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Sample GSM959630 Query DataSets for GSM959630
Status Public on Sep 05, 2012
Title LS180_MED1_125
Sample type SRA
Source name LS180_MED1_125
Organism Homo sapiens
Characteristics cell line: LS180 cells
passage number: 12-24
cell type: cultured CRC cells
antibody: MED1 (Santa Cruz, M-255, sc-8998)
Treatment protocol Cells were treated with 10-7M 1,25(OH)2D3 [125] or with ethanol vehicle [Veh] for 3 hours prior to ChIP assay
Growth protocol Cells were grown in normal MEM-alpha with 10% standard FBS serum, 1% Non-essential Amino Acids, 1% Sodium Pyruvate and 1% Penicillin-Streptomycin
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation was performed by treating LS180 cells for 3 hrs with vehicle or 10-7M 1,25(OH)2D3 as was optimized as previously reported. ChIP samples were created from 100 million cells per sample. The treated cells were washed several times with PBS and then subjected to a 15 minute cross-linking reaction with 1.5% formaldehyde. After the cross-linking reaction, isolated cell extracts were sonicated to prepare chromatin fragments (average DNA size of 500-600 bp DNA as assessed by agarose gel electrophoresis) using a Fisher Model 100 Sonic Dismembranator at a power setting of 2. Pre-cleared samples were subjected to immunoprecipitation using either a control IgG antibody or the indicated experimental antibody. The precipitated DNA was then washed, the cross-links reversed and the DNA fragments purified using Qiagen QIAquick PCR Purification Kits (Valencia, CA). The isolated DNA (or DNA acquired prior to precipitation (input)) was then subjected to quantitative real time PCR (qPCR) and further preparation for ChIP-chip or ChIP-seq analysis. ChIP-DNA was prepared and amplified using the Illumina ChIP-seq DNA preparation kit (1003473, #11257047 RevA), clusters formed and sequenced on the Illumina GAIIx sequencers by the University of Wisconsin - Madison DNA Sequencing Facility in the University of Wisconsin- Madison Biotechnology Center. DNA clusters were generated using either a Standard Cluster Generation kit (ver. 4) on an Illumina cluster station (Illumina, San Diego, CA), [for all samples sequenced before April, 2010] or using a cBot Single Read Cluster Generation kit on an Illumina cBot (Illumina) [after April, 2010] according to the manufacturer's instructions, to obtain an average of 2.0×107 clusters for each lane on a flowcell. All sequencing runs for 36mers were performed on an Illumina Genome Analyzer IIx using the Illumina Sequencing kit (ver. 4).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description ChIP-DNA
Data processing ChIP-seq runs were all 36bp. All samples were mapped from fastq files using Bowtie [-m 1 -- best] to hg18 [UCSC human genome build 18]. Replicate lanes were validated separately for reproducibility and then combined for greater read depth.
Peaks were called by using HOMER [] and QuEST [].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding with the following exception: clonal filter = 5.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: hg18
Supplementary_files_format_and_content: Bowtie files are the bowtie aligned files, bedGraph files are for display in the UCSC genome browser and the peaks.bed files are the resulting peaks found with QuEST and HOMER
Submission date Jul 11, 2012
Last update date May 15, 2019
Contact name Mark B Meyer
Phone 608-890-0857
Organization name University of Wisconsin-Madison
Department Nutritional Sciences
Lab Meyer Lab
Street address 1415 Linden Dr.
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
Platform ID GPL10999
Series (1)
GSE39277 Corepressors (NCoR and SMRT) as well as Coactivators are Recruited to Positively Regulated 1α,25-Dihydroxyvitamin D3-Responsive Genes
SRA SRX159191
BioSample SAMN01087383

Supplementary file Size Download File type/resource
GSM959630_LS180_MED1_125.bedGraph.gz 47.7 Mb (ftp)(http) BEDGRAPH
GSM959630_LS180_MED1_125.bowtie.txt.gz 1.0 Gb (ftp)(http) TXT
GSM959630_LS180_MED1_125_peaks.bed.gz 25.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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