|
| Status |
Public on May 01, 2019 |
| Title |
Viable_paternal_excess_2 [Bisulfite-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Endosperm
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Ler female x 4N Col nrpd1 male
developmental stage: 7 days after pollination
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Plants were grown in a growth-chamber with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at seven DAP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Endosperm was hand dissected from seeds at 7 DAP. DNA was extracted from dissected endosperm using the QiaAMP DNA microkit. Breifly, dissected tissue was incubated in ATL buffer and Proteinase K overnight. 80-100 ng of DNA obtained for each sample was subjected to bisulfite treatment using Methylcode Bisulfite conversion kit (Invitrogen).
Purified, bisulfite converted DNA was used as input for library construction using Illumina Truseq DNA methylation kit.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Bisulfite sequencing
Viable_paternal_excess_2
|
| Data processing |
Reads that were obtained were filtered for quality with “trim_galore --phred64 --fastqc --stringency 5 --length 15 --paired --clip_R1 2 --clip_R2 2”.
The reads were then aligned to TAIR10 using “bismark -N 1 -L 20”.
Duplicate reads were removed using bismark.
Bismark methylation extractor was used to obtain unfiltered per base methylation data. Custom scripts previously described were used to obtain per base methylation and to identify DMRs.
We used a custom script (https://github.com/clp90/imprinting_analysis/tree/master/helper_scripts) to identify allele specific reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Contains output from script for DMR detection and includes methylation per window, significance of difference in tab delimited files. Generated based on data from both biological replicates.
Supplementary_files_format_and_content: List of detected DMRs for CHH, CHG and CG methylation in comparisons between Balanced, Lethal and Viable paternal excess endosperm in bed format. Generated based on data from both biological replicates.Briefly, differences in methylation were calculated genome-wide for 300 bp sliding windows with 200 bp overlaps. To be included, windows had at least 3overlapping cytosines in both genotypes with a read depth of at least 6 reads per cytosine. Windows called as significantly different were at least 10% different between tested genotypes for CHH methylation, 20% for CHG methylation and 30% for CG methylation. Significance of difference was calculated by F.E.T with a Bonferroni- Hochberg correction (p<0.01).
Supplementary_files_format_and_content: Methylation level at single base resolution in CHH,CHG and CG context in Balanced, lethal and viable paternal excess endosperm in tdf format. Only cytosines passing coverage thresholds are included here. Each *tdf file for a genotype includes data from both biological replicates
|
| |
|
| Submission date |
Feb 22, 2019 |
| Last update date |
May 01, 2019 |
| Contact name |
satyaki P Rajavasireddy |
| E-mail(s) |
satyaki@wi.mit.edu
|
| Phone |
6072290279
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Gehring Lab
|
| Street address |
455 Main Street
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE126929 |
Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage [Bisulfite-seq] |
| GSE126932 |
Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage |
|
| Relations |
| BioSample |
SAMN10987546 |
| SRA |
SRX5408225 |
