SC_EXP_9778_3#2
Illumina HiSeq 2000 paired end sequencing
Illumina sequencing of library 7211735, constructed from sample accession ERS206040 for study accession ERP015660.  This is part of an Illumina multiplexed sequencing run (9778_3).  This submission includes reads tagged with the sequence CGATGT.
7211735
qPCR only
SC
SC_EXP_9778_3#2
The Wellcome Trust Sanger Institute
SC_EXP_9778_3#2
BISULFITE_CONVERSION_PERCENT
99.9%
BISULFITE_CONVERSION_PROTOCOL
QIAGEN EpiTect Bisulfite - FFPE protocol
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL
TruSeq DNA LT Sample Prep-Kit Set A (July 2012, Illumina, FC-121-2001) - 30C for 10 minutes
DNA_PREPARATION_ADAPTOR_SEQUENCE
AD002 (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG)
DNA_PREPARATION_ADAPTOR_SOURCE
Methylated adaptors (Illumina ME-100-0010)
DNA_PREPARATION_FRAGMENT_SIZE_RANGE
280bp average size (50bp-650bp)
DNA_PREPARATION_INITIAL_DNA_QNTY
1ug
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION
450-550bp average size - AMPure XP beads (Agencourt)
EXPERIMENT_TYPE
DNA Methylation
EXTRACTION_PROTOCOL
AllPrep DNA/RNA Mini Kit (QIAGEN 80204)
EXTRACTION_PROTOCOL_SONICATION_CYCLES
200
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR
Covaris E210
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE
PCR Primer Cocktail - TruSeq DNA LT sample preparation kit (Illumina, FC-121-2001)
LIBRARY_GENERATION_PCR_NUMBER_CYCLES
10 cycles
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE
Pfu Turbo Cx Hotstart DNA polymerase
LIBRARY_GENERATION_PCR_PRIMER_CONC
PCR Primer Cocktail - TruSeq DNA LT sample preparation kit (Illumina, FC-121-2001) (1.5ul/50ul reaction)
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL
AMPure XP beads (Agencourt) 1:1
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE
PCR Primer Cocktail - TruSeq DNA LT sample preparation kit (Illumina, FC-121-2001)
LIBRARY_GENERATION_PCR_TEMPLATE_CONC
5-10ng/ul
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM
95C for 2min; 10 cycles of: 95C for 30 sec, 60C for 20 sec, 72C for 45 sec; 72C for 5min; hold at 4C