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| Status |
Public on Jun 03, 2014 |
| Title |
ARF6 ChIP-Seq |
| Sample type |
SRA |
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| Source name |
Etiolated ARF6p::ARF6-Myc in arf6;arf8 seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Etiolated seedlings
antibody: anti-myc antibody
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| Growth protocol |
Transgenic plants expressiong ARF6-Myc driven by native ARF6 promoter (ARF6p::ARF6-Myc) are grown in the dark for 5 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and ARF6-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 HiSeq following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Chromatin IP against ARF6 transcription factor
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| Data processing |
ARF6 binding peaks were identified using ChIP-Seq analysis R (CSAR) software with parameters (backg=10, norm=-1, test="Ratio", times=1e6, digits=2) (Muino et al., 2011)
Genome_build: TAIR9
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| Submission date |
Oct 28, 2013 |
| Last update date |
Jan 18, 2022 |
| Contact name |
Eunkyoo Oh |
| Organization name |
Carnegie Institution
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| Department |
Plant Biology
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| Street address |
260 Panama Street
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL13222 |
| Series (2) |
| GSE51770 |
Interactions of ARF6 with PIF4, BZR1, and RGA integrate auxin signaling with environmental and other hormonal signals in Arabidopsis [ChIP-Seq] |
| GSE51773 |
Interactions of ARF6 with PIF4, BZR1, and RGA integrate auxin signaling with environmental and other hormonal signals in Arabidopsis |
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| Relations |
| BioSample |
SAMN02385021 |
| SRA |
SRX368984 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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