alias: 2013_07_31_FISH_SR_Q33_A/fastq/Project_GH/Sample_GH278A_3/GH278A_3_NoIndex_L005_R1_001.fastq.gz
expected_number_runs: 1
center_name: UCSD

STUDY_REF: The San Diego Epigenome Center
SAMPLE_DESCRIPTOR: SRS267132

LIBRARY
LIBRARY_NAME: GH278A_L5.2013_07_31
LIBRARY_STRATEGY: TAB-Seq
LIBRARY_SOURCE: GENOMIC
LIBRARY_SELECTION: RANDOM
LIBRARY_LAYOUT: SINGLE
POOLING_STRATEGY: none
LIBRARY_CONSTRUCTION_PROTOCOL: See http://www.nature.com/nprot/journal/v7/n12/full/nprot.2012.137.html

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

PLATFORM
ILLUMINA
INSTRUMENT_MODEL: Illumina HiSeq 2000
SEQUENCE_LENGTH: 100

BASE CALLS
Illumina HiSeq Control Software 2.0.12.0

QUALITY SCORES
Illumina HiSeq Control Software 2.0.12.0

ATTRIBUTES
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: See http://www.nature.com/nprot/journal/v7/n12/full/nprot.2012.137.html
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris
EXTRACTION_PROTOCOL_SONICATION_CYCLES: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200?500 bp.
DNA_PREPARATION_INITIAL_DNA_QNTY: 5ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 200-500bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Standard Illumina adaptor sequence
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: TruSeq
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 250-600
BISULFITE_CONVERSION_PROTOCOL: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)
BISULFITE_CONVERSION_PERCENT: 99.6512
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: not measured
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2min 95C, 30s 98C, 10x (15s 98c, 30s 60C, 4min 72C), 10min 72C, hold 4C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 80
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: standard Illumina TruSeq
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: standard Illumina TruSeq
LIBRARY_GENERATION_PCR_PRIMER_CONC: undiluted Illumina TruSeq kit PCR primers
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.