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Sample GSM2127103 Query DataSets for GSM2127103
Status Public on Apr 20, 2016
Title ChIP-seq mouse 3T3 shOSR1 OSR1(1)
Sample type SRA
 
Source name NIH/3T3 tet-on 3G cells
Organism Mus musculus
Characteristics protocol: shRNA (Osr1 knockdown)
Extracted molecule genomic DNA
Extraction protocol [ChIP-seq SELEX] 300ng of the resultant library mouse genomic DNA was run again with the new empty sepharose beads and GST-Osr1 beads, and the process was repeated four times.Eluted DNA was purified by MinElute Reaction Cleanup Kit (Qiagen). The DNA ends were repaired and generated a protruding 3’ A as described above. Following ligation of a pair of Solexa adaptors to the repaired ends, 150 to 400bp fragments were recovered from agarose gel. Then DNA was amplified using the index primers for 18 cycles and the 150-400bp fragments were isolated from agarose gel again.
[ChIP-seq SELEX] The libraries enriched at rounds two, three, and four were sequenced using Illumina high throughput sequencing
[RNA-seq] For mRNA-seq library prep: a random primer (invitrogen cat# 48190-011) was used to prime the purified PolyA tailed-RNA and the cDNA synthesis was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen cat# 11917-010) according to the users manual. The ds cDNA was subject to sonication in Diagenode's Bioruptor (level M, total of 30 minutes of 20 seconds ON and 20 seconds OFF) to a size range of 100-400bp. Indexed library was prepared using Illumina's multiplexing sample prep oligonucleotide kit (Ref# 1005709) with Epicentre's End-It DNA End-repair Kit (Epcentre, cat# ER81050) according to the user's manual and Illumina's multiplexing sample preparation guide.
[RNA-seq] The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10”; 68°C, 30”; 72°C, 30” for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq2000.
[bPPI-seq] Total RNAs of sorted cells were extracted using QIAzol (Qiagen) and purified with miRNeasy micro kit (Qiagen) and DNase set (Qiagen). Purified RNAs were reverse transcribed using PrimeScript Reverse Transcriptase (Takara) with an oligo dT primer. The cDNAs were amplified by VNC-specific and T7 primers and fragmented to 200 to 500bp by sonication. The DNA ends were repaired using End-It DNA End-repair Kit (Epicentre), followed by treatment with Klenow Fragment exo- (New England Biolabs) to generate a protruding 3’A base used for adaptor ligation. Following ligation of a pair of top-Phops-oligo-17bp/T7MmeI-18bp adaptors, the fragments between 250-650bp were isolated from agarose gel. Then the DNA was amplified by MmeI-SD1/2/3 and T7 primers to add an MmeI recognition site at both ends, followed by digestion with MmeI (New England Biolabs).
[bPPI-seq] After treatment with Klenow Enzyme (New England Biolabs), indexed libraries were prepared with a Multiplexing Sample Preparation Oligonucleotide Kit (Illumina) according to the user's manual. The fragments between 250-500bp were isolated for sequencing on an Illumina next generation sequencing platform.
[ChIP-seq] Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
[ChIP-seq] Libraries were prepared according to Illumina's instructions. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3′ A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. Libraries were sequenced on the Hi-seq following the manufacturer's protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description 3T3 shRNA (Osr1 knockdown), Osr1ChIP antibody (Santa Cruz, catalog# sc68392)
GA8172
Data processing [ChIP-seq] Basecalls performed using RTA 1.7 or Illumina Casava1.7
[ChIP-seq] ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed for further analysis in each library.
[ChIP-seq] We identified Enriched-ChIP iregions using MACS.
[RNA-seq] Basecalls performed using RTA 1.7 or Illumina Casava1.7
[RNA-seq] RNA-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 for further analysis in each library.
[RNA-seq] We computed the rpkm value for each gene.
[bPPI-seq] Basecalls performed using RTA 1.7 or Illumina Casava1.7
[bPPI-seq] bPPI-seq reads were mapped to the mouse genome (mm9) using tophat, and the parameter multihits =15.
[bPPI-seq] We computed the rpkm value for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: [ChIP-seq] Bed: plain text file. Each line is a peak region. The six columns are chrom, start position, end position, peak name, and -10log10(p-value).
Supplementary_files_format_and_content: [RNA-seq] rpkm: plain text file. Each row is a gene.The three columns are gene, rpkm value, and readcount.
Supplementary_files_format_and_content: [bPPI-seq] rpkm: plain text file. First few rows include the information of the rpkm calculations. Then the four columns are gene, accession number, rpkm value, and readcount.
 
Submission date Apr 19, 2016
Last update date May 15, 2019
Contact name Keji Zhao
E-mail(s) zhaok@nhlbi.nih.gov
Organization name national Institute of Health
Department National Heart, Lung, and Blood Institute
Street address Building 10 Room 7B06A
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
 
Platform ID GPL13112
Series (1)
GSE80425 Genome-wide identification of H2A.Z-interacting proteins by bPPI-seq
Relations
BioSample SAMN04869770
SRA SRX1712808

Supplementary file Size Download File type/resource
GSM2127103_GA8172_shOsr1_Osr1_mm9_macs_w_input_peaks.bed.gz 24.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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