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Sample GSM3597821 Query DataSets for GSM3597821
Status Public on May 02, 2019
Title E10_5_Isl1_hypo_OFT_RV_RNA_seq_rep2
Sample type SRA
 
Source name E10_5_Isl1_hypo_OFT_RV
Organism Mus musculus
Characteristics embryonic stage: E10.5
tissue: dissected outflow tract and right ventricle
strain: C57BL/6
genotype: Isl1 hypomorph
Extracted molecule polyA RNA
Extraction protocol Outflow tract and right ventricle of E10.5 control and Isl1 hypomorphic embryos were dissected and stored at −80 °C in Qiazol. After genotyping, total RNA from single embryos was extracted using Rneasy Microarray Tissue Kit (Qiagen #73304). The integrity of RNA was assessed on Bioanalyzer 2100 (Agilent). For RNA-Seq of control and Isl1 hypomorphic tissue samples, 100 ng of total RNAs was used for library preparation and sequenced on BGISEQ-500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description E10_5_Isl1_hypo_OFT_RV_RNA_seq.bw
E10_5_Isl1_hypo_OFT_RV_quanty_transcripts_diff_expr.txt
Data processing RNA-Seq reads were mapped to the mm9 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000). Samples were quantified using analyzeRepeats.pl (mm9 –count exons –strand both –noadj). Differential expression (fold change >1.5; log2 fold change <−0.58, >0.58; p-value < 0.05) was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR. The KNIME 2.9.1 platform (Konstanz, Germany) was used to filter differentially regulated genes.
Genome_build: mm9
Supplementary_files_format_and_content: bw, differential expressed DESEq2 file
 
Submission date Feb 11, 2019
Last update date May 03, 2019
Contact name Gergana Dobreva
E-mail(s) Gergana.Dobreva@medma.uni-heidelberg.de
Organization name Medical Faculty Mannheim/University of Heidelberg
Department Cardiovascular Genomics and Epigenomics
Lab AG Dobreva
Street address Ludolf-Krehl-Str. 7-11
City Mannheim
State/province Baden Württemberg
ZIP/Postal code 68167
Country Germany
 
Platform ID GPL23479
Series (2)
GSE80383 Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate
GSE126403 Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [Isl1_Hypo_E10_5_RNA_seq]
Relations
BioSample SAMN10910899
SRA SRX5360295

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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