alias: WGBS_Lib 71
center_name: BI
expected_number_runs: 3

STUDY_REF: G1828
SAMPLE_DESCRIPTOR: BioSam 1242

LIBRARY
LIBRARY_NAME: WGBS_Lib 71
LIBRARY_STRATEGY: Bisulfite-Seq
LIBRARY_SOURCE: GENOMIC
LIBRARY_SELECTION: RANDOM
LIBRARY_LAYOUT: SINGLE
POOLING_STRATEGY: none
LIBRARY_CONSTRUCTION_PROTOCOL: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

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: 99

BASE CALLS
GAPipeline RTA1.15.19.5

QUALITY SCORES
GAPipeline RTA1.15.19.5

ATTRIBUTES
BISULFITE_CONVERSION_PROTOCOL: 2x5hrs Epitect Kit
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
EXTRACTION_PROTOCOL_SONICATION_CYCLES: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: T4 Ligase (2,000U/ul) 16C o/n
DNA_PREPARATION_ADAPTOR_SEQUENCE: Illumina paired end adapter
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE1.0
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 250-400
BISULFITE_CONVERSION_PERCENT: 99.5%
EXTRACTION_PROTOCOL: Standard Protocol (Smith et al., Methods 48, 226-232)
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25uM
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 130-280
EXPERIMENT_TYPE: DNA Methylation
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: Smith et al., Methods 48, 226-232
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: SPRI Beads
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE2.0
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: NA
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Pfu Turbo Cx hot start
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5-8
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris S2 (TM)