alias: WGS_Lib 4
center_name: BI
expected_number_runs: 3

STUDY_REF: G1828
SAMPLE_DESCRIPTOR: BioSam 1820

LIBRARY
LIBRARY_NAME: WGS_Lib 4
LIBRARY_STRATEGY: WGS
LIBRARY_SOURCE: GENOMIC
LIBRARY_SELECTION: RANDOM
LIBRARY_LAYOUT: SINGLE
POOLING_STRATEGY: none
LIBRARY_CONSTRUCTION_PROTOCOL: Genomic DNA (0.5~1.5µg) was fragmented to 100-1,000 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with paired-end adapters. Adapter-attached DNA fragments of 470-570 bp, which contain 350-450 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were utilized as templates for PCR enrichment (5-6 cycles) by using Phusion HF polymerase (NEB). The PCR amplified DNA fragments were purified using 1.5X of Agencourt AMPure XP beads (Beckman Coulter) to remove PCR primers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit (Invitrogen). Library sequencing was performed using 101 BP PE Illumina

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: 101

BASE CALLS
GAPipeline RTA1.15.19.5

QUALITY SCORES
GAPipeline RTA1.15.19.5

ATTRIBUTES
EXTRACTION_PROTOCOL_SONICATION_CYCLES: Covaris shearing conditions: four cycles of two consecutive treatments (T1-Duty cycle 5%, Intensity 5, cycle per burst 200, duration 30 sec; T2-Duty cycle 1%, Intensity 5, cycle per burst 200, duration 5 sec).
EXPERIMENT_TYPE: Whole Genome Sequencing
EXTRACTION_PROTOCOL: Standard Protocol (Smith et al., Methods 48, 226-232)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris S2 (TM)