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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 09, 2010 |
| Title |
Ath_met1_flowers_bisulfite |
| Sample type |
SRA |
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| Source name |
Flowers
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| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Columbia-0
genotype: met1
sample type: Flowers
tissue: Flowers
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Bisulfite conversion of unmethylated cytosines
all sequences are Cycles 1..5: BS-Seq FW=tctgt, BS-Seq RC=tccat
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| 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.
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| Submission date |
Apr 02, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
matteo Pellegrini |
| E-mail(s) |
matteop@mcdb.ucla.edu
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| Phone |
310-825-0012
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| Organization name |
UCLA
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| Department |
MCD Biology
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| Lab |
Matteo Pellegrini
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| Street address |
621 Charles Young Drive South
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL9302 |
| Series (1) |
| GSE21152 |
Conservation and divergence of methylation patterning in plants and animals |
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| Relations |
| SRA |
SRX018783 |
| BioSample |
SAMN00010922 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM530101_090306_HWI-EAS399_S014_3126D_L2_processed_chromStrandZeroBasedCoordAthTAIR9_observeMethOrUnme.txt.gz |
21.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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