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Sample GSM5630049 Query DataSets for GSM5630049
Status Public on Oct 01, 2023
Title aSHF, mutant, biological rep1 (miRNA)
Sample type RNA
 
Source name aSHF, mutant
Organism Mus musculus
Characteristics tissue: aSHF
genotype: Mef2c-AHF-Cre/+; Dgcr8 f/f
developmental stage: embryonic day E9.5
Treatment protocol Embryos were isolated on embryonic day E9.5 and immediate processed for microdissection of aSHF and OFT-RV tissues following by fast freezing at -80C. After multiple litter collections and genotyping, the tissues were pooled according to genotype for total RNA extraction.
Growth protocol Embryos at E9.5 (19 - 21 somite pairs) were used for quentitative gene expression studies of microdissected anterior second heart field and outflow tract with the right ventricle.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions-miRNeasy Mini Kit QIAGEN 217004.
Label biotin
Label protocol The sense-strand cDNA was amplified and converted from 100 nanograms (ng) starting total RNA using Ambion WT Expression Kit.
 
Hybridization protocol A total of 3.8 mg of cDNA from the last step was hybridized to the Affymetrix Mouse GeneST 1.0 or miRNA 4.0 chip. Hybridization, washing, staining and scanning were performed in the Genomics Core at Einstein (https://www.einstein.yu.edu/research/shared-facilities/cores/46/genomics/) according to the Affymetrix manual.
Scan protocol Scanning were performed in the Genomics Core at Albert Einstein College using Genechip G7 scanner.
Description miRNA expression data from E9.5 aSHF
Data processing Data analysis was performed in the R statistical package. GeneChip data were pre-processed by the ‘oligo’ package (PMID: 20688976), which implements Robust Multichip Average (RMA) algorithm with background correction, quantile normalization and gene level summarization (PMID: 12925520).
 
Submission date Oct 18, 2021
Last update date Oct 01, 2023
Contact name Silvia Elisa Racedo
E-mail(s) silvia.racedo@einsteinmed.org
Organization name Albert Einstein College of Medicine
Department Genetics
Lab Morrow Lab
Street address 1301 Morris Park Ave
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL19117
Series (1)
GSE186064 Dgcr8 function in the anterior second heart field

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
14q0_st 0.882774995
14qI-1_st 0.771859901
14qI-1_x_st 0.846253829
14qI-2_st 0.43991731
14qI-3_x_st 0.623902531
14qI-4_st 0.742699859
14qI-4_x_st 0.665090396
14qI-5_st 0.763811143
14qI-6_st 0.669442649
14qI-7_st 1.104185848
14qI-8_st 0.72858437
14qI-8_x_st 0.722463046
14qI-9_x_st 0.49517666
14qII-1_st 1.040533147
14qII-1_x_st 1.071226853
14qII-10_st 0.623647555
14qII-11_st 0.905869818
14qII-12_st 0.84896362
14qII-12_x_st 0.870178696
14qII-13_st 0.858167934

Total number of rows: 36353

Table truncated, full table size 984 Kbytes.




Supplementary file Size Download File type/resource
GSM5630049_BM5447-miRNA4-8.2.CEL.gz 734.3 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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