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Sample GSM1211400 Query DataSets for GSM1211400
Status Public on Oct 15, 2013
Title Cont 0h rep2
Sample type RNA
Source name FDCPmix_Cont 0h
Organism Mus musculus
Characteristics cell line: FDCPmix
infected with: Empty vector
Treatment protocol GATA1ERT and Pu.1ERT were subcloned into the pHR-SIN-CSGWEmGFP lentiviral expression construct under control of the SFFV promoter. Gata2 and Pu.1 shRNAs were subcloned into Lentilox 3.7. Recombinant plasmids were packaged into lentiviral particles esssentially by published procedures. FDCPmix cells were transduced at an MOI of between 50 and 200. For gene expression analysis, samples of FDCPmix cells in self-renewal conditions were transduced with lentiviral particles encoding GATA1ERT or PU.1ERT fusion proteins linked to ires-GFP, with empty virus used as a control. GFP+ cells were sorted after 3 days and expanded for a further 7 days under standard conditions, before re-sorting on GFP and addition of 2M 4OH-tamoxifen. Cells were harvested after 0h and 24h of induction and total RNA analyzed by microarray.
Growth protocol FDCPmix were grown in 20% Fischer's medium.
Extracted molecule total RNA
Extraction protocol Total RNA was isolate using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).
Label Cy3
Label protocol Total RNA (150ng) and Agilent One-Color RNA Spike-In were reverse-transcribed and linearly amplified in the presence of Cy3-labeled CTP using Low RNA Input One-Color Kit (Agilent) following Agilent protocols, to generate Cy3-labeled cRNA for hybridisation to high-density microarrays. Quality and yield/specific activity of cRNA were determined using RNA 6000 Nano kit and spectrophotometer (NanoDrop ND- 1000). All samples generated comparable quality cRNA profiles, with specific activities in the range of 10.3 to 12.2 pmol Cy3/mg cRNA.
Hybridization protocol Each Cy3-labeled cRNA sample (1.6ug as per NanoDrop reading) was hybridised to an individual 44K subarray of 4x44K high-density microarray slide (Whole Mouse Gene Expression Microarrays, Agilent), washed, scanned and feature-extracted as per Agilent protocols.
Scan protocol Scanning and feature extraction was performed as per Agilent protocols
Description ER_2
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent v10.1.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Aug 19, 2013
Last update date Oct 15, 2013
Contact name Shamit Soneji
Organization name BMC
Street address Sölvegatan 19
City Lund
ZIP/Postal code 221 84
Country Sweden
Platform ID GPL7202
Series (2)
GSE49990 Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors [ER]
GSE49991 Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_52_P756921 3.523
A_52_P1133703 9.714
A_52_P1052870 4.948
A_52_P1021909 6.179
A_51_P133060 1.365
A_51_P287221 6.099
A_52_P112159 5.012
A_51_P378063 4.972
A_52_P289204 6.284
A_51_P439156 7.022
A_52_P2181 7.788
A_52_P53154 2.667
A_52_P527925 6.99
A_52_P315910 5.667
A_52_P519870 7.935
A_52_P96087 6.775
A_51_P137808 7.078
A_52_P552026 8.987
A_52_P42395 5.814
A_52_P350876 5.235

Total number of rows: 41278

Table truncated, full table size 766 Kbytes.

Supplementary file Size Download File type/resource
GSM1211400_US10020348_251486830449_S01_GE1_107_Sep09_1_2.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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