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Status |
Public on Apr 03, 2013 |
Title |
Empty_ChIP-seq |
Sample type |
SRA |
|
|
Source name |
HEK293T_Empty_ChIP-seq
|
Organism |
Homo sapiens |
Characteristics |
cell line: HEK293T transfection: empty vector 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.
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|
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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)
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|
|
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 |
SRX210720 |
BioSample |
SAMN01831454 |