|
| Status |
Public on Apr 08, 2014 |
| Title |
Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Cytosine base modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) are present in mammalian DNA. Here, reduced bisulfite sequencing is developed for quantitatively sequencing 5fC at single-base resolution. This method is then applied with oxidative bisulfite sequencing to gain a map of 5mC, 5hmC and 5fC in mouse embryonic stem cells.
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| |
|
| Overall design |
12 samples, reduced representation bisulphite treatment: 4 replicates each for bisulphite (BS), oxidative BS (oxBS) and reduced BS (redBS) for the detection of 5mC, 5hmC and 5fC. Mouse (strain B6C) embryonic stem cells.
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| |
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| Contributor(s) |
Booth MJ, Marsico G, Bachman M, Beraldi D, Balasubramanian S |
| Citation(s) |
24755596 |
| |
| Submission date |
Apr 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Giovanni Marsico |
| E-mail(s) |
persego@gmail.com
|
| Organization name |
CRUK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (12)
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| Relations |
| BioProject |
PRJNA243936 |
| SRA |
SRP041010 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56572_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
| GSE56572_README_supplementary_files.txt |
2.5 Kb |
(ftp)(http) |
TXT |
| GSE56572_genome.cnt_met.mat.txt.gz |
257.7 Mb |
(ftp)(http) |
TXT |
| GSE56572_genome.loci.txt.gz |
339.6 Mb |
(ftp)(http) |
TXT |
| GSE56572_genome.pct_met.BS.bed.gz |
225.7 Mb |
(ftp)(http) |
BED |
| GSE56572_genome.pct_met.mat.txt.gz |
362.9 Mb |
(ftp)(http) |
TXT |
| GSE56572_genome.pct_met.oxBS.bed.gz |
224.5 Mb |
(ftp)(http) |
BED |
| GSE56572_genome.pct_met.redBS.bed.gz |
225.6 Mb |
(ftp)(http) |
BED |
| GSE56572_genome.tot_reads.mat.txt.gz |
325.7 Mb |
(ftp)(http) |
TXT |
| GSE56572_glmnonsig_hmC_fC_BScounts_all_new.txt.gz |
30.5 Mb |
(ftp)(http) |
TXT |
| GSE56572_glmsig_fC_new.txt.gz |
226.1 Kb |
(ftp)(http) |
TXT |
| GSE56572_glmsig_hmC_fC_BScounts_new.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE56572_glmsig_hmC_new.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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