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| Status |
Public on Apr 05, 2018 |
| Title |
Autism_placenta_029 |
| Sample type |
SRA |
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| Source name |
placenta
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| Organism |
Homo sapiens |
| Characteristics |
developmental timepoint: full term birth
Sex: male
diagnosis: autism
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples of the placenta were frozen immediately after birth. DNA was purified using Qiagen's Puregene kit and sonicated to about 200 bp.
Methylated adapters were added with the NEBNext DNA library prep kit. Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit, amplified for 14 cycles with PfuTurbo Cx, and purified with AMPure beads.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
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: hg19
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.
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| Submission date |
Apr 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Janine LaSalle |
| E-mail(s) |
jmlasalle@ucdavis.edu
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| Organization name |
UC Davis
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| Street address |
Medical Microbiology and Immunology
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE67615 |
DNA methylation in the placentas of typically developing and autistic children |
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| Relations |
| BioSample |
SAMN03463205 |
| SRA |
SRX980539 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1652149_autism_029_placenta_methylation.tar.gz |
114.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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