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Sample GSM4832852 Query DataSets for GSM4832852
Status Public on Mar 11, 2024
Title Dorsal tissue at E10.5, biological rep 2
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 2.79991089215888
11298_at 3.78840562820636
11302_at 4.61489998591386
11303_at 3.41004980017525
11304_at 3.03250774141411
11305_at 2.94072211140033
11306_at 3.30299619695881
11307_at 4.10836989169167
11308_at 3.40553838271254
11350_at 3.6736707883543
11352_at 2.88156248139941
11354_at 2.45672919774857
11363_at 3.33978397936101
11364_at 3.05889630598029
11370_at 3.62432252707966
11409_at 3.20750711297069
11416_at 3.00533562347132
11418_at 3.26741621527692
11419_at 3.38768118864969
11421_at 3.48386142630829

Total number of rows: 25429

Table truncated, full table size 662 Kbytes.




Supplementary file Size Download File type/resource
GSM4832852_DT2_E10.5.CEL.gz 6.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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