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| Status |
Public on Jan 26, 2010 |
| Title |
WT_ES_cell_bisulfite |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
cell type: Embyonic stem cell
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted from mouse tissues were treated with sodium bisulfite and then used to generate Illumina/Solexa sequencing libraries as described previously (Cokus et al., Nature 451, 215-219), except that fewer cycles of PCR amplification were used (15 cycles instead of 18 cycles). For PGC samples, due to the limited sources of tissue, the input DNA amount for libraries had to be reduced to as low as 150 ng. Therefore, the enzymatic reaction steps used for library construction (including reagents and adapters for PCR) were scaled down to accommodate the reduced input amount. On the other hand, more DNA template (in volume) was used in each PCR reaction and more duplicate PCR reactions were performed in parallel in order to obtain equivalent amounts of product as for the other libraries.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Bisulfite conversion of unmethylated cytosines
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| Data processing |
Illumina Genome Analyzer 300 tiles/lane (samples 1..4, 6..8), Illumina Genome Analyzer 330 tiles/lane (sample 5), Illumina Genome Analyzer II 100 tiles/lane (samples 9..12)
Illumina_native (_sig2, _seq, _prb): samples 1..8 are by Solexa pipeline 0.2.2.4/OS X, 36 physical cycles all given to Solexa pipeline, autocalibration from all tiles and cycles of lane 4 on same flow cell which was one of two genomic libraries (#1 for samples 1..4/6/8, #2 for samples 5/7) with high representation of A/C/G/T; samples 9..12 are by Solexa pipeline 1.3rc5/Linux, 55 physical cycles all given to Solexa pipeline, autocalibration from all tiles and cycles of Phi-X library on lane 4 of same flow cell.
BSseq--chrStrandCoord-observeMethOrUnme processing was similar to a previous study (Cokus et al., Nature 451, 215-219) with some adjustments; briefly: (1) GMM (sig2V9) fits were made to _sig2 files and movies manually inspected; (2) PWM-based probabilistic alignment (CokusAlignment) was performed (cycles 10..36 for samples 1/2/6/8, cycles 6..32 for samples 3..5/7, cycles 6..55 for samples 9..12) against reference genome UCSC mm9 (chr1..19, X, Y; no rnd or chrU or chrM, except samples 9..12 included chrM from NCBI gi 34538597) with per-read FW/RC probability scoring priors derived from cycles 1..5 of _prb files; (3) only reads aligning to exactly one genomic 27-mer (samples 1..8) or 50-mer (samples 9..12) that is BS-unique were retained; (4) non-conversion filtering was performed; and (5) data from cycles 15..31 (samples 1/2/6/8), cycles 11..27 (samples 3..5/7), and cycles 20..46 (samples 9..12) was gathered.
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| Submission date |
Jan 25, 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 |
GPL9185 |
| Series (1) |
| GSE19960 |
Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by Aid deficiency |
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| Relations |
| SRA |
SRX016287 |
| BioSample |
SAMN00008348 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM500951_071121_HWI-EAS172_200C0_L7_processed.txt.gz |
10.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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