|
| Status |
Public on Nov 01, 2013 |
| Title |
Col H3K4m3 ChIP (replicate 1) |
| Sample type |
SRA |
| |
|
| Source name |
3 week leaf tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Wild type
ecotype: Columbia
antibody: anti-H3K4m3 (Diagenode pAb-003-050)
|
| Growth protocol |
All plants were grown at 22 degrees celsius in constant light.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
extracted by ChIP followed by phenol-chloroform exctract as described
Illumina TruSeq DNA Prep Kit
immunoprecipitated formaldehyde-crosslinked leaf tissue
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane
ChIP-seq -- Reads were filtered for full-length (50bp) reads. Reads containing adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Technical sequencing replicates for each respective genotype to increase coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)
|
| |
|
| Submission date |
Jul 22, 2013 |
| 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) |
| GSE49090 |
Interplay Between Active Chromatin Marks and RNA-directed DNA Methylation in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN02261575 |
| SRA |
SRX326935 |
