|
| Status |
Public on Jun 27, 2013 |
| Title |
FANCD2_IP_UV treated |
| Sample type |
SRA |
| |
|
| Source name |
FANCD2_IP_UV treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human cell lines (kidney, embryonic)
antibody: FANCD2
cell line: 293T
|
| Treatment protocol |
UV treatment (30J), harvest post 3hour after UV treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Briefly, we mapped the reads with Bowtie version 0.12.7 to hg19 using the parameters -n 1 (which restricts the number of missmatches allowed in the alignment seed region to 1) and -m 1 (which suppresses all alignments for a read if more than 1 alignment exists for that read in the genome).
For each report we generated we first use a program called "makeTagDirectory.pl" to prepare the read data for analysis by HOMER (e.g., it normalizes and provides basic QC).
Then we use a program called 'analyzeChIP-Seq.pl' in HOMER that automates the analysis by stringing the following functions (programs) together into a pipeline: Peak finding / Transcript detection / Feature identification (findPeaks)
Genome_build: mm9
Supplementary_files_format_and_content: HOMER Peaks Text files
|
| |
|
| Submission date |
May 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
eunmi Park |
| E-mail(s) |
eunmi_park@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
44 Binney street
|
| City |
BOSTON |
| State/province |
MA |
| ZIP/Postal code |
02210 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46902 |
FANCD2 Activates Transcription of TAp63 and Suppresses Tumorigenesis |
|
| Relations |
| SRA |
SRX277586 |
| BioSample |
SAMN02143979 |
