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| Status |
Public on Mar 12, 2014 |
| Title |
TT_SOX2_AF2018 |
| Sample type |
SRA |
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| Source name |
TT_SOX2_AF2018
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| Organism |
Homo sapiens |
| Characteristics |
cell lines: TT
antibody: SOX2
antibody vendor: R&D (AF2018)
antibody lot#: KOY0112011
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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 |
IP
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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 |
SAMN02142034 |
| SRA |
SRX277134 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1139035_TT_AF2018_summits.bed.gz |
151.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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