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Sample GSM2424475 Query DataSets for GSM2424475
Status Public on Dec 01, 2017
Title CD34_RUNX1_1
Sample type RNA
 
Source name human primary CD34 cells transduced with shRUNX vector
Organism Homo sapiens
Characteristics cell type: primary CD34+ cells
Treatment protocol Cells were lentivirally transduced with specific shvectors or a control shvector targeted against LacZ. Transduction was monitored by GFP, only cells with more than 95% GFP positiv cells were further processed. Cells were harvested 5 days after transduction.
Growth protocol K562 cells were grown under standard conditions (ATCC). Human CD34+ cells were purified from mobilised apharesis samples with magnetic CD34+ antibody beads (Miltenyi). Cells were maintained and transduced in serum free expansion medium (StemSpan, StemCell Technologies)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies). mRNA was reverse-transcribed using oligo-dT and random hexameric primers and was quantified via qRT-PCR analysis using SYBR Green (Invitrogen/Life Technologies).
Label cy3
Label protocol Microarrays were done using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Cat. N°: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol. Global gene expression analysis was applied using the SurePrint G3 Human Gene Expression 8x60K v2 Microarray Kit, Product number G4851B, (Agilent Microarray Design ID 039494). 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer's recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.
 
Hybridization protocol The hybridizations were performed for 17 hours at 10 rpm and 65°C in the hybridization oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.
Scan protocol Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 3 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.
Data processing Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 11.5.1.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma packages of Bioconductor.
 
Submission date Dec 12, 2016
Last update date Dec 01, 2017
Contact name Gabriela Salinas
E-mail(s) [email protected]
Organization name Universitaetsmedizin Goettingen
Department Department of Pathology
Lab NGS Integrative Genomics
Street address Kreuzbergring 57
City Goettingen
State/province Lower-Saxony
ZIP/Postal code 37075
Country Germany
 
Platform ID GPL13497
Series (1)
GSE92251 Gene expression alterations upon knock down of transcription factors

Data table header descriptions
ID_REF
VALUE quantile normalized signal intensity

Data table
ID_REF VALUE
A_23_P100001 206.573895
A_23_P100022 134.6576235
A_23_P100056 2.45249201
A_23_P100074 1411.138802
A_23_P100127 1078.079606
A_23_P100141 168.4662455
A_23_P100189 36.05856965
A_23_P100196 2159.29438
A_23_P100203 1206.332315
A_23_P100220 113.7979635
A_23_P100240 8.1652353
A_23_P10025 5.356543685
A_23_P100292 9946.989625
A_23_P100315 2189.53018
A_23_P100326 5149.277435
A_23_P100344 708.2591795
A_23_P100355 2729.510075
A_23_P100386 9.40626941
A_23_P100392 749.232306
A_23_P100420 800.891469

Total number of rows: 34127

Table truncated, full table size 808 Kbytes.




Supplementary file Size Download File type/resource
GSM2424475_US22502691_252665213249_S01_GE1_107_Sep09_1_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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