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Sample GSM838021 Query DataSets for GSM838021
Status Public on Dec 01, 2013
Title Ubiq_DMSO_rep1
Sample type SRA
Source name 3T3-L1 cells (ATCC #CL-173)
Organism Mus musculus
Characteristics epitope: 3FLAG
treatment: DMSO
antibody: M2 (Sigma Aldrich)
molecule: 3FLAG-ubiquitin
Treatment protocol Treatment was performed with 25 microM lactacystin or 0.1% DMSO (mock) for three hours.
Growth protocol 3T3-L1 cells were obtained by ATCC and cultured at undifferentiated state (as fibroblasts) following standard recommendations. 15 Mio cells were processed for an average ChIP-seq run.
Extracted molecule genomic DNA
Extraction protocol After fixation in PBS/1% para-Formaldehyde (37ÂșC, 10 min), nuclei were isolated by lysis in Triton-X100 buffer and sonicated to ca. 200 bp length. DNA was co-immunoprecipitated with the respective antibodies over night.
Libraries were prepared according to Illumina's instructions (New England Biolabs, Cat. No. E6200). 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 (32 to 52 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 was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Steady state ubiquitin
Data processing Alignment: Sequence reads were obtained and mapped to the mouse mm9 genome using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (, version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: The bigwigs were created with the following steps: Reads were aligned to the reference genome using bowtie with at most 2 mismatches. The SAM file with those alignments was converted to BAM format and then sorted using samtools, and then the sorted alignments were converted to wig format using a custom python script. Finally, the wigs were converted to bigWigs using wigToBigWig (which can be downloaded from
Submission date Nov 21, 2011
Last update date May 15, 2019
Contact name Andre Catic
Organization name Baylor College of Medicine
Street address One Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platform ID GPL13112
Series (1)
GSE33821 A functional map of DNA-associated proteolysis
SRA SRX110450
BioSample SAMN00761836
Named Annotation GSM838021_Ubiq_DMSO_rep1.bigwig

Supplementary file Size Download File type/resource
GSM838021_Ubiq_DMSO_rep1.bigwig 4.6 Gb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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