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Sample GSM4832851 Query DataSets for GSM4832851
Status Public on Mar 11, 2024
Title Dorsal tissue at E10.5, biological rep 1
Sample type RNA
 
Source name Dorsal tissue at E10.5
Organism Mus musculus
Characteristics tissue: dorsal aortic tissue
isolation: Tissue isolated by laser microdissection
developmental stage: E10.5
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 10.5.
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 dorsall aortic tissue at E10.5
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)
GSE159588 Molecular analysis of the subaortic hematopoietic stem cell niche [E10.5_1]
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
11287_at 2.55680046282659
11298_at 3.80916180321003
11302_at 4.25247172751312
11303_at 3.50593617180555
11304_at 2.76781172627699
11305_at 3.17692022437547
11306_at 3.07756169305628
11307_at 4.44480643615898
11308_at 4.06366208212784
11350_at 3.31467456687972
11352_at 3.0604996119306
11354_at 2.34839163949864
11363_at 3.0271482324943
11364_at 3.09417762496595
11370_at 3.35903927499463
11409_at 4.01518194929449
11416_at 2.72357081065316
11418_at 3.40672399431777
11419_at 2.80205016536534
11421_at 3.23146219688003

Total number of rows: 25429

Table truncated, full table size 662 Kbytes.




Supplementary file Size Download File type/resource
GSM4832851_DT1_E10.5.CEL.gz 7.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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