|
| Status |
Public on Jul 08, 2012 |
| Title |
Col-0 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Etiolated seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Etiolated seedlings
genotype/variation: Col-0
antibody: anti-myc antibody
vendor/catalog#: Cell Signaling #2276
|
| Growth protocol |
Transgenic plants expressiong PIF4-myc driven by native PIF4 promoter (pPIF4::PIF4-myc) are grown in the dark for 5 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and PIF4-myc-DNA complexes were isolated with anti-myc antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Genome Analyzer IIx following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against PIF4 transcription factor
|
| Data processing |
Alignment : The raw sequence data were processed using Illumina sequence data analysis pipeline GAPipeline1.3.2. Sequences in Solexa FASTQ format were mapped to the Arabidopsis genome, TAIR9. Only unique mapping reads were used to determine PIF4 binding peaks.
Peaks: Peak detection was performed with Plant Research International ChIP-seq Analysis Tool (PRI-CAT) (http://www.ab.wur.nl/pricat/)
Genome Build:
Col.aln: Arabidopsis genome (TAIR9)
|
| |
|
| Submission date |
Jan 24, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eunkyoo Oh |
| Organization name |
Carnegie Institution
|
| Department |
Plant Biology
|
| Street address |
260 Panama Street
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11221 |
| Series (2) |
| GSE35315 |
Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses [ChIP-seq] |
| GSE37160 |
Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses |
|
| Relations |
| SRA |
SRX117694 |
| BioSample |
SAMN00778982 |
