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| Status |
Public on May 17, 2017 |
| Title |
GB0883_H2A-rep2 |
| Sample type |
SRA |
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| Source name |
NIH/3T3 tet-on 3G cells_expressing GFPN-H2A
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| Organism |
Mus musculus |
| Characteristics |
cell line origin: 3T3
cell line: NIH/3T3 tet-on 3G cells
genotype/variation: expressing GFPN-H2A
facs population: GFP-positive cells
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| 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
bPPI-seq
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| 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
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| Submission date |
May 16, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Keji Zhao |
| E-mail(s) |
zhaok@nhlbi.nih.gov
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| Organization name |
national Institute of Health
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| Department |
National Heart, Lung, and Blood Institute
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| Street address |
Building 10 Room 7B06A
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE80425 |
Genome-wide identification of H2A.Z-interacting proteins by bPPI-seq |
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| Relations |
| BioSample |
SAMN07126200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2628250_GB0883_h2a_rep2_wo_last_exon_2.bed.gz |
23.9 Mb |
(ftp)(http) |
BED |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
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