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Sample GSM1216744 Query DataSets for GSM1216744
Status Public on Nov 26, 2013
Title FAIRE_DL23_nt
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
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 library strategy: FAIRE-seq
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.
FAIRE sample was generated from 10x106 DLD1-F3 cells as described in detail (Simon et al., 2012). Briefly, cells were crosslinked in 1% formaldehyde (for 5 minutes at room temperature), lysed, collected in buffer with protease inhibitors (Roche) and dounced with a tight pestle. Nuclei were collected through centrifugation, lysed and DNA was sheared using Biorupter Sonicator. FAIRE DNA was obtained through phenol/chloroform/isoamyl alcohol and chloroform/isoamyl (SIGMA) extraction. DNA was treated with DNase-free RNase and proteinase K (Ambion), decrosslinked overnight at 65C and purified with Qiaquick PCR purification kit (Qiagen).
Library strategy OTHER
Library source genomic
Library selection other
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
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.
BioSample SAMN02335196
SRA SRX340065

Supplementary file Size Download File type/resource
GSM1216744_FAIREDL23nt.bed.gz 77.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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