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Sample GSM4832869 Query DataSets for GSM4832869
Status Public on Mar 11, 2024
Title Ventral tissue at E12.5, biological rep 1
Sample type RNA
 
Source name Ventral tissue at E12.5
Organism Mus musculus
Characteristics tissue: ventral aortic tissue
isolation: Tissue isolated by laser microdissection
developmental stage: E12.5
strain: C57Bl/6
Treatment protocol Unfixed embryos were embedded in OCT medium in presence of isopentane cooled at -65°C. Twenty μm cryostat sections were then prepared and stained before laser micro-dissection. The dorsal tissue localized in between the notochord and the roof of the aorta and the ventral tissue underneath the aorta were isolated from the same embryos.
Growth protocol Embryos were collected from pregnant C57B/6 mice at embryonic day 12.5.
Extracted molecule total RNA
Extraction protocol Microdissected tissues were collected on appropriate caps and then proceeded for RNA extraction using Acturus Picopure RNA isolation kit. RNAs were eluted in a final volume of 13 μl and their concentrations and integrity quantified on a bioanalyzer (Agilent).
Label biotin
Label protocol Between 200 and 1000 pg of total RNA was reverse transcribed following the Ovation Pico V2 system (Nugen) and the resulting double strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, sens target DNA was fragmented and biotin labelled using Encore Biotin Module kit (Nugen).
 
Hybridization protocol After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.
Scan protocol After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.
Description Gene expression data from ventral aortic tissue at E12.5
Data processing The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. RMA normalization is performed using R with Version 21 of Entrezgene CDF brain array.
 
Submission date Oct 19, 2020
Last update date Mar 11, 2024
Contact name Charles Durand
E-mail(s) charles.durand@sorbonne-universite.fr
Phone +33 1 44 27 22 84
Organization name Sorbonne University
Department Laboratory of Developmental Biology
Lab CNRS UMR7622
Street address 9, quai saint-Bernard
City Paris
ZIP/Postal code 75005
Country France
 
Platform ID GPL23092
Series (2)
GSE159591 Molecular analysis of the subaortic hematopoietic stem cell niche [E12.5]
GSE159592 Molecular analysis of the subaortic hematopoietic stem cell niche

Data table header descriptions
ID_REF
VALUE Log2-RMA signal.

Data table
ID_REF VALUE
100009600_at 3.20771387117768
100009609_at 2.03194396129383
100009614_at 2.83774041322794
100009664_at 3.1298217187265
100012_at 2.89625619510713
100017_at 3.56864610830868
100019_at 5.1771294194335
100033459_at 2.16255321489442
100034251_at 4.07188618518429
100034675_at 2.79719297172944
100034728_at 10.1810101734556
100034729_at 1.690041083125
100034739_at 3.42497498724417
100034748_at 3.52942173026012
100036518_at 1.99915928462655
100036520_at 2.96506460889724
100036521_at 2.85019802753813
100036523_at 5.23101197118644
100036537_at 4.91185269018759
100036768_at 2.84209736874898

Total number of rows: 25429

Table truncated, full table size 662 Kbytes.




Supplementary file Size Download File type/resource
GSM4832869_VT2_E12.5.CEL.gz 8.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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