GSM1657732: CCA1-ChIP_IonPGM; Arabidopsis thaliana; ChIP-Seq - SRA

SRX997424: GSM1657732: CCA1-ChIP_IonPGM; Arabidopsis thaliana; ChIP-Seq
1 ION_TORRENT (Ion Torrent PGM) run: 2.9M spots, 445.4M bases, 336.7Mb downloads

Submitted by: Gene Expression Omnibus (GEO)

Study: Genome-wide identification of CCA1-bound genes in Arabidopsis by ChIP-Seq

PRJNA281176 • SRP057254 • All experiments • All runs

show Abstracthide Abstract

LHY and CCA1 encode single MYB transcription factors, involved in circadian clock. However, direct target genes of LHY and CCA1 in a genomic scale were largely unknown. To reveal bound genes by CCA1, chimeric protein CCA1-FLAG was expressed under CCA1 promoter in cca1 lhy (CCA1pro:CCA1-FLAG/ cca1 lhy). ChIP was performed using anti-FLAG antibody (F3165; SIGMA), which was bound to Dynabeads Protein G (100-03D; Life Technologies), and ChIP DNA were analyzed by IonPGM or Illumina GAII. Overall design: Chromatin immunoprecipitation was performed for CCA1-FLAG-expressing Arabidopsis. ChIP DNA was analyzed 2 types of deep sequencers (Illumina GAII and IonPGM).

Sample: CCA1-ChIP_IonPGM

SAMN03485816 • SRS911633 • All experiments • All runs

Organism: Arabidopsis thaliana

Library:

Instrument: Ion Torrent PGM

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: Nuclei isolated from fixed plants, were sonicated and immunoprecipitated with anti-FLAG antibody (F3165, SIGMA), according to the method (Nakamichi et al., PNAS,109:17123-17128, 2012). Libraries were prepared according to suppliers' instructions, Ion Plus Fragment library Kit (4471252, Life Technologies) for IonPGM, and ChIP-Seq Sample Prep Kit (Part# IP-102-1001, Illumina) for Illumina GAII.

Experiment attributes:

GEO Accession: GSM1657732

Links:

External link: GEO Sample GSM1657732

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 2.9M spots, 445.4M bases, 336.7Mb

Run	# of Spots	# of Bases	Size	Published
SRR1976455	2,931,193	445.4M	336.7Mb	2016-03-11

ID:: 1448310

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