_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM432634


title: AdultMale_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400667

source_name: AdultMale

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Male 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

value: AdultMale


title: E8-12_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM432636


title: E12-16_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM432634


title: E8-12_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM432636


title: E8-12_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM432636


title: E8-12_INPUT


title: Illumina sequencing of small RNAs from post-gastrulation C. elegans embryos

status: Public on Sep 06 2009

city: Berlin

first: Jonas

last: Maaskola

address: Robert-Roessle Str. 10

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max-Delbrueck Centrum Berlin-Buch

description: Post-gastrulation embryos.

data_processing: Removal of 3' adapter sequences by searching for best matches of adapter prefixes up to edit distance 4.

source_name: Post-gastrulation embryo

growth_protocol: Strains were maintained using standard methods (Brenner, 1974) on OP50 seeded NGM plates or in liquid culture.

extract_protocol: Library preparation as well as cluster generation and deep sequencing was performed according to the 5’ ligation dependent (5’monophosphate dependent) manufacturer’s protocol (Digital Gene Expression for small RNA, Illumina). Rougly 60,000 embryos (~10µg total RNA) were used for small RNA library preparation. Small RNAs were size selected between 18 and 40 nt according to the ssDNA marker in the small RNA sequencing kit (Illumina).

treatment_protocol: Embryos were left to develop for three hours after isolation by bleaching. Hatched L1s were removed by a second round of bleaching.

tag: developmental stage

value: Post-gastrulation embryo

tag: meoh-fixed

tag: sorted

tag: resorted


title: E4-8_PolII_ChIPSeq_1

description:
PolII_ChIPSeq_1
corresponding input record: GSM432635

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 4-8 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.


title: MDBK_BHV1_infection_MOI_0.75

status: Public on Jul 29 2009

city: Brisbane

first: Evgeny

last: Glazov

address: Ipswich Road

department: Diamantina Institute

country: Australia

institute: University of Queensland

data_processing: processed fasta files contain non-redundant sets of sequences generated from raw data after trimming 3' sequencing adapter (5'-TCGTATGCCGTCTTCTGCTTG-3'); Example of record ID is as follows >Cnt.F.txt_184803_2, where second numeral _184803_  represent sequnce read count and last numeral _2 represent unique numeric csequence ID.

organism: Bos taurus

source_name: MDBK Bovine kidney cell line - infection - MOI 0.75

growth_protocol: The BoHV-1 virus utilised for this study was recovered using the infection clone, pBACBHV-37 (Mahony 2002), of the BoHV-1 strain V155 (Snowden, 1964) as previously described in Madin-Darby Bovine Kidney (MDBK) cells (ATCC number CCL-22) (Madin 1958).  The MDBK cells were maintained in Earle's minimal essential medium containing non-essential amino acids, glutaMAX, 25 mM HEPES and 5% (v/v) foetal calf serum at 37oC in a 5% CO2 atmosphere.  All reagents utilised for cell and virus propagation were obtained from Invitrogen Australia unless otherwise stated.

extract_protocol: MDBK cells were seeded into flasks 24 h prior use and infected at approximately 80% confluency with BoHV-1 and incubated at 37C in an atmosphere of 5% CO2.  The MDBK monolayers were infected at multiplications of infectivity (MOI) of either 0.75 or 7.5.  At 6 h, 12, h or 24 h post-infection monolayers were harvested and total RNA recovered using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.  Total RNA was recovered from mock infected MDBK monolayers for control purposes. The total RNA was resuspended in diethyl pyrocarbonate treated water.  The RNA was quantified using a NanoDrop spectrophotometer and either used immediately or stored at -70CC until required. The small RNA fraction (<400 nucleotides) was recovered from total RNA using previously described methods (Mitter 2003).  Briefly, polyethylene glycol 8000 and sodium chloride were added to the total RNA solution and the volume adjusted to give final concentrations of 10% (w/v) and 100 mM respectively, followed by incubation on ice for 30 min. The samples were centrifuged at 10,000 g for 10 min at 4C. The supernatant was transferred to a new microfuge tube and 3 volumes of 100% ethanol added.  The small RNA was allowed to precipitate by incubation overnight at -20oC prior to recovery by centrifugation at 10,000 g at 4C for 30 min. The resultant RNA pellet was washed once with 75% ethanol and air-dried.  The small RNA pellet was subsequently resuspended in de-ionised formamide for electrophoresis and northern blotting analyses.  The concentration and quality of the small RNA fractions were estimated using a NanoDrop Spectrophotometer or gel electrophoresis, respectively.

