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Sample GSM530099 Query DataSets for GSM530099
Status Public on Apr 09, 2010
Title Ath_wildtype_flowers_bisulfite
Sample type SRA
 
Source name Flowers
Organism Arabidopsis thaliana
Characteristics strain: Columbia-0
genotype: wild type
sample type: Flowers
tissue: Flowers
Extracted molecule genomic DNA
Extraction protocol BS-Seq DNA library construction and high-throughput sequencing by Illumina/Solexa Genome Analyzer were performed according to published protocols (Cokus et al., Nature 451, 215-219), except that a total number of six PCR cycles were removed from the library generation procedure. NEBNext DNA sample preparation kit (New England BioLabs) and CpGenome DNA Modification Kit (Chemicon) were used during library construction.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer II
 
Description Bisulfite conversion of unmethylated cytosines
all sequences are Cycles 1..5: BS-Seq FW=tctgt, BS-Seq RC=tccat
Data processing Illumina Genome Analyzer 200 tiles/lane (sample 1), Illumina Genome Analyzer II 100 tiles/lane (samples 2/3/4/7/9), Illumina Genome Analyzer 300 tiles/lane (samples 5/6/8/10/11/13/14), Illumina Genome Analyzer 330 tiles/lane (sample 12)
Illumina_native (_sig2, _seq, _prb): All samples are single end by Solexa pipeline 0.2.2.4/OS X with all physical cycles given to the pipeline, except samples 2/3/4 are by Solexa pipeline 1.3rc5/OS X and samples 7/9 are by Solexa pipeline 1.3rc5/Linux. All lanes are single end 36 cycles, except lanes for samples 7/9 are single end 55 cycles. Autocalibration on each flow cell was from all tiles and cycles of lane 4 on the same flow cell, which was one of four genomic libraries (#1 for flow cells 070625_SLXA-EAS20_5701 / 071030_HWI-EAS172_14517, #2 for 090306_HWI-EAS399_S014_3126D / 090616_HWI-EAS399_S022_30155, #3 for 080604_HWI-EAS172_20DYB, and #4 for the remaining six) with high representation of A/C/G/T.
 
Submission date Apr 02, 2010
Last update date May 15, 2019
Contact name matteo Pellegrini
E-mail(s) matteop@mcdb.ucla.edu
Phone 310-825-0012
Organization name UCLA
Department MCD Biology
Lab Matteo Pellegrini
Street address 621 Charles Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL9302
Series (1)
GSE21152 Conservation and divergence of methylation patterning in plants and animals
Relations
SRA SRX018781
BioSample SAMN00010920

Supplementary file Size Download File type/resource
GSM530099_090306_HWI-EAS399_S014_3126D_L1_processed_chromStrandZeroBasedCoordAthTAIR9_observeMethOrUnme.txt.gz 27.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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