NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1510113 Query DataSets for GSM1510113
Status Public on Sep 22, 2015
Title Ctrl_BM1
Sample type RNA
 
Source name Bone marrow HSCs
Organism Mus musculus
Characteristics tissue: bone marrow
treatment: control
cell type: CD150+CD48-Lin-kit+Sca1+ HSCs
age: 8-10 week
Treatment protocol HSCs from control mice or after 7 days of G-CSF treatment or 14 days after Pten deletion
Growth protocol HSCs harvested directly from mouse by flow cytometry
Extracted molecule total RNA
Extraction protocol RNA was prepared using the nucelospin RNA isolation kit (Machery-Nagel)
Label Cy3
Label protocol cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul). The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes. Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol. cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf
 
Hybridization protocol The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul). The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655). Hybridization was carried out at 65C for 20 hours. Washing procedures were carried out according to Agilent gene expression protocols.
Scan protocol Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.
Description Gene expression in HSCs
Data processing Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).
 
Submission date Sep 23, 2014
Last update date Sep 22, 2015
Contact name Jeffery Magee
E-mail(s) magee_j@kids.wustl.edu
Organization name Washington University School of Medicine
Department Internal Medicine - Cardiovascular Division
Street address 660 S Euclid Ave.
City St Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL11202
Series (1)
GSE61655 Pten cell autonomously regulates HSC mobilization and function via G-CSF independent mechanisms

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity in log2 scale

Data table
ID_REF VALUE
A_55_P1989846 9.93461
A_55_P1991598 11.597
A_55_P2022211 12.207
A_55_P1980764 12.9764
A_55_P1964375 8.75156
A_51_P128876 15.291
A_55_P2121042 5.22134
A_52_P219230 5.21616
A_51_P207591 4.80402
A_55_P2131920 5.20777
A_55_P2404223 10.1106
A_55_P2101944 16.6749
A_52_P358860 10.5478
A_51_P119031 6.24203
A_51_P309854 4.82451
A_51_P343900 11.6684
A_51_P234359 8.82459
A_51_P487813 10.8905
A_52_P613977 11.9677
A_55_P1957209 5.17615

Total number of rows: 39429

Table truncated, full table size 827 Kbytes.




Supplementary file Size Download File type/resource
GSM1510113_252665511168_S01_GE1_107_Sep09_red_only_1_1.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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