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| Status |
Public on Dec 30, 2010 |
| Title |
TBP_ChIPSeq |
| Sample type |
SRA |
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| Source name |
whole embryo
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| Organism |
Xenopus tropicalis |
| Characteristics |
development stage: 12
antibody: SL33 against TBP
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| Growth protocol |
Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 3% cysteine and collected at Nieuwkoop-Faber stage 12
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin (400 embryos) was fixed in 1% formaldehyde, sheared using a Branson sonifier, immunoprecipitated using 2 µl of antibody (SL33 against TBP, Ruppert et al. 1996,PMID: 9064287), washed, decrosslinked, DNA was purified and sequenced using a Illumina Genome Analyzer according to the manufacturer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin IP against TBP
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| Data processing |
Reads were mapped to the X.tropicalis genome (version JGI4.1) with ELAND, reads in identical positions were removed and peaks were called using MACS with p-value 1e-7
The included bed-files contain xenTro2/JGI4.1 coordinates. These tab-delimited files contain up to 6 columns according to the BED specification.
1) chromosome
2) start
3) end
4) score (see description below)
5) not used
6) strand
The file TBP.bed contains the coordinates of the filtered unique 35-basepair reads, mapped strand-specific to the xenTro2 genome.
The TBP_peaks.bed file contain the peaks as determined by MACS using a p-value threshold of 1e-7. The score column contains the number of reads in the peak as determined by MACS.
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| Submission date |
Apr 22, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
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| Phone |
+31 24 3610541
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| Organization name |
Radboud University
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| Department |
Molecular Developmental Biology
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| Street address |
Geert Grooteplein 28
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| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
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| Platform ID |
GPL9405 |
| Series (1) |
| GSE21482 |
Nucleotide composition-linked divergence of vertebrate core promoter architecture |
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| Relations |
| SRA |
SRX019583 |
| BioSample |
SAMN00011915 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM537039_TBP.bed.gz |
68.9 Mb |
(ftp)(http) |
BED |
| GSM537039_TBP_peak.bed.gz |
60.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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