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Sample GSM1116509 Query DataSets for GSM1116509
Status Public on Apr 09, 2013
Title gSOC1 negative 3
Sample type SRA
 
Source name SOC1p:gSOC1;soc1-2 #9 apices
Organism Arabidopsis thaliana
Characteristics genotype/variation: SOC1p:gSOC1;soc1-2
Growth protocol 15 days SD + 3 days LD
Extracted molecule genomic DNA
Extraction protocol Material collection: ZT4. ChIP protocol using anti-GFP Ab (Abcam #ab290)
Libraries were prepared according to manufacture's instructions of the ChIP-seq sample prep kit from Illumina. 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 (3’ to 5’ 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 from 150-400 bp was band isolated from an agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Sample 5
Data processing Base calling: Illumina SCS/RTA version 2.8
Read filtering and trimming: SHORE import version 0.8 (shore.sf.net). Filtering parameters: “-n 10% -c -k 32”
Read mapping: SHORE mapflowcell version 0.8 (shore.sf.net) utilizing GenomeMapper version 0.4.4 (http://1001genomes.org/software/genomemapper.html). mapflowcell alignment parameters “-n 4 --select=10,11,12,13 --restrict=on”
Peak calling: SHORE peak version 0.8 (shore.sf.net). Peak calling on all 3 replicates using default peak calling parameters, TAIR10 genome annotation file provided via “-a”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak region list generated by SHORE peak (SOC1_SUMMARY.txt), see README.txt for format description.
 
Submission date Apr 08, 2013
Last update date Sep 04, 2019
Contact name Felix Ott
Organization name Max Planck Institute for Developmental Biology
Street address Spemannstr. 35-39
City Tuebingen
ZIP/Postal code 72076
Country Germany
 
Platform ID GPL11221
Series (1)
GSE45846 Characterization of SOC1’s central role in flowering by the identification of its upstream and downstream regulators
Relations
Reanalyzed by GSE136843
SRA SRX262131
BioSample SAMN02009206

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

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