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Sample GSM3597841 Query DataSets for GSM3597841
Status Public on May 02, 2019
Title E8_75_Isl1_wt_RNA_seq_rep4
Sample type SRA
 
Source name E8_75_Isl1_wt
Organism Mus musculus
Characteristics embryonic stage: E8.75 (6 somites)
tissue: pharyngeal mesoderm and hearts
strain: C57BL/6
genotype: wild-type
Extracted molecule polyA RNA
Extraction protocol Pharyngeal mesoderm and hearts of E8.75 control and Isl1 KO 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−/− tissue samