|
| Status |
Public on Dec 04, 2014 |
| Title |
dnTCF1Emut 0hrs |
| Sample type |
SRA |
| |
|
| Source name |
DLD1 colon cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1 colon cancer cells
genotype/variation: dnTCF1Emut
time (induction): 0hrs
chip antibody: Anti-FLAG Beads Sigma (A2220)
|
| Treatment protocol |
Used 1ug/mL Doxycycline for dnTCF1E induction
|
| Growth protocol |
Grew cells in RPMI complete with doxycycline free FBS. Cells were grown in RPMI complete with 10ug/mL blasticidin and 300ug/mL zeocin for 24 hours before induction
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Used anti-FLAG conjugated magnetic beads from Sigma (A2220) to immunoprecipitate FLAG-tagged dnTCF1EWT and FLAG-tagged dnTCF1Emut
All libraries were prepared using the NEXTflex ChIP Seq kit from Biooscientific using 10ng as starting material
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
0hrs (no doxycycline - no dnTCF1Emut overexpressed) ChIP-seq from dnTCF1Emut cell line. First replicate
dnTCF1Emut 0hrs (a)
dnTCF1Emut 0hrs (b)
|
| Data processing |
Demultiplexing and basecalls performed using CASAVA v1.8.2
Biological replicates FASTQ files pooled
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 v2.0.0 allowing up to 3 mismatches
Peaks were called using MACS v1.3 using only one unique read per genome position and a default peak score cutoff of 50
Genome_build: hg19
Supplementary_files_format_and_content: Peak files annotated using HOMER v3.16 and wiggle files generated using MACS v1.3
|
| |
|
| Submission date |
Dec 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Zeller |
| E-mail(s) |
zellerm@uci.edu
|
| Organization name |
University of California, Irvine
|
| Department |
Computer Science
|
| Lab |
Pierre Baldi
|
| Street address |
241 ICS 2
|
| City |
Irvine |
| State/province |
California |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE53536 |
DNA binding activities of the C-clamp |
|
| Relations |
| BioSample |
SAMN02483535 |
| SRA |
SRX396838 |
| Named Annotation |
GSM1295634_MUT_0_peaks.bed.gz |
| Named Annotation |
GSM1295634_MUT_0_treat_afterfiting.wig.gz |