value: MDBK bovine kidney cell line


title: E12-16_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM432634


title: MDBK_BHV1_infection_MOI_7.5

source_name: MDBK Bovine kidney cell line - infection - MOI 7.5


title: genomic DNA control

status: Public on Jul 26 2009

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description: genomic DNA control

data_processing: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. More details as described in Jin et al., 2008

source_name: genomicDNA

growth_protocol: Growth protocol as described in Jin et al., 2008

extract_protocol: Extract protocol as described in Jin et al., 2008

treatment_protocol: Treatment protocol as described in Jin et al., 2008

tag: HeLa


title: MDBK_mock_infection_control

description: Control

source_name: MDBK Bovine kidney cell line - control


title: H2A.Z (high salt) ChIP

description: Chromatin IP


title: input (low salt) control

description: input control

source_name: input


title: H3.3-H2A.Z double ChIP

description: Chromatin IP

source_name: Double ChIP


title: H3.3 ChIP

description: Chromatin IP


title: H2A.Z (low salt) ChIP

description: Chromatin IP


title: E16-20_CBP_ChIPSeq_1

description:
CBP_ChIPSeq_1
corresponding input record: GSM400659

value: CBP

tag: antibody provider

value: Dr. Mattias Mannervik in Stockholm University


title: Illumina sequencing of small RNAs from living one cell C. elegans embryos

description: Living one-cell embryos. The embryos were sorted a single time, yielding a purity of about 70%.

source_name: Living one-cell embryo

treatment_protocol: Living one cell stage embryos obtained by eFACS.

value: one-cell embryo

tag: strain

tag: purity


title: E4-8_INPUT_PolII


title: P1.c (yr.+6)

status: Public on Jul 17 2009

type: RNA

city: Brussels

first: Karen

last: Willard-Gallo

address: 127 Blvd de Waterloo

department: Institut Bordet

country: Belgium

institute: Université Libre de Bruxelles

description:
CD3- CD4+ T-cells from blood obtained during follow-up (year  +6).
T-lymphoma stage of lymphocytic variant of hypereosinophilic syndrome.

hyb_protocol: 15µg of cRNA was hybridized following the standard protocol for Affymetrix’s Genechips hybridization

scan_protocol: Chips were scanned using GCF3000 scanner and processed using GCOS operating software

data_processing: Data were processed using GCOS operating software

label: biotin

source_name: Patient 1

label_protocol: 1.5µg of total RNA was labeled following the standard protocol for Affymetrix’s Genechips hybridization

extract_protocol: Total RNA was extracted using TriPure Isolation Reagent (Roche Applied Science) as manufacturer's recommendations. ). The quality of the RNA was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)

treatment_protocol:
Isolated PBMC were frozen.
Thawed CD3-CD4+ T-cells were purified using magnetic beads and 18h-cultured in X-vivo medium

tag: cell type

value: CD3- CD4+ T-cells

tag: tissue

value: blood

tag: time

value: year +6 (follow-up)

tag: disease state


title: P2.b (yr.0)

description:
CD3- CD4+ T-cells from blood obtained at diagnosis (year 0).
Pre-malignant stage of lymphocytic variant of hypereosinophilic syndrome.

source_name: Patient 2

value: year 0 (diagnosis)


title: P3.b (yr.0)

source_name: Patient 3

value: Pre-malignant stage of lymphocytic variant of hypereosinophilic syndrome


title: P1.a (yr.+6)

value: T-lymphoma stage of lymphocytic variant of hypereosinophilic syndrome


title: Methyl-Seq_human T cells

status: Public on Aug 11 2009

city: Singapore

first: Jung Kyoon

last: Choi

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description:
Based on the affinity of the MBD2b/MBD3L1 complex (MIRA technique)
Processed_data_file: tcell_met.bed

data_processing: Alignment: Sequence reads were obtained and mapped to the human genome (hg18) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 150 bp to create summary windows. The read count from every 150-bp window was used as a measure of DNA methylation level.

source_name: T cells

extract_protocol: Genomic DNA was purified by using the DNeasyR Blood & Tissue Kit (Qiagen). The Methylated CpG Island Recovery Assay (MIRA, a methylated-DNA enrichment technique) was carried out as follows. The purified genomic DNA was sonicated to 100 ~ 500 bp in size and incubated with the prepared GST-MBD2b protein, His-MBD3L1 protein, and the JM110 bacterial DNA. The MagneGST beads (Promega) were preblocked with the JM110 bacterial DNA and incubated at 4°C in the MIRA binding buffer (10 mM Tris-HCl, pH 7.5; 50 mM NaCl; 1 mM EDTA; 1 mM DTT; 3mM MgCl2; 0.1% Triton X-100; 5% glycerol; 25 ug/ml BSA) and then washed in the washing buffer (10 mM Tris-HCl, pH 7.5; 300 mM NaCl; 1 mM EDTA; 3 mM MgCl2; 0.1% Triton X-100). DNA elution was done by incubation at room temperature for 5 minutes and 56°C for 30 minutes with RNase A and Proteinase K. Additional purification of the eluted DNA fragments was done using the QIAquick PCR purification kit (Qiagen).

value: CD4+ T cells


title: P1.c (yr.+4)

description:
CD3- CD4+ T-cells from blood obtained during follow-up (year  +4).
Pre-malignant stage of lymphocytic variant of hypereosinophilic syndrome.

