GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM838662 Query DataSets for GSM838662
Status Public on May 21, 2013
Title INK4A/ARF -/- mNPC 1 BMI1
Sample type SRA
Source name INK4A/ARF -/- mNPC 1 BMI1
Organism Mus musculus
Characteristics cell type: Adult Neural Progenitor cells
genetic background: INK4a/Arf FVB
genotype: INK4A/ARF -/-
chip antibody: anti-BMI1
chip antibody manufacturers: Millipore, Abcam, Abnova
chip antibody catalog #'s: 05-1321, ab14389, H00000648-M02
chip antibody lot #'2: NG1681858, 859827, 08071-S1
Treatment protocol GBM1 were cultured in presence of Doxyclyne (48h), Arvanil (24h) and BMP7 (3h), only for the ATF3 ChIP-seq experiment.
Growth protocol Mouse cells were grown as in Bruggeman, 2007, human cells as in Pollard 2009
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina's instructions. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA, library fragments of ~230 bp (insert plus adaptor and PCR primer sequences) were selected from an agarose gel. The final size-selected lib. was amplified by 15 cycle of PCR followed by column purification of amplified DNA. The purified DNA was captured on an Illumina flow cell for cluster generation. ChIP was performed by cross-linking proteins to DNA using 2mM DSG and 1% formaldehyde solution (Gargiulo et al, 2009). Immunoprecipitated DNA (ChIP-seq) and Input DNA were Libraries were sequenced on the Genome Analyzer of HiSeeq2000 following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Alignment used BWA, and peak calling used MACS, and Clustering used
mm9 and hg19
Genome build: mm9
Submission date Nov 23, 2011
Last update date May 15, 2019
Contact name Gaetano Gargiulo
Organization name Max Delbrüch Center
Department Molecular Oncology
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
Platform ID GPL11002
Series (1)
GSE33912 Functional Identification of Critical Bmi1 target genes in Neural Progenitor and Malignant Glioma cells
SRA SRX109471
BioSample SAMN00760904

Supplementary file Size Download File type/resource
GSM838662_mNPCs_1_s6_first_chipseq.bam 349.6 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap