NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1059959 Query DataSets for GSM1059959
Status Public on Oct 02, 2014
Title PIF1-peaks-3
Sample type SRA
 
Source name whole seedlings
Organism Arabidopsis thaliana
Characteristics developmental satge: 3-day-old
growth conditions: dark-grown
chip antibody: anti-Myc (Abcam, ab9132)
genotype/variation: PIF1
Treatment protocol Under green safelight, 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 0.2 g stratified seeds were irradiated with WL at 21 ºC for 3 h to induce germination and grown in darkness at 21 ºC for 3 d before harvest.
Extracted molecule genomic DNA
Extraction protocol For each PIF-ChIP and each WT control ChIP three independent libraries were generated pooling DNA of four ChIP assays of two biological replicates each using the NEXTflex ChIP-seq kit and 6 NEXTflex ChIP-Seq Barcodes (Bioo Scientific) according to the manufacturer’s instructions. Adapter-ligated DNA-fragments of 200-300 bp were gel-purified, validated by Bioanalyzer 2000 (Agilent) and quantified by the KAPA Library Quantification Kit (KAPABiosystems). Six libraries were pooled on a single lane and sequenced by 50-cycle single-end sequencing on the Illumina HiSeq platform.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description PIF1-peaks-3.txt
Data processing Base-callling was performed using Illumina pipeline CASAVA-1.8.0.
Reads passed quality filtering were aligned to the chromosomes 1-5 of the TAIR10 genome assembly using Bowtie-0.12.7 with the following settings: -v 2 --best --strata -m 1 -5 3
Peak-calling was performed using MACS-1.4.1 with the following settings: -g 150000000 --off-auto --nomodel --shiftsize=60 -w -S.
Genome_build: TAIR10
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 Jan 04, 2013
Last update date Sep 04, 2019
Contact name james m tepperman
E-mail(s) jmtepp@berkeley.edu
Phone 510-559-5935
Organization name Plant Gene Expression Center/UC Berkeley
Department Plant and Microbial Biology
Lab QUAIL
Street address 800 Buchanan St.
City Albany
State/province CA
ZIP/Postal code 94710
Country USA
 
Platform ID GPL13222
Series (2)
GSE43283 Genome-wide identification of PIF1-binding sites and direct-target genes of PIF1 transcriptional regulation in skotomorphogenesis
GSE43286 Genome-wide identification of PIF-binding sites and direct-target genes of PIF transcriptional regulation in skotomorphogenesis
Relations
Reanalyzed by GSE136843
SRA SRX214144
BioSample SAMN01882323

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap