NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4074145 Query DataSets for GSM4074145
Status Public on Jun 21, 2020
Title 192CS17
Sample type SRA
 
Source name seedling
Organism Arabidopsis thaliana
Characteristics genotype: ELF3pro::ELF3-MYC elf3-1
cultivar: Col-0
tissue: seedling
photoperiod: Short day (8L/16D)
temperature: 17C
replicate: single
fragmentation method: sonication
chip antibody: Anti-c-Myc agarose affinity gel antibody (Sigma, A7470)
Growth protocol Seedlings were grown for 10 days under SDs at either 17 or 22 ºC and shifted to 27 ºC for 2 h at ZT8 or kept at its respective temperature.
Extracted molecule genomic DNA
Extraction protocol 3 g of seedlings for each treatment were fixed under vacuum for 20 min in 1xPBS (10 mM PO43−, 137 mM NaCl, and 2.7 mM KCl) containing 1% Formaldehyde (F8775 Sigma). The reaction was quenched by adding glycine to a final concentration of 62 mM. ChIP experiments were performed as described19. Anti-c-Myc agarose affinity gel antibody (Sigma, A7470), Anti-HA−Agarose (Sigma, A2095) or Anti-Flag® M2 Affinity Gel (Sigma, A2220) were used for immunoprecipitation.
Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1024) or using NEBNext® Ultra™ II DNA Library Prep Kit (New England BioLabs) and samples were sequenced on the Illumina NextSeq 500 platform.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Genome_build: TAIR10
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. PCR duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control 192CS19 using MACS2 with argument "--keep-dup 1 -p 0.1".
Supplementary_files_format_and_content: *.bam: Genomic alignements that were sorted, deduplicated and filtered for uniq-mapped reads.
Supplementary_files_format_and_content: *_RPKM.bw: RPKM-normalised bigwig track at 10bp resolution
Supplementary_files_format_and_content: *.narrowPeak: containing MACS2-called peaks. as described
 
Submission date Sep 11, 2019
Last update date Jun 21, 2020
Contact name Philip Wigge
E-mail(s) wigge@igzev.de
Organization name Cambridge University
Department Sainsbury Laboratory
Street address 47 Bateman street
City Cambridge
ZIP/Postal code CB2 1LR
Country United Kingdom
 
Platform ID GPL19580
Series (1)
GSE137264 RNA-Seq and ChIP-Seq profiling of ELF3, an prion-like domain-containig in ELF3 that functions as a thermosensor in Arabidopsis.
Relations
BioSample SAMN12727730
SRA SRX6830807

Supplementary file Size Download File type/resource
GSM4074145_192CS17.supp.ELF3myc-17C-ZT10_S17_Ath-TAIR10_RPKM.bw 26.9 Mb (ftp)(http) BW
GSM4074145_192CS17.supp.ELF3myc-17C-ZT10_S17_Ath-TAIR10_peaks.narrowPeak.gz 460.3 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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