NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2143798 Query DataSets for GSM2143798
Status Public on Nov 22, 2016
Title HSC_WT_P14_16451
Sample type RNA
 
Source name Bone marrow
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: P14
genotype: wildtype
tissue: HSC
Treatment protocol No treatments. Cells were harvested directly from mice by flow cytometry
Growth protocol HSCs and HPCs harvested directly from mouse by flow cytometry
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Qiagen RNAeasy micro plus columns
Label Cy5
Label protocol RNA samples were amplified using SIGMA WTA2 RNA amplification system. Amplified 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 May 05, 2016
Last update date Nov 22, 2016
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 GPL10787
Series (1)
GSE81153 Fetal and neonatal hematopoietic progenitors are functionally and transcriptionally resistant to Flt3-ITD mutations.

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity in log2 scale based on the rProcessedSignal field

Data table
ID_REF VALUE
A_55_P2051983 4.77586
A_52_P169082 8.84685
A_30_P01028193 4.75594
A_52_P237997 8.88374
A_51_P414243 13.8566
A_55_P2136348 4.7294
A_51_P108228 5.66133
A_30_P01033363 8.85783
A_55_P2049737 6.60436
A_30_P01024440 12.3506
A_30_P01025554 13.2368
A_30_P01031558 11.9209
A_30_P01030675 5.4409
A_51_P328014 12.6131
A_30_P01019108 10.2939
A_55_P2056220 10.1002
A_55_P1985764 14.2437
A_52_P108321 11.6765
A_55_P2018002 8.04935
A_52_P123354 11.9006

Total number of rows: 55681

Table truncated, full table size 1191 Kbytes.




Supplementary file Size Download File type/resource
GSM2143798_US82600140_252800520967_S01_GE1_107_Sep09_red_only_2_4.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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