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| Status |
Public on Jul 26, 2015 |
| Title |
CCA1_ChIPSeq_Input |
| Sample type |
SRA |
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| Source name |
Arabidopsis thaliana seedlings, WS-2 ecotype
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: WS-2
harvest time: ZT2
light regime: Comstant Light after entrainment in 12h:12h Light: Dark
plant tissue: whole seedlings
plant stage: 14 day old seedlings
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| Growth protocol |
Plants were grown on MS media plus agar on plates in 12h:12h light:dark cycles. 14d old whole seedlings were harvested.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Plants were harvested, fixed via vacuum infiltration with 1% formaldehyde fir 20 minutes. The reaction was stopped with 0.125 M glycine. Nuclei were isolated, lysed, and sonicated. Chromatin was immunoprecipitated with anti-GFP or IgG (mock control & input).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Input DNA
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| Data processing |
BaseCalls Using Illumina CASAVA 1.8
Adaptor removal using TagDust v1.12
Adaptor removal using Trimmomatic v0.33
Duplicate removal using PRINSEQ v 0.20.4
Data were aligned to genome using Bowtie 2.2.1 selecting the best mapped read using MAPQ
Tag Directories were made using HOMER v4.7, peaks were called using HOMER v4.7 and the parameters findPeaks LL1 -P .1 -LP .1 -poisson .1 -fragLength 100 -style factor -i Input
Peaks were annotated using HOMER v4.7 and assignment to nearest TSS or using GenomicRanges and assignment to all TSS within 1kb of peak
Genome_build: TAIR10
Supplementary_files_format_and_content: Peaks file- .peaks.txt tab-delimited Top peaks passing IDR threshold, peakID, Chromosome, start,stop, strand (N/A), Normalized Tag counts, Focus ratio, PeakScore, Control Tag counts, Fold change vs Control, p-value vs control, Fold Change vs Local, p-value vs Local , Clonal Fold change
Supplementary_files_format_and_content: UCSCbedFiles- ucsc.bedGraph.gz Normalized read counts in UCSC friendly bed format
Supplementary_files_format_and_content: Annotated Peaks- .txt tab-delimited Top peaks annotated to nearest TSS in TAIR: peakID, Chromosome, start,stop, strand (N/A), Peak score, Focus ratio, Annotation, Distance to TSS, Nearest Promoter Udm Ebtrez ID, Nearest Unigene ID, Nearest Refseq, Gene Name, Gene Alias, Gene Description, Gene Type, CpG%, GC%
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| Submission date |
Jul 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Colleen J Doherty |
| E-mail(s) |
colleen_doherty@ncsu.edu
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| Organization name |
North Carolina State University
|
| Department |
Biochemistry
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| Lab |
Colleen Doherty
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| Street address |
128 Polk Hall CB7622
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| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695-7622 |
| Country |
USA |
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| Platform ID |
GPL9302 |
| Series (1) |
| GSE70533 |
Genome-wide Identification of CCA1 Targets Uncovers an Expanded Clock Network in Arabidopsis |
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| Relations |
| BioSample |
SAMN03840357 |
| SRA |
SRX1081595 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1808455_Input.ucsc.bedGraph.gz |
64.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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