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Sample GSM2628252 Query DataSets for GSM2628252
Status Public on May 17, 2017
Title GB0888_H2AZ-rep2
Sample type SRA
 
Source name NIH/3T3 tet-on 3G cells_expressing GFPN-H2A.Z
Organism Mus musculus
Characteristics cell line origin: 3T3
cell line: NIH/3T3 tet-on 3G cells
genotype/variation: expressing GFPN-H2A.Z
facs population: GFP-positive cells
Extracted molecule total RNA
Extraction protocol 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).
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 idolated for sequencing on an Illumina next generation sequencing platform.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Description bPPI-seq
Data processing library strategy: bait Protein-Protein Interaction-sequencing (bPPI-seq)
Basecalls performed using RTA 1.7 or Illumina Casava1.7
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.
Filtered reads that are mapped in the last exons
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plan text file. Each line is a read. The six columns are chrom, start position, end position, fragment size, index, strand direction
 
Submission date May 16, 2017
Last update date Jan 23, 2018
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 GPL21493
Series (1)
GSE80425 Genome-wide identification of H2A.Z-interacting proteins by bPPI-seq
Relations
BioSample SAMN07126204

Supplementary file Size Download File type/resource
GSM2628252_GB0888_h2aZ_rep2_wo_last_exon_2.bed.gz 17.6 Mb (ftp)(http) BED
Raw data provided as supplementary file
Processed data provided as supplementary file

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