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Sample GSM2356940 Query DataSets for GSM2356940
Status Public on Oct 21, 2016
Title pol 3
Sample type RNA
 
Source name BM LSK SLAM, POL5551 infusion mouse 3
Organism Mus musculus
Characteristics tissue: bone marrow
gender: male
treatment: POL5551 treated (continuos infusion, 2 wks, 100 mg/kg/day)
Treatment protocol HSCs from control mice or after 2 or 5 days of G-CSF treatment or 14 days after POL5551 infusion start
Growth protocol HSCs harvested directly from mouse by flow cytometry
Extracted molecule total RNA
Extraction protocol RNA was prepared using the NucleoSpin® RNA XS Isolation kit (Macherey-Nagel, Bethlehem, PA, USA) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy5
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 8x60K microarrays (G4852B-074809). 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.
Data processing Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).
 
Submission date Oct 20, 2016
Last update date Oct 21, 2016
Contact name Darja Karpova
E-mail(s) d.karpova@wustl.edu
Phone +1-314-362-9335
Organization name Washington University School of Medicine
Department Oncology, BMT
Lab John F. DiPersio
Street address 660 S Euclid Ave
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21163
Series (1)
GSE88999 Gene expression profiling of differentially treated hematopoietic stem cells (LSK SLAM)

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

Data table
ID_REF VALUE
A_52_P355169 11751
A_52_P281702 20431
A_55_P1966204 2953
A_51_P246543 2220
A_55_P2088615 4060
A_66_P101782 2654
A_51_P337675 3724
A_55_P1964348 8790
A_52_P642167 1638
A_51_P186703 2837
A_51_P494125 1350
A_55_P1960053 880
A_66_P114333 4836
A_55_P2923578 989
A_55_P2177910 8020
A_55_P2128153 7176
A_52_P520495 1210
A_55_P1967291 2474
A_66_P119504 468
A_55_P2801312 1111

Total number of rows: 49665

Table truncated, full table size 879 Kbytes.




Supplementary file Size Download File type/resource
GSM2356940_US82600140_257480910187_S01_GE1_107_Sep09_red_only_2_3.txt.gz 12.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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