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Sample GSM1216739 Query DataSets for GSM1216739
Status Public on Nov 26, 2013
Title CHIP_DL23_nt_H3
Sample type SRA
 
Source name DL23 cell line with pcDNA3-HA-FOXO33-ER
Organism Homo sapiens
Characteristics cell line: DL23 cell line with pcDNA3-HA-FOXO33-ER
chip antibody: H3
chip antibody vendor: Abcam
chip antibody cat. #: ab1791
Growth protocol DLD1 and DLD1-F3 cells were grown on RPMI-1640 medium with 10% FCS and standard supplements
Extracted molecule genomic DNA
Extraction protocol Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD sequencer to produce 50-bp long reads.
4-hydroxy-tamoxifen (4OHT) from Sigma, was dissolved in ethanol and added to cells at a final concentration of 1uM. Cells were treated with PKB inhibitor VIII (Santa Cruz) at a concentration of 10uM. Cells were grown in the absence or 4 hour presence of 4OHT or PKB inhibitor. Three independent batches of chromatin were obtained for all three conditions and mixed, with a total of 80x106 cells per IP. IPs were performed for 16h with the following antibodies: 2.5 ug of H3K4me1, H3K4me3 and H3K27ac and total H3 from Abcam (ab8895, ab8580 and ab4729, ab1791) and 16ug of ╬▒FOXO3 (Santa Cruz, H144) for the FOXO3-ER (2) ChIP-seq. The second H3K27ac(2) ChIP-seq was performed on an independent fourth batch of chromatin.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB 5500xl Genetic Analyzer
 
Data processing Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin, 2009). Non-uniquely placed reads were discarded.
Cisgenome v2.0 software package was used to calculate reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated genes.
Genome_build: hg19
Supplementary_files_format_and_content: alignment file (chr;start;end;strand)
 
Submission date Aug 27, 2013
Last update date May 15, 2019
Contact name Michal Mokry
E-mail(s) m.mokry@umcutrecht.nl
Organization name Wilhelmina Children's Hospital, University Medical Center Utrecht
Street address Lundlaan 6
City Utrecht
ZIP/Postal code 3584 EA
Country Netherlands
 
Platform ID GPL16288
Series (1)
GSE50243 FOXO3 selectively amplifies enhancer activity to establish target gene regulation.
Relations
BioSample SAMN02335209
SRA SRX340060

Supplementary file Size Download File type/resource
GSM1216739_CHIPDL23ntH3.bed.gz 88.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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