|
| Status |
Public on Mar 28, 2013 |
| Title |
placenta 3 - MethylC-seq |
| Sample type |
SRA |
| |
|
| Source name |
placenta
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta from full-term pregnancy
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue DNA was purified using Qiagen's Puregene kit.
The genomic DNA was sonicated to ~300 bp and methylated Illumina adapters were ligated to the ends. 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurboCx Hotstart DNA Polymerase (Stratagene) for 14 cycles using Illumina's standard amplification protocol.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the genome using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment. BS Seeker parameters: -e 85 -m 3 -a adapter2.
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%
Genome_build: hg18
Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site
|
| |
|
| Submission date |
Feb 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Janine LaSalle |
| E-mail(s) |
jmlasalle@ucdavis.edu
|
| Organization name |
UC Davis
|
| Street address |
Medical Microbiology and Immunology
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE39775 |
Examination of four human tissue samples by MethylC-seq |
| GSE39777 |
Comparison of DNA methylation in human tissues |
|
| Relations |
| SRA |
SRX237632 |
| BioSample |
SAMN01921692 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1083881_placenta3_MethylC-seq_chr1.BED.gz |
11.9 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr10.BED.gz |
7.1 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr11.BED.gz |
6.9 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr12.BED.gz |
6.8 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr13.BED.gz |
4.2 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr14.BED.gz |
4.5 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr15.BED.gz |
4.4 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr16.BED.gz |
5.7 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr17.BED.gz |
6.0 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr18.BED.gz |
3.6 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr19.BED.gz |
5.6 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr2.BED.gz |
11.3 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr20.BED.gz |
3.9 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr21.BED.gz |
2.0 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr22.BED.gz |
3.0 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr3.BED.gz |
8.6 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr4.BED.gz |
7.6 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr5.BED.gz |
7.8 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr6.BED.gz |
7.7 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr7.BED.gz |
8.0 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr8.BED.gz |
6.8 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chr9.BED.gz |
6.0 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chrX.BED.gz |
4.5 Mb |
(ftp)(http) |
BED |
| GSM1083881_placenta3_MethylC-seq_chrY.BED.gz |
433.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