value: year +4 (follow-up)


title: P1.c (yr.0)


title: P2.a (yr.0)


title: P1.b (yr.0) Stim

hyb_protocol: 15µg of cRNA was hybridized following the standard protocol for Affymetrix Genechip hybridization

label_protocol: 1.5µg of total RNA was labeled following the standard protocol for Affymetrix Genechip hybridization

growth_protocol: CD3-CD4+ T-cells were cultured 18h in X-vivo medium supplemented with rhIL2, anti-CD2 and anti-CD28 antibodies

treatment_protocol:
Isolated PBMC were frozen.
Thawed CD3-CD4+ T-cells were purified using magnetic beads


title: P3.b (yr.0) Stim

growth_protocol: CD3-CD4+ T-cells were cultured 18h in X-vivo medium supplemented with rhIL2, anti-CD2 and anti-CD28 antibodies.

treatment_protocol:
Isolated PBMC were frozen.
Thawed CD3-CD4+ T-cells were purified using magnetic beads.


title: P1.a (yr.+4)


title: P3.a (yr.0) Stim


title: P1.a (yr.0) Stim


title: P1.c (yr.0) Stim


title: P1.b (yr.+6)


title: P1.b (yr.+4)


title: P2.a (yr.0) Stim


status: Public on Jul 15 2009

city: Palo Alto

first: Ghia

last: Euskirchen

address: 1501 S. California Ave.

department: Genetics

institute: Stanford University

data_processing: Sequence tags were obtained and aligned to the Saccharomyces cerevisiae from SGD2 (Apr 2008 build) and Escherichia coli K12 MG1655 (U00096) genomes using the Illumina/Solexa Analysis Pipeline. The analysis allowed 2 mismatches per mapped read and only uniquely aligned reads were retained. In sample 1 (Nucleosomes assembled on yeast and E. coli DNA by salt dialysis) and sample 2 (Nucleosomes assembled on yeast and E. coli DNA by ACF), each sequencing tag represents one end of a mono-nucleosomal DNA fragment. Therefore, we extended each tag to 146 bp in the 3’ direction to represent a whole mono-nucleosome, and then we piled up all extended sequencing tags in a sample to obtain the nucleosome density profile along the genome. The identical approach was also used in sample 3 (Yeast-Ecoli control, sonicated) to serve as control.

organism:
Escherichia coli
Saccharomyces cerevisiae

source_name: yeast and E. coli

extract_protocol: Yeast DNA was prepared from exponentially growing cells that were treated with Zymolyase. The resulting spherophasts were resuspended in Qiagen buffer G2 with 200μg/ml RNase A and then incubated with Proteinase K (8mg, Qiagen) for 30 minutes at 50C. After removal of cellular debris by centrifugation, DNA was precipitated with ethanol, isolated by spooling, and further purified using a Qiagen Genomic-tip 500/G according to the manufacturer’s instructions. E. coli DNA was isolated using a Qiagen Genomic-tip 500/G according to the manufacturer's instructions. Purified genomic DNA preparations from Saccharomyces cerevisiae as well as from Escherichia coli were sonicated separately to yield fragments that ranged in length from 5 to 10 kb. The resulting yeast and E. coli DNA samples were combined in a 3:1 mass ratio, and assembled into chromatin using a purified system containing recombinant Drosophila NAP-1 and ACF as well as purified native histones from Drosophila embryos. Chromatin was extensively digested with micrococcal nuclease to yield core particles. The ~147 bp DNA fragments derived from the core particles were purified by agarose gel electrophoresis. Mononucleosomal DNA was treated with calf intestinal alkaline phosphatase (New England Biolabs) to remove 3’ phosphate groups left after the micrococcal nuclease treatment. Libraries were prepared according to Illumina’s instructions accompanying the DNA Sample Kit (Part# 0801-0303) and sequenced on the Genome Analyzer following the manufacturer’s protocols.

value: Yeast BY4730 (MAT a, leu2∆0, met15∆0, ura3∆0)

value: E. coli JS5


title: Yeast-E. coli control, sonicated

extract_protocol: Yeast DNA was prepared from exponentially growing cells that were treated with Zymolyase. The resulting spherophasts were resuspended in Qiagen buffer G2 with 200μg/ml RNase A and then incubated with Proteinase K (8mg, Qiagen) for 30 minutes at 50C. After removal of cellular debris by centrifugation, DNA was precipitated with ethanol, isolated by spooling, and further purified using a Qiagen Genomic-tip 500/G according to the manufacturer’s instructions. E. coli DNA was isolated using a Qiagen Genomic-tip 500/G according to the manufacturer's instructions. Purified genomic DNA preparations from Saccharomyces cerevisiae as well as from Escherichia coli were sonicated separately to yield fragments that ranged in length from 5 to 10 kb. Fragments were purified by agarose gel electrophoresis. Libraries were prepared according to Illumina’s instructions accompanying the DNA Sample Kit (Part# 0801-0303) and sequenced on the Genome Analyzer following the manufacturer’s protocols.


