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Sample GSM1181983 Query DataSets for GSM1181983
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
BioSample SAMN02228435
SRA SRX318859

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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