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| Status |
Public on Feb 19, 2019 |
| Title |
BB608-STAT3 |
| Sample type |
SRA |
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| Source name |
FaDu Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HNSCC cell line FaDu
treatment: BB608
chip antibody: STAT3 (Santa Cruz sc-482)
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| Treatment protocol |
FaDu cells were treated with DMSO or 1 uM BB608 for 2 hours. 15 min prior to harvest, cells were stimulated with 20 ng/ml OSM for the STAT3 ChIP samples, or with 20 ng/ml IFN-gamma for the STAT1 samples.
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| Growth protocol |
FaDu cells were maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum and 1% pennicillyn/streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-IT® ChIP-Seq Kit (Active Motif) was used for chromatin preparation and ChIP using antibodies for STAT1 (Santa Cruz sc-345) or STAT3 (Santa Cruz sc-482).
ChIP-IT® ChIP-Seq Kit (Active Motif) was used for library construction.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
STAT3 Analysis.txt
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| Data processing |
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis
Intervals (Peaks) were determined using the MACS peak finding algorithm (see Zhang et al., Genome Biology 2008, 9:R137). Using our default cutoff of p-value = 1e-7,
the tag number of all samples is reduced (by random sampling) to the number of tags present in the smallest sample.
Genome_build: hg19
Supplementary_files_format_and_content: STAT1 Analysis.txt, STAT3 Analysis.txt
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| Submission date |
Feb 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Harry Rogoff |
| Organization name |
Boston Biomedical, Inc.
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| Street address |
640 Memorial Dr.
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE78212 |
Effect of BB608 on STAT3 DNA Binding in HNSCC Cell Line |
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| Relations |
| BioSample |
SAMN04510486 |
| SRA |
SRX1597600 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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