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Reference Epigenome: ChIP-Seq Analysis of H3K27ac in IMR90 Cells
ChIP-Seq Analysis of H3K27ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.


Project News:
2010/2/25:
EXPERIMENT XML file 'renlab.H3K27ac.IMR90-03.01.experiment.xml' uploaded



alias: renlab.H3K27ac.IMR90-03.01
expected_number_runs: 1
expected_number_spots: 15006490
expected_number_reads: 15006490
center_name: UCSD

STUDY_REF: The San Diego Epigenome Center
SAMPLE_DESCRIPTOR: IMR90-05

LIBRARY
LIBRARY_NAME: YL58
LIBRARY_STRATEGY: ChIP-Seq
LIBRARY_SOURCE: GENOMIC
LIBRARY_SELECTION: ChIP
LIBRARY_LAYOUT: SINGLE
LIBRARY_CONSTRUCTION_PROTOCOL: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

SPOT
NUMBER_OF_READS_PER_SPOT: 1
READ_INDEX: 0
READ_CLASS: Application Read
READ_TYPE: Forward
BASE_COORD: 1

PLATFORM
ILLUMINA
INSTRUMENT_MODEL: Illumina Genome Analyzer II
CYCLE_SEQUENCE: ACGT
CYCLE_COUNT: 36

BASE CALLS
SEQUENCE_SPACE: Base Space
BASE_CALLER: Illumina Genome Analyzer Pipeline Software version 1.4

QUALITY SCORES
Quality Type: phred
QUALITY_SCORER: Illumina Genome Analyzer Pipeline Software version 1.4
NUMBER_OF_LEVELS: 80
MULTIPLIER: 1

ATTRIBUTES
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 120
CHIP_PROTOCOL: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 500 micrograms
CHIP_PROTOCOL_BEAD_TYPE: magnetic anti-rabbit
CHIP_PROTOCOL_BEAD_AMOUNT: 33,500,000
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 micrograms
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: Ab4729
CHIP_ANTIBODY_LOT: 34624

 

 


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