title: P1.b (yr.0)


title: D4

description: CD4+ T-cells

source_name: Healthy control 4

treatment_protocol:
Isolated PBMC were frozen.
Thawed CD4+ T-cells were purified using magnetic beads and 18h-cultured in X-vivo medium

value: CD4+ T-cells

value: control


title: Kc167_42.6

city: St Louis

first: Marijke

middle: Jeltje

last: van Baren

state: MO

address: One Brookings Drive

department: CSE

institute: Washington University

description:
Oligo-dT selected, double stranded cDNA single read sequencing
processed data file: 42_6.gff
processed data file: Kc167.wig (linked as a supplementary file to the Series GSE17107 record)

data_processing: Reads were aligned to the reference genome (Drosophila melanogaster, BDGP Release 5) and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .wiggle files which indicate the number of reads that map to each base in the genome.

molecule: polyA RNA

source_name: Kc167 cell line

growth_protocol: Schneider's medium + 10% heat-inactivated FCS

extract_protocol: TRIzol Dnase Rneasy

tag: cell line

tag: replicate

value: technical


title: Kc167_42.4

description:
Oligo-dT selected, double stranded cDNA single read sequencing
processed data file: 42_4.gff
processed data file: Kc167.wig (linked as a supplementary file to the Series GSE17107 record)


title: P1.a (yr.0)

description:
CD3- CD4+ T-cells from blood obtained at diagnosis (year 0)
Pre-malignant stage of lymphocytic variant of hypereosinophilic syndrome


title: Kc167_42.2

description:
Oligo-dT selected, double stranded cDNA single read sequencing
processed data file: 42_2.gff
processed data file: Kc167.wig (linked as a supplementary file to the Series GSE17107 record)


title: Nucleosomes assembled on yeast and E. coli DNA by salt dialysis

extract_protocol: Yeast DNA was prepared from exponentially growing cells that were treated with Zymolyase. The resulting spherophasts were resuspended in Qiagen buffer G2 with 200μg/ml RNase A and then incubated with Proteinase K (8mg, Qiagen) for 30 minutes at 50C. After removal of cellular debris by centrifugation, DNA was precipitated with ethanol, isolated by spooling, and further purified using a Qiagen Genomic-tip 500/G according to the manufacturer’s instructions. E. coli DNA was isolated using a Qiagen Genomic-tip 500/G according to the manufacturer's instructions. Purified genomic DNA preparations from Saccharomyces cerevisiae as well as from Escherichia coli were sonicated separately to yield fragments that ranged in length from 5 to 10 kb. The resulting yeast and E. coli DNA samples were combined in a 3:1 mass ratio, and assembled into chromatin by purified native histones from Drosophila embryos through salt dialysis. Chromatin was extensively digested with micrococcal nuclease to yield core particles. The ~147 bp DNA fragments derived from the core particles were purified by agarose gel electrophoresis. Mononucleosomal DNA was treated with calf intestinal alkaline phosphatase (New England Biolabs) to remove 3’ phosphate groups left after the micrococcal nuclease treatment. Libraries were prepared according to Illumina’s instructions accompanying the DNA Sample Kit (Part# 0801-0303) and sequenced on the Genome Analyzer following the manufacturer’s protocols.


title: L1_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400663

data_processing: Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300Â bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

tag: development point

tag: antibody

tag: antibody manufacturer

value: Abcam


title: D2

description: CD4+ T-cells

source_name: Healthy control 2

extract_protocol: Total RNA was extracted using TriPure Isolation Reagent (Roche Applied Science) as manufacturer's recommendations. The quality of the RNA was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)


title: Yeast Exponential phase glucose GCC library with MspI site

status: Public on Jul 21 2009

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

data_processing: Data was processed using the Flp_spin_man program suite in conjunction with SOAP

organism: Saccharomyces cerevisiae

source_name: Exponential yeast cells

growth_protocol: Saccharomyces cerevisiae (BY4741 [Mata his3delta1 leu2delta0 met15delta0 ura3delta0]) was cultured (30oC, 160rpm) to an A600 = 0.6 on synthetic complete medium containing amino acid supplements and glucose (2 % w/v).

extract_protocol: Samples (residuals of 108 cells in 52.6µl) were digested (37°C, 2hr) with MspI (100U, Fermentas) in a final volume of 100 ml.  MspI was inactivated by the addition of 1% SDS (final v/v) and incubation (65°C, 20mins). Reactions were diluted in 2ml T4 ligation buffer (NEB) containing 1% Triton X-100. T4 DNA Ligase (20U, Invitrogen) was added and the reaction incubated (16°C, 2hrs). Samples were reverse cross-linked (65°C, O/N) in the presence of Proteinase K (7-11ug, Roche), 20µl EDTA (0.5M), 12µl NaCl (5M), 1.2µl Tris-HCl (1M).  RNase (20µg) was added and incubated (37°C, 15mins) prior to three Phenol:Chloroform (1:1) extractions.  Samples were column purified (Zymo Clean and Concentrator) and eluted in 10µl milliQ H2O.  DNA (5µg in 100µl) was sequenced using the Illumina Solexa platform (Allan Wilson Centre, Massey University).

