|
| Status |
Public on Sep 27, 2013 |
| Title |
Input_DNA_G18 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MD-231, input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MD-231
chip antibody: none
|
| Growth protocol |
MDA-MD-231 cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (PAA) and penicillin/streptomycin (PAA). Neuronal progenitor cells (NPCs) were isolated from mouse brain at E13.5 and expanded in cell culture as neurospheres.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using chloroform/phenol extraction.
Libraries were constructed following manufacturer's instructions (NEB Next ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequnecing quality was checked with the FastQC script.
Reads were aligned to the genome (mm9 (NPC), hg19 (MDA-MD-231)) with BOWTIE v0.12.7.
Peak calling was performed with MACS v1.4.2 using default parameters but a p value of 1e-10 and input samples as control files.
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS14 output bed file (contains peak localisation).
|
| |
|
| Submission date |
Jul 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
|
| Department |
Chair for Biochemistry and Molecular Biology
|
| Lab |
Martin Eilers
|
| Street address |
Am Hubland
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE48602 |
Miz1 is required to maintain autophagic flux |
|
| Relations |
| BioSample |
SAMN02228435 |
| SRA |
SRX318859 |
