|
| Status |
Public on Nov 08, 2016 |
| Title |
400nM_2_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
H1-hESCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1-hESCs
treatment: 2 (O=C(CCCOC1=C2C(C=CO2)=CC3=C1OC(C=C3)=O)NCCOCCOCC(N[C@@H](CCCCNC(CCCC[C@@H]4[C@]5([H])[C@](NC(N5)=O)([H])CS4)=O)C(NCCOCCOCC(NCCC[N+](C)([H])CCCNC(CCNC(C6=CC(NC(C7=CC(NC(C8=NC(NC(C9=CC(NC(CCCNC(C%10=NC(NC(C%11=CC(NC(C%12=CC(NC(C%13=C(Cl)C=CS%13)=O)=CN%12C)=O)=CN%11C)=O)=CN%10C)=O)=O)=CN9C)=O)=CN8C)=O)=CN7C)=O)=CN6C)=O)=O)=O)=O)=O)
treatment_length: 24 h
|
| Treatment protocol |
H1-hESCs were treated with molecule for 24 h.
|
| Growth protocol |
E8 with Matrigel-coated plates
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed again with PBS, and isolated with Accutase per manufacturer’s directions. COSMIC was performed as described previously (Erwin et al. Angew. Chem. Int. Ed. 2014, 53, 38, 10124).
Sequencing libraries for Input and AP DNA were labeled with a DNA barcode for multiplexing, and prepared for sequencing with the TruSeq ChIP Sample Prep Kit (Illumina, Inc., San Diego, CA) per manufacturer’s directions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: COSMIC-seq
Base pairs were called with Casava v.1.8.2 (Illumina).
Reads were de-multiplexed with the barcode to yield only the 51 bp genomic fragment. Reads were filtered and trimmed to eliminate low-quality reads and adapter sequences, and mapped to the human genome (hg19) with Bowtie v 1.0 (best -m 1) to yield unique alignments.
HOMER (http://biowhat.ucsd.edu/homer/) was used to produce a signal track. The tag density for each factor was normalized to 10^7 tags and Input DNA. Peaks were called with SPP v 1.10.1 with the default parameters of the IDR methodology according to ENCODE guidelines (Landt et al Genome Res. 2012, 22, 1813).
Genome_build: hg19
Supplementary_files_format_and_content: *.bed files contain the COSMIC-seq peak locations. *.bedgraph files contain signal tracks.
|
| |
|
| Submission date |
Sep 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aseem Ansari |
| Organization name |
University of Wisconsin-Madison
|
| Department |
Biochemistry and The Genome Center
|
| Lab |
Ansari
|
| Street address |
440 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE70267 |
COSMIC-seq of bioactive N-methylpyrrole/N-methylimidazole polyamides |
|
| Relations |
| BioSample |
SAMN05829388 |
| SRA |
SRX2192509 |