treatment_protocol: Chromatin was prepared using a modification of Dekker.{Dekker, 2002 #11} Briefly, Cells were cross-linked (2% v/v formaldehyde, 10 mins, room temperature, with stirring) and quenched (0.125M glycine).


title: D1

description: CD4+ T-cells

source_name: Healthy control 1

extract_protocol: Total RNA was extracted using TriPure Isolation Reagent (Roche Applied Science) as manufacturer's recommendations. The quality of the RNA was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc).


title: D3

description: CD4+ T-cells

source_name: Healthy control 3


title: H3K36me3_ChIPSeq

status: Public on Jul 08 2009

first: Emily

last: Hodges

address: 1 Bungtown Road

description: Chromatin IP against H3K36me3

data_processing: Alignment: Sequence reads from ChIP-seq experiments were mapped to the human genome (March 2006) with the RMAP program, allowing at most 2 mismatches in 36 bases. Reads mapped ambiguously to multiple locations in the genome were ignored in subsequent analysis.

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were grown in DMEM containing 15% FBS, L-glutamine, non-essential amino acids, and penicillin/streptomycin.

extract_protocol: Chromatin immunoprecipitation was performed with rabbit anti-trimethyl histone H3K36 (Abcam, ab32356) and rabbit anti-dimethyl histone H3K4 (Abcam, ab9050) according to previously described methods (Steger et al. 2008). Following elution, IP samples were treated with RNaseA at 65ºC overnight followed by proteinase K at 42ºC for 2 hours. DNA was isolated by phenol:chloroform extraction and ethanol precipitation.  ChIP DNA was prepared for Illumina sequencing according to the protocol described by Robertson et al (Robertson et al. 2007) and the manufacturer's recommendations.

value: Human breast adenocarcinoma cell line


title: H3K4me2_ChIPSeq

description: Chromatin IP against H3K4me2


title: CHPSKN1_Biulfite_seq

description: Targeted bisulfite sequencing

data_processing: Alignment: Sequence reads from BS capture experiments were mapped to the human genome (March 2006) with the RMAPBS program, freely available from the authors as Open Source software under the GNU Public License.  Reads mapped ambiguously to multiple locations in the genome were ignored in subsequent analysis.

source_name: CHP-SKN1 cells

growth_protocol: CHP-SKN1 cells were grown in 15 cm plates with DMEM medium containing 20% FBS supplemented with L-glutamine, non-essential amino acids and penicillin/streptomycin. MDA-MB-231 cells were grown in DMEM containing 15% FBS, L-glutamine, non-essential amino acids, and penicillin/streptomycin.

extract_protocol: Purified cell-line DNA was randomly fragmented by sonication and subsequently treated with a mixture of T4 DNA Polymerase, E. coli DNA polymerase I Klenow fragment, and T4 polynucleotide kinase to repair, blunt and phosphorylate ends according to the manufacturer’s instructions (Illumina). The repaired DNA fragments were subsequently 3’ adenylated using Klenow exo- fragment (Illumina). After each step, the DNA was recovered using the QIAquick PCR Purification kit (Qiagen). Adenylated fragments were ligated to Illumina-compatible paired-end adaptors synthesized with 5’-methyl-cytosine instead of cytosine (Illumina) and fragments ranging from 150-300 bp were extracted by gel purification using the QIAquick gel extraction kit (Qiagen) followed by elution in 30ul elution buffer. Following size selection and gel purification, the adapter-ligated DNA was divided into two separate reactions to ensure optimal DNA concentration for subsequent cytosine conversion reactions. Fragments were denatured and treated with sodium bisulfite using the EZ DNA methylation gold kit according to the manufacturer’s instructions (Zymo). Lastly, the sample was desulfonated and the converted, adaptor-ligated fragments were PCR enriched using paired-end adaptor-compatible primers 1.0 and 2.0 (Illumina) and Expand High Fidelity PLUS PCR system (Roche), a specialized polymerase capable of amplifying the highly denatured, uracil-rich templates. PCR reactions contained 1x Expand HiFi PLUS reaction buffer, 200μM each dNTP, 1μM each primer, 2.5mM MgCl2, and 2.5 U Expand HiFi PLUS enzyme. The reactions were performed under the following conditions: 94ºC for 2 minutes, 25 cycles of 94ºC for 15 seconds, 65ºC for 30 seconds and 72ºC for 30 seconds, followed by 72ºC for 7 minutes.  Following amplification, the samples were hybridized to capture arrays and captured fragments were recovered and sequenced.

value: Human primary dermal fibroblasts


title: MDAMB231_Bisulfite_seq

description: Targeted bisulfite sequencing


title: Kc167_42.3

description:
Oligo-dT selected, double stranded cDNA single read sequencing
processed data file: 42_3.gff
processed data file: Kc167.wig (linked as a supplementary file to the Series GSE17107 record)


title: P2.b (yr.0) Stim


title: Kc167_42.7

description:
Oligo-dT selected, double stranded cDNA single read sequencing
processed data file: 42_7.gff
processed data file: Kc167.wig (linked as a supplementary file to the Series GSE17107 record)


title: adult skin

status: Public on Jul 10 2009

first: Mike

last: Gilchrist

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: Cambridge University

description: Small RNAs were sequenced from Xenopus tropicalis adult skin

data_processing:
Reads stripped of adaptor sequence to make tags. Tags with exact mapping to genome submitted.

library strategy: RNA-Seq. 10µg RNA of miRvana size-selected RNA was again size-selected to 18-30 nucleotides on a denaturing polyacrylamide gel and small RNA libraries were cloned through ligation of a 5' and 3' adapter according to the manufacturerâ€™s protocol (Illumina, San Diego, CA, USA).
library source: RNA
library selection: 18-42 nucleotides

organism: Xenopus tropicalis

source_name: Xenopus tropicalis adult skin

extract_protocol: Ovarian lobes were removed from Xenopus tropicalis females and collagenase treated for 3 h. Oocytes were staged and washed in modified Barth’s solution (8.8mM NaCl, 1mM KCl, 330µM Ca(NO3)2, 410µM CaCl2, 820µM MgSO4, 2.4mM NaHCO3, 10 mM HEPES-NaOH pH7.4). Total RNA was isolated from staged oocytes of Xenopus tropicalis or from different adult tissues of Xenopus tropicalis using Trizol reagent (Invitrogen, Carlsbad CA, USA) and according to the manufacturer’s protocol. Total RNA extracted was enriched for small RNAs using the miRVana kit (Ambion, Austin TX, USA), resolved in a 15% denaturing polyacrylamide gel and stained using SYBR green (Invitrogen). 10µg RNA of miRvana size-selected RNA was again size-selected to 18-30 nucleotides on a denaturing polyacrylamide gel and small RNA libraries were cloned through ligation of a 5' and 3' adapter according to the manufacturer’s protocol (Illumina, San Diego, CA, USA).

tag: genotype

value: wild type

tag: developmental stage

value: adult


title: small RNAs from Medicago truncatula, Jemalong A17, Root tips

status: Public on Jul 07 2009

city: Castanet Tolosan

first: Jerome

last: Gouzy

address: 24 Chemin de Borde Rouge, BP52627

department: LIPM

country: France

institute: INRA/CNRS

description: root smallRNAs 13-45nt

data_processing: Sequence adaptors (3’ ATTGATGGTGCCTACACTCTG or 5’ GCACATCGTAGCCACCTGATA, GCACATCGTAGCTGCCTGATA, GCACATCGTAGCGTCCTGATA were identified using crossmatch (-minmatch 8 -minscore 10). Reads with patterns: 3’A-smallRNA-5’A,  3’A-smallRNA and smallRNA-5’A were reverse-complemented.

organism: Medicago truncatula

source_name: Root apexes

growth_protocol: Surface-sterilized seeds of Medicago truncatula Jemalong A17 were germinated on 1.5% agar plates at 4 °C for 1 week in the dark and then grown at 23°C, 16h day, in perlite/sand (3:1).

extract_protocol: Total RNA extraction was performed with Trizol reagent

value: Jemalong A17

value: Root

tag: development stage

value: Root tips (1-2cm)

tag: specific growth conditions

value: Root tips (1-2 cm) were obtained from plants 10-12 days post-germination grown in sand:perlite pots disposed on a metal grid, with root tips growing in a rich SN/2 nutritive solution.


title: adult liver

description: small RNAs were sequenced from Xenopus tropicalis adult liver

source_name: Xenopus tropicalis adult liver


title: HPC-7_Scl_Chip-Seq (Scl_lane7 and Scl_lane8)

status: Public on Jun 19 2009

first: Samuel

middle: David

last: Foster

state: Cambridgeshire

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

department: Department of Haematology

institute: Cambridge Institute for Medical Research

description: Chromatin IP against Scl protein

data_processing: Sequence data was aligned using Solexa alignment software.

organism: Mus musculus

growth_protocol: HPC-7 cells were grown in 10% conditioned mSCF and were routinely counted and split every day to be kept at a confluence between 0.7-2 x 106 cells per ml).

