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Status |
Public on Mar 12, 2014 |
Title |
TT_input |
Sample type |
SRA |
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Source name |
TT_input
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Organism |
Homo sapiens |
Characteristics |
cell lines: TT antibody: none
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Growth protocol |
RPMI1640 +10% FBS
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Extracted molecule |
genomic DNA |
Extraction protocol |
Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified and subjected to standard Illumina library construction.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
Input
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Data processing |
Bowtie alignment read counts normalization in 100kb window size Peak calling (MACS 1.4.1) Genome_build: hg18 Supplementary_files_format_and_content: MACS_peak files
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Submission date |
May 10, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Shouyong Peng |
E-mail(s) |
shouyongpeng@gmail.com
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Organization name |
Dana-Farber Cancer Institute
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Department |
Medical Oncology
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Lab |
Bass
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Street address |
450 Brookline Avenue
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02215 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE46837 |
SOX2 and p63 occupancy in human squamous carcinoma cell lines and embryonic stem cells. |
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Relations |
BioSample |
SAMN02142033 |
SRA |
SRX277133 |
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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