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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 21, 2013 |
| Title |
hGBM 5 Input |
| Sample type |
SRA |
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| Source name |
hGBM 5 INPUT
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Glioblastoma Multiforme stem like
genotype: Multiple genetic aberrations
chip antibody: none
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| Treatment protocol |
GBM1 were cultured in presence of Doxyclyne (48h), Arvanil (24h) and BMP7 (3h), only for the ATF3 ChIP-seq experiment.
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| Growth protocol |
Mouse cells were grown as in Bruggeman, 2007, human cells as in Pollard 2009
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Alignment used BWA, and peak calling used MACS, and Clustering used http://bips.u-strasbg.fr
mm9 and hg19
Genome build: hg19
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| Submission date |
Nov 23, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Gaetano Gargiulo |
| E-mail(s) |
gaetano.gargiulo@mdc-berlin.de
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| Organization name |
Max Delbrüch Center
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| Department |
Molecular Oncology
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| Street address |
Robert-Rössle-Straße 10
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE33912 |
Functional Identification of Critical Bmi1 target genes in Neural Progenitor and Malignant Glioma cells |
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| Relations |
| SRA |
SRX109483 |
| BioSample |
SAMN00760916 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM838674_hGBM5_control_s7_second_chipseq.bam |
4.7 Gb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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