|
| Status |
Public on Aug 05, 2012 |
| Title |
NRPE1 ChIP rdm1 mutant |
| Sample type |
SRA |
| |
|
| Source name |
floral tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: rdm1-1 (eco. C24) with NRPE1-FLAG transgene
genetic background: C24
tissue: floral
genotype: rdm1-1
transgene: NRPE-FLAG
chip antibody: anti-FLAG
sample type: Genomic DNA isolated from immunoprecipitated chromatin using FLAG antibody
chip antibody manufacturer: Sigma
chip antibody catalog #: M8823-5ml
chip antibody lot #: 041M6135
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples 1..7 / 8..11 / 12..13 / are by NEBNext DNA sample preparation protocol using Illumina PE adapters / Illumina TruSeq small RNA / converted and fragmented genomic DNA library as described in Cokus et al., Nature 2008 /
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
immunoprecipitated formaldehyde-crosslinked leaf tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
|
| Data processing |
ChIPseq 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 2 mismatches and retaining only uniquely mapping reads.
genome build: TAIR8
Fixed step (50bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 50bp bins / total unique mapping reads)
|
| |
|
| Submission date |
Jul 10, 2012 |
| 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) |
| GSE39247 |
The DDR complex facilitates the genome-wide association of RNA Polymerase V to promoters and evolutionarily young transposons |
|
| Relations |
| SRA |
SRX159111 |
| BioSample |
SAMN01087298 |
