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| Status |
Public on Jul 09, 2013 |
| Title |
NT2 input 2 |
| Sample type |
SRA |
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| Source name |
NT2 input 2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Ntera2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from NT2 cells and was either fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI (DRIP-seq 1) or BamHI, NcoI, ApaLI, NheI and PvuII (DRIP-seq 2). Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
Sequencing library was constructed using standard Illumina protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
gDNA digested with BamHI, NcoI, ApaLI, NheI and PvuII
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| Data processing |
Library strategy: DRIP-seq
Fastq reads were aligned to hg19 using BWA version 0.6.1
Peak calling was performed using MACS 1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated by MACS
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| Submission date |
Mar 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoong Wearn Lim |
| E-mail(s) |
ywlim@ucdavis.edu
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| Organization name |
University of California, Davis
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| Department |
Molecular and Cellular Biology
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| Lab |
Chedin
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| Street address |
One Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE45530 |
DNA-RNA Immunoprecipitation sequencing (DRIP-seq) of human NT2 cells |
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| Relations |
| SRA |
SRX255722 |
| BioSample |
SAMN01992771 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not applicable for this record |
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