|
| Status |
Public on Sep 25, 2013 |
| Title |
batch5_chrom2_LoVo_PCF11_Goat_PassedQC |
| Sample type |
SRA |
| |
|
| Source name |
LoVo
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LoVo
cell type: colon adenocarcinoma
hgn: PCF11
antibody: Santa Cruz Biotechnology, Inc. : sc-161998
control sample: batch5_chrom2_LoVo_IgG_Goat
qc successful: PassedQC
number of peaks, fdr < 5%: 823
fraction of peaks close to tss: 0.381531
lowest e-value for a high complexity de novo motif: 1.1e-10
|
| Growth protocol |
LoVo (ATCC CCL-229) colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed according to Illuminas standard protocol. The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane. Sequencing was performed using one lane of Illumina GAIIx, or alternatively, samples were indexed with DNA barcodes and four to six different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-seq that passed automated QC; > 300 peaks, located close to TSS and/or enriched in high complexity motif(s)
|
| Data processing |
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_PCF11_PassedQC_peaks.txt: hg18
|
| |
|
| Submission date |
Sep 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Enge |
| E-mail(s) |
martin.enge@ki.se
|
| Organization name |
Karolinska Institute
|
| Department |
Dep of Oncology-Pathology
|
| Street address |
CCK, Z4
|
| City |
Stockholm |
| ZIP/Postal code |
S-171 76 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE51142 |
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites [Validation Set] |
|
| Relations |
| BioSample |
SAMN02363708 |
| SRA |
SRX360032 |