extract_protocol: Chromatin was fixed in 0.4% formaldehyde, sheared to 200-500bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

value: Early haematopoietic cell line dervied from ES cells


title: small RNAs from Medicago truncatula, Jemalong A17, Mature nodules

description: nodule smallRNAs 13-45nt

source_name: Mature nodules

value: Nodule

value: Mature nodules (1 month after inoculation with S. meliloti 2011)

value: One week old seedlings, grown in low nitrogen conditions, were inoculated with S. meliloti 2011 strain and mature nodules were harvested   four weeks after inoculation


title: dme_endosperm_BS_seq

status: Public on Jun 16 2009

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description:
DNA methylation analysis of Arabidopsis tissue by bisulfite sequencing
library_strategy: Other (BS-seq)
library_source: genomic
library_selection: random

data_processing:
Processed data files (.gff): alignment, single_C_fractional_methylation, and 50bp_window_fractional_methylation files, are linked below as supplementary files.
Alignment: We used Perl scripts to convert all the Cs in the ‘forward’ reads (and in the scaffold) to Ts, and all the Gs in the ‘reverse’ reads and scaffold to As, and initially aligned the converted reads to the converted TAIR8 scaffold using SeqMap as individual reads, allowing up to two mismatches per read. We subsequently used a Perl script to insure that paired reads mapped to opposite strands within 300 bp of each other.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Each processed data file has 9 tab-delimited columns (described in the README.txt file attached to the Series record).

organism: Arabidopsis thaliana

source_name: dme endosperm

growth_protocol: Standard long day growth conditions

extract_protocol: Seeds at the mid-torpedo stage to early-maturation stage (7-9 days after pollination, ecotype Col-0) were dissected in 0.3 M sorbitol, 5 mM MES (pH 5.7) on a slide under a dissecting microscope. We synthesized custom Illumina adapters in which cytosines were replaced by 5-methylcytosines, so that the adapters would survive bisulfite conversion. We chose to synthesize paired ends (PE) adapters, which allow each molecule to be sequenced from both ends, thus facilitating subsequent alignment to the genomic scaffold. We isolated 0.5-1 micrograms of genomic DNA from endosperm dissected from wild type and dme seeds, as well as control wild type embryos and aerial tissues. Specifically,plant tissues were ground in CTAB (cetyltrimethylammonium bromide) and genomic DNA was isolated as described by Murray and Thompson (Nucleic Acids Research. 8: 4321-4325, 1980, PMID: 7433111). DNA was sheared by sonication to fragments of 100-500 bp, and the adapters were ligated following the Illumina protocol. The library was then treated twice with sodium bisulfite (which converts unmethylated Cs to Us) using the Qiagen EpiTect kit, and amplified by 18 cycles of PCR using PfuTurboCx DNA polymerase (Stratagene), a proofreading enzyme that tolerates uracil in the template strand. Bands around 300 bp were gel-purified and cloned for validation.

tag: ecotype

value: dme (DEMETER) mutant

value: endosperm


title: WT_endosperm_BS_seq

source_name: Wild-type endosperm

value: wild-type


title: Beihai_adullt_1

status: Public on Jun 30 2009

city: Shenzhen

first: li

last: qibin

address: Beishan, Yantian

country: China

institute: Beijing Genomic Institute

description: total RNAs extracted from a pool of 12 adult Chinese Amphioxus

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

Alignment: Unique small RNA sequences were aligned against amphioxus genome (Branchiostoma floridae v2.0) by SOAP, tolerating one mismatch.

organism: Branchiostoma belcheri

source_name: 12 adult Chinese Amphioxus

growth_protocol: Adults of Chinese amphioxus, Branchiostoma belcheri (Gray), were collected from Beihai, Guangxi, China, and kept alive with seawater and sea algae.

extract_protocol: 12 adult animals were pooled together and total RNA was extracted from pooled samples using Trizol Reagent (Invitrogen). Briefly, small RNA molecules between 18-30 nt were PAGE purified and ligated to a pair of Solexa adaptors, the small RNA molecules were amplified using the adaptor primers for 17 cycles, and the fragments around 90bp (small RNA + adaptors) were isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer.

tag: organism type

value: Branchiostoma belcheri (Gray)


title: Illumina sequencing of small RNAs from FACS-sorted planarian neoblasts

status: Public on Jul 01 2009

first: Marc

middle: Riemer

last: Friedlaender

state: Berlin

address: Robert-Rössle-Str. 10

institute: MDC, Berlin-Buch

description: small RNAs

data_processing: Output from Bustard application (part of Solexa/Illumina package), adapters clipped and reads with more than one uncalled nucleotide or homo-nucleotides stretches of 7 nt or longer were discarded, as were reads that did not map to the genome (for details on mapping protocol, see Friedlander et al. PNAS, 2009).

