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Sample GSM1817673 Query DataSets for GSM1817673
Status Public on Jul 23, 2015
Title mRS_CTCF_ChIP-seq
Sample type SRA
 
Source name Mouse Round spermatids
Organism Mus musculus
Characteristics cell line: mRS
chip antibody: custom mouse monoclonal CTCF (characterized in PMID:15731119)
Treatment protocol For ChIP-seq 100 million of asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication.
Growth protocol K562, Delta47, Ovcar8, NHDF and MCF7 cell lines were grown in DMEM supplemented with 10% FCS and penicillin-streptomycin.
Extracted molecule genomic DNA
Extraction protocol After overnight incubation with DiaMag magnetic beads (Diagenode, Inc.) and CTCF or BORIS monoclonal or polyclonal antibodies (characterized and described by PMID:15731119; PMID: 21659515; PMID:20231363), precipitated chromatin was then washed, decrosslinked, and digested with proteinase K. The resulting DNA was purified using phenol/chloroform/isoamyl alcohol. DNA concentration was assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries.
TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Sequences generated by the Illumina genome analyzer (36bp and 50bp reads) were aligned against either human (build hg19) or mouse (build mm9) genome using Bowtie program (http://bowtie-bio.sourceforge.net). The alignment was performed with default parameters except the sequence tags that mapped to more than one location in the genome were excluded from the analysis using –m1 option.
Peaks were called using Model-based Analysis for ChIP-Seq (MACS) (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (part of MACS) to call sub-peaks, summit of peaks and improve peak resolution.
For the Illumina RNA-seq library, fastq.gz files were mapped to UCSC Human reference (build hg19) using TopHat2 with the default parameter setting of 20 alignments per read and up to 2 mismatches per alignment.
For Ion Torrent RNA-seq sequencing, fastq.gz files were mapped to UCSC Human reference (build hg19) using two-step alignments. First, the reads were aligned with TopHat2. Second, the unmapped reads from the first step are then extracted and aligned with Bowtie2 with –local mode and --very-sensitive-local option.
For both Illumina and Ion Torrent RNA-seq, the resulting aligned reads (BAM files) were then analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build hg19). The expression of each transcript was quantified as the number of reads mapping to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM).
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Narrow peak (bed) and wig files were generated by MACS
 
Submission date Jul 10, 2015
Last update date May 15, 2019
Contact name Elena Pugacheva
E-mail epugacheva@niaid.nih.gov
Organization name NIH
Department NIAID
Lab LIG
Street address Bldg.29B
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
 
Platform ID GPL13112
Series (1)
GSE70764 Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
Relations
BioSample SAMN03854459
SRA SRX1091832

Supplementary file Size Download File type/resource
GSM1817673_mRS_CTCF.wig.gz 442.6 Mb (ftp)(http) WIG
GSM1817673_mRS_CTCF_NarrowPeaks.bed.gz 316.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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