|
Status |
Public on Jun 01, 2014 |
Title |
mom1_Bisulfite-Seq |
Sample type |
SRA |
|
|
Source name |
adult leaf tissue
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: mom1-2 tissue: leaf developmental stage: adult
|
Growth protocol |
All plants were grown at 22 degrees celsius in constant light.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted by Qiagen DNeasy Plant Mini Prep kit libraries were prepared using LT Illumina TruSeq kit followed by bisulfite conversion with Qiagen Epitect Bisulfite conversion and subsequent PCR amplification
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
BS-seq reads for 131216 libraries were mapped with BSmap (Xi Y, Li W, 2009 BMC Bioinformatics) allowing up to 2 mismatches and retaining only uniquely mapping reads.. Genome_build: TAIR10 Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced). Only cytosines with 5X coverage were plotted. Note: No strand information given for cytosines.
|
|
|
Submission date |
Apr 28, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Christopher Joel Hale |
E-mail(s) |
chris.joel.hale@gmail.com
|
Organization name |
University of Washington
|
Department |
Pathology
|
Lab |
Center for Precision Diagnostics
|
Street address |
1959 NE Pacific St., HSC H-458
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL13222 |
Series (1) |
GSE54677 |
Transcriptional gene silencing by Arabidopsis Microrchidia homologues involves the formation of heteromers |
|
Relations |
BioSample |
SAMN02739353 |
SRA |
SRX528713 |