|
| Status |
Public on Apr 03, 2013 |
| Title |
Myc_Idax_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T_Myc_Idax_ChIP-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
transfection: wild-type Myc-Idax
antibody: Anti-c-Myc; Sigma, Cat#: A7470-1ML (Agarose Affinity Gel)
|
| Growth protocol |
Stable HEK293T cells were generated by transfecting empty vector, wild-type Myc-Idax or DNA-binding mutant of Myc-Idax (Myc-IdaxDBM).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated and chromatin was sheared using Covaris S2 instrument and protein-DNA complexes were isolated by antibody.
ChIP-seq library was constructed using TruSeq Sample Prep kit (Illumina) and Illumina HiSeq sequencing was performed as per manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using 'HiSeq Control Software' version 1.5.15.1
Sequencing reads were mapped against hg19 using bowti (bowtie-0.12.7 -n 2 -l 28 -m 3 -k 1 --best --chunkmbs 512 -p 8 -S -q)
Peaks were called using MACS (1.4.1) using default parameter settings for human (hs)
Enrichment profiles along selected annotations were calculated using custom scripts inside of the R/Bioconductor environment.
Genome_build: hg19
Supplementary_files_format_and_content: wiggle files were generated as follows: i) reads are extended to the length of estimated average fragment length. ii) coverage is calculated in the single nucleotide-level and its normalised by the number of million mapped reads (RPM)
|
| |
|
| Submission date |
Dec 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Lukas Chavez |
| E-mail(s) |
l.chavez@dkfz.de
|
| Organization name |
German Cancer Research Center (DKFZ)
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE42958 |
Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX |
|
| Relations |
| SRA |
SRX210718 |
| BioSample |
SAMN01831452 |
