NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2065410 Query DataSets for GSM2065410
Status Public on Jun 18, 2017
Title IMR90 senescent 2
Sample type genomic
 
Channel 1
Source name nucleolus-associated DNA
Organism Homo sapiens
Characteristics sample type: isolated, non amplified, nucleolar DNA
cell line: IMR90
Treatment protocol Nucleolus-associated DNA was isolated as discribed below
Growth protocol 5% CO2, 37°C, 10% FCS, DMEM, 1g/L Glucose
Extracted molecule genomic DNA
Extraction protocol 1x10^8 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. After washing cells 2 times with ice-cold PBS they were scraped off and pooled in 100 mL 1xPBS and centrifuged (750 g, 5 min, 4°C). Supernatant was discarded or used for DNA precipitation and cells were resuspended in 1 mL HMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 12 mM MgCl2, 1 mM TCEP, PI). Cells were sonicated on ice for 3x10 sec with fine tip (Branson sonifier, 65% output, 70% duty cycle). After centrifugation (15000 g, 30 sec) the supernatant was set aside for DNA precipitation or discarded. The pellet was resuspended in 1 mL LMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 1 mM MgCl2, 1 mM TCEP, PI), sonicated on ice for 2x10 sec (as before) and centrifuged (15000 g, 2 min). Supernatant was set aside for DNA precipitation and the pellet was resuspended in 200 µL 20 mM Tris pH 8.1. RNA was digested by adding 3 µL of RNAse A (10 mg/mL) and incubation for 1 h at 37°C. Proteins were deigested by adding 5 µL Proteinase K and incubation for 8 h at 37°C and the cross-link was reversed for 8 h at 65°C. Finally DNA was precipitated.
Label Cy3
Label protocol 2µg of DNA was submitted to Nimblegen and processed there. Nucleolus-associated DNA was labelled with Cy3 and the control DNA with Cy5.
 
Channel 2
Source name genomic DNA
Organism Homo sapiens
Characteristics sample type: genomic DNA
cell line: IMR90
Treatment protocol Genomic DNA was isolated with standard protocols from proliferating IMR90 cells.
Extracted molecule genomic DNA
Extraction protocol 1x10^8 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. After washing cells 2 times with ice-cold PBS they were scraped off and pooled in 100 mL 1xPBS and centrifuged (750 g, 5 min, 4°C). Supernatant was discarded or used for DNA precipitation and cells were resuspended in 1 mL HMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 12 mM MgCl2, 1 mM TCEP, PI). Cells were sonicated on ice for 3x10 sec with fine tip (Branson sonifier, 65% output, 70% duty cycle). After centrifugation (15000 g, 30 sec) the supernatant was set aside for DNA precipitation or discarded. The pellet was resuspended in 1 mL LMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 1 mM MgCl2, 1 mM TCEP, PI), sonicated on ice for 2x10 sec (as before) and centrifuged (15000 g, 2 min). Supernatant was set aside for DNA precipitation and the pellet was resuspended in 200 µL 20 mM Tris pH 8.1. RNA was digested by adding 3 µL of RNAse A (10 mg/mL) and incubation for 1 h at 37°C. Proteins were deigested by adding 5 µL Proteinase K and incubation for 8 h at 37°C and the cross-link was reversed for 8 h at 65°C. Finally DNA was precipitated.
Label Cy5
Label protocol 2µg of DNA was submitted to Nimblegen and processed there. Nucleolus-associated DNA was labelled with Cy3 and the control DNA with Cy5.
 
 
Hybridization protocol Hybridization was performed at Nimblegen due to their protocols.
Scan protocol Scanning was perfomred at Nimblegen due to their protocols.
Description Nucleolus-associated DNA from senescent IMR90 cells was labelled with Cy3 and hybridized against genomic DNA labelled with Cy5 on NimbleGen Human CGH 4.2M Whole-Genome Tiling Array v1.0 arrays.
Data processing Data were preprocessed at Nimblegen, due to their protocols.
 
Submission date Feb 17, 2016
Last update date Jun 18, 2017
Contact name Stefan Dillinger
E-mail(s) stefan.dillinger@ur.de
Organization name University Regensburg
Street address Universitätsstr. 31
City Regensburg
ZIP/Postal code 93051
Country Germany
 
Platform ID GPL15746
Series (1)
GSE78043 Mapping of nucleolus-associated chromosomal domains during replicative senescence.

Data table header descriptions
ID_REF
VALUE scaled, log2 (Nucleolus-associated/genomic) ratio

Data table
ID_REF VALUE
CHR10FS064161750 -0.257
CHR10FS004720970 0.097
CHR10FS113188736 0.357
CHR10FS122624666 0.015
CHR10FS108377382 0.413
CHR10FS132679612 0.302
CHR10FS065046330 -0.170
CHR10FS068540792 0.101
CHR10FS063078649 -0.477
CHR10FS100129665 -0.385
CHR10FS068500675 0.102
CHR10FS017492721 -0.452
CHR10FS024205096 0.238
CHR10FS092464006 0.198
CHR10FS130961947 0.381
CHR10FS050901581 -0.155
CHR10FS112087279 -0.943
CHR10FS081238934 -0.217
CHR10FS131954696 0.045
CHR10FS108788266 0.622

Total number of rows: 4200002

Table truncated, full table size 95972 Kbytes.




Supplementary file Size Download File type/resource
GSM2065410_IMR90_senescent_02.txt.gz 171.6 Mb (ftp)(http) TXT
GSM2065410_IMR90_senescent_genomic_02.pair.gz 80.2 Mb (ftp)(http) PAIR
GSM2065410_IMR90_senescent_no_ass_02.pair.gz 80.8 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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