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Sample GSM1267924 Query DataSets for GSM1267924
Status Public on Jun 12, 2014
Title SP1KO hemogenic endothelium II (HE2) replicate1
Sample type RNA
Source name from differentiation of ES cells
Organism Mus musculus
Characteristics cell type: hemogenic endothelium II
strain: C57BL/6
genotype: Sp1 -/- knock-out
Growth protocol ES cells were trypsinised and allowed to form embryoid bodies by plating in base methylcellulose (Stem Cell Technologies M3134) supplemented with 10% FCS, 100 units/ml Penicillin and 100 µg/ml Streptomycin, 1 mM glutamine, 0.15 mM MTG, 10 g/ml insulin (Sigma), 5% IL-3 conditioned media, 10 ng/ml recombinant mouse M-CSF (R&D Systems), 100 units/ml IL-1 (Peprotech) at a cell concentration previously determined to give similar numbers of EB. After at least 14 days EB were counted and assessed for the number of EB.
Extracted molecule total RNA
Extraction protocol RNA was extracted from cells using TRIzol® (Invitrogen) according to manufacturer’s instruction. First strand cDNA synthesis was carried out using Superscript II (Invitrogen) according to manufacturer’s instructions using 250-500 ng of RNA. Real Time PCR was carried out using ABI SYBR® green master mix with 5 µl of diluted cDNA and 0.25 µM primer per 15 µl reaction on an ABI 7900HT machine.
Label Cy3
Label protocol 25ng of each source sample RNA was labelled with Cy3 dye as per the protocol detailed in the Low Input Quick Amp Labelling Kit (Agilent Technologies – 5190-2305). A Specific Activity of greater than 6.0 was confirmed by measurement of 260 nm and 550 nm wavelengths with a NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol Hybridization samples were prepared for a 8-pack microarray using 600 ng cRNA each according to the hybridization protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), loaded onto the 8-pack array slide and hybridized at 65 °C overnight
Scan protocol After washing the microarray was scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays (Dye channel: Green; Scan region: Scan Area (61 x 21.6 mm); Scan resolution (μm): 3; Tiff: 20 bit)
Description SP1_KO_HE2_12
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) (protocol GE1_107_Sep09, Grid: 028005_D_F_20100614 and platform Agilent SurePrint G3 Mouse GE 8x60K). The raw data output by Feature Extraction Software was analysed using the LIMMA R package with quantile normalization and background subtraction.
Submission date Nov 19, 2013
Last update date Jun 12, 2014
Contact name Salam Adli Assi
Organization name University of Birmingham
Department Institute for Cancer and Genomic Sciences
Street address IBR
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
Platform ID GPL13912
Series (2)
GSE52497 A crucial role of the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification [array]
GSE52499 A crucial role of the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification

Data table header descriptions
VALUE Normalized log2 signal intensity

Data table
1 15.15
2 6.02
3 6.04
4 6.14
5 7.03
6 6.24
7 6.10
8 11.07
9 6.41
10 6.37
11 7.29
12 6.34
13 9.73
14 11.73
15 6.65
16 6.10
17 12.47
18 9.84
19 11.61
20 16.08

Total number of rows: 62976

Table truncated, full table size 678 Kbytes.

Supplementary file Size Download File type/resource
GSM1267924_SP1KO_HE2_12.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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