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Sample GSM958274 Query DataSets for GSM958274
Status Public on Feb 01, 2013
Title WT-ChIP-2
Sample type SRA
 
Source name whole seedlings
Organism Arabidopsis thaliana
Characteristics developmental satge: 2-day-old
growth conditions: true dark
genotype: WT
chip antibody: anti-Myc (Abcam, ab9132)
Treatment protocol Under green safelight, about 4 g of seedlings were cross-linked in 72 ml of 1% fresh formaldehyde solution for 5 plus 10 min by vacuum infiltration, and then were quenched by adding 5 ml of 2M of glycine with 5 min of vacuum infiltration. Seedlings were rinsed by sterile distilled water, dried by paper towels, and then frozen in liquid nitrogen.
Growth protocol Stratified seeds were irradiated with WL at 21 ºC for 3 h to induce germination, followed by a FR pulse for 15 min to suppress pseudo dark effects, and grown in darkness at 21 ºC for 2 d before harvest.
Extracted molecule genomic DNA
Extraction protocol The ChIP-seq library was constructed according to Illumina’s instruction with some modifications. Four ChIP samples from technical replicates of each biological replicate were pooled together and concentrated to increase the starting amount of DNA. The end repair of DNA fragments was performed using End-It DNA End-Repair Kit (Epicentre). The A-tailing was added to the end-repaired DNA fragments using Klenow Fragment (NEB), and then Illumina’s PE adapters were ligated by T4 DNA Ligase (Promega) at 16 ºC overnight. The adapter-ligated DNA fragments in the 200-300 bp size-range were selected by the gel purification, and then were amplified using Phusion High-Fidelity DNA Polymerase (NEB) with the Illumina PE PCR primer set. The library was purified using an Agencourt AMPure XP system (Beckman Coulter Genomics), and then validated by Bioanalyzer 2000 (Agilent).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description PIF3-peaks-2.xlsx
Data processing Base-callling was performed using Illumina pipeline CASAVA-1.7.0.
Reads that have no unrecognized nucleotides (Ns) and passed quality filtering were aligned to the TAIR9 genome assembly using Bowtie-0.12.7 with the following settings: -v 2 --best --strata -m 1.
Only reads mapped uniquely to the nuclear genome with the lowest number of mismatches were retained for binding-peak identification.
The aligned reads from the two technical sequencing replicates of both libraries were combined and processed as single dataset in the 1st and 2nd biological replicates.
Peak-calling was performed using MACS-1.4.0rc2 with the following settings: gsize=1.1e8, bw=100, nomodel, shiftsize=50, slocal=1000, llocal=2000, and p=1e-5.
Genome_build: TAIR9
Supplementary_files_format_and_content: Tabular files generated by MACS containing peaks information, including chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region, fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage.
 
Submission date Jul 10, 2012
Last update date Sep 04, 2019
Contact name Yu Zhang
E-mail(s) yuzhang@berkeley.edu
Phone 1-510-559-5889
Organization name UC Berkeley
Department Plant and Microbial Biology
Lab Peter H. Quail
Street address 800 Buchanan Street
City Albany
State/province California
ZIP/Postal code 94710
Country USA
 
Platform ID GPL11221
Series (2)
GSE39215 Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]
GSE39217 Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis
Relations
Reanalyzed by GSE136843
SRA SRX159031
BioSample SAMN01086901

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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