organism: Schmidtea mediterranea

source_name: planarian

extract_protocol: total RNA, ~15-40nt RNAs isolated using Novex 15% TBE-Urea gel (invitrogen)

value: FACS-sorted neoblast stem cells


title: Embryo_BS_seq

source_name: Embryo

value: embryo


title: 18dpp_homo_tdrd6-KO

status: Public on Jul 25 2009

first: Vasily

last: Vagin

institute: Cold Spring Harbor

description:
19-33 nt RNA isolated from testes of 18 days old mice
library_strategy: sequential ligation of 3' and 5' linkers using T4 RNA ligase follwed by PCR amplification
library_source: small RNA
library_selection: other

data_processing: Reads were aligned to the reference genome allowing zero mismatches. Number of mapping in the genome and genomic annotation were extracted.

source_name: testes

extract_protocol: total RNA was size selected (19-33nt)

value: 18dpp mouse testes


title: HPC-7_Scl_Chip-Seq (Scl_vancouver)

description: Chromatin IP against Scl protein

data_processing: Sequence data was aligned using Eland alignment software.


title: CD4+ T cell RNA-Seq

status: Public on Jun 15 2009

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description: RNA-seq

data_processing: Illumina Genome Analyzer Pipeline version 1.0 produced an output containing sequences in seq and prb formats. First 30 bases of sequences were matched to both the hg18 human genome and a library of (26+26)-bp exon junction sequences using ELAND. Exons sequences were retrieved from Ensembl database (version 50).

source_name: CD4+ T cell mRNA

extract_protocol: polyA RNA purified from total RNA

value: CD4+ T cell


title: 18.5dpc_homo_tdrd1-KO

address: 1 Bungtown Rd

description:
19-33 nt RNA isolated from testes of 18.5dpc embryos
library_strategy: sequential ligation of 3' and 5' linkers using T4 RNA ligase follwed by PCR amplification
library_source: small RNA
library_selection: other

value: 18.5dpc embryo testes


title: small RNAs from Medicago truncatula, Jemalong A17, Root tips + NaCl 100 mM 1 hour

description: root+NaCl smallRNAs 13-45nt

source_name: Root apexes + NaCl

tag: strain

value: Jemalong A17

value: Root tips (1-2 cm) were obtained from plants 10-12 days post-germination grown in sand:perlite pots disposed on a metal grid, with root tips growing in a rich SN/2 rich nutritive solution. Plants were transferred for 1 h in SN/2 + NaCl 100 mM.


title: 25dpp_homo_tdrd6-KO

description:
19-33 nt RNA isolated from testes of 25 days old mice
library_strategy: sequential ligation of 3' and 5' linkers using T4 RNA ligase follwed by PCR amplification
library_source: small RNA
library_selection: other

value: 25dpp mouse testes


title: Yeast Exponential phase glucose GCC library without MspI site

source_name: Exponential yeast cells


title: 18.5dpc_hetero_tdrd1-KO


title: Input Lane 5

city: Salt Lake City

first: Bradley

middle: R.

last: Cairns

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: HHMI and Huntsman Cancer Institute

description: Input control

data_processing: Reads were aligned to Hg18/ NCBI 36.1/ H_sapiens_Mar_2006 using the Illumina Pipeline's ELAND extended aligner and enriched regions relative to input identified using the USeq analysis package (http://useq.sourceforge.net, Nix et al BMC Bioinfo Dec 5:9(1):523 (2008)).

source_name: Sperm Pooled Donors

growth_protocol: Sperm samples were obtained from four known fertile donors attending the University of Utah Andrology laboratory, consented for research.

extract_protocol: Sperm samples were collected after 2-5 days abstinence and subjected to an ISolate density gradient (to purify viable, motile, mature sperm) and treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H2O) for 20 min on ice to eliminate white blood cell contamination. Samples were centrifuged at 10,000 G for 3 min and the sperm pellet was resuspended in 1X PBS and used immediately for chromatin preparation. Chromatin was prepared as previously described by Zalenskaya et al Biochem Biophys Res Commun 279, 213-8 (2000) in the absence of crosslinking reagent. Sperm was treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were used for chromatin immunopreciptation (below), or the DNA extracted and gel purified (~140-155bp) for  array analysis. All Chromatin IPs (ChIPs) were performed as previously described by Gordon et al Mol Cell Biol 27, 4058-69 (2007).

value: sperm


title: Input Lane 4

description: Input control


title: 6w_homo_tdrd6-KO

description:
19-33 nt RNA isolated from testes of 6 weeks old mice
library_strategy: sequential ligation of 3' and 5' linkers using T4 RNA ligase follwed by PCR amplification
library_source: small RNA
library_selection: other

value: 6 weeks  old testes


title: Input Lane 3

description: Input control

source_name: Sperm Donor D1


title: Input Lane 2

description: Input control


title: 6w_hetero_tdrd6-KO

value: 6 weeks old mouse testes


title: Histone-Mnase Lane 11

description: Histone bound DNA enrichment via Mnase digestions and nucleosome purification

source_name: Sperm Donor D3


title: 25dpp_hetero_tdrd6-KO


title: Histone-Mnase Lane 12

source_name: Sperm Donor D4