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| Status |
Public on Oct 19, 2016 |
| Title |
PolII ChIP-exo |
| Sample type |
SRA |
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| Source name |
K562
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Haematopoietic and lymphoid
histology: Haematopoietic neoplasm
protein-dna complex: PolII
protocol: ChIP-exo
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| Treatment protocol |
For PIP-seq, cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine
For ChIP-exo, cells were crosslinked with 1% formaldehyde for 15 min and quenched with 2.5M glycine
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| Growth protocol |
Cells were grown in DMEM under standard conditions
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-exo, lysates were clarified from sonicated nuclei and Protein(TFIIB, PolII)-DNA complexes were isolated with IgG antibody.
PIP-Seq libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pubmed/23746353
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
PSU57041
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| Data processing |
Basecalls performed using CASAVA version 1.7 for Illumina single reads, bcl2fastq ver 2.16 for NextSeq paired reads
PIP-seq and ChIP-exo reads were aligned to theCRch37(hg19) genome assembly using bwa version 0.6.2 for single reads, and bwa mem version 0.7.9a for paired reads
Genome_build: GRch37/hg19
Supplementary_files_format_and_content: BED format, TFIIB PIP-seq peaks are called using Genetrack and requiring simultaneous enrichment of TFIIB ChIP-exo and GRO-cap
Supplementary_files_format_and_content: BED graph format, PolII PIP-seq ('T' filtered), Input PIP-seq and ChIP-exo samples are converted into Genetrack scidx (Strand coordinated index) format, and Bedgraph files have been generated accordingly.
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| Submission date |
Jan 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bongsoo Park |
| E-mail(s) |
bxp12@psu.edu
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| Phone |
814-441-3861
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| Organization name |
Penn State University
|
| Street address |
453 North Frear Building
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE76955 |
Genome-wide uniformity of human “open” pre-initiation complexes |
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| Relations |
| BioSample |
SAMN04420778 |
| SRA |
SRX1534080 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2041448_57041hg19.bedgraph.gz |
46.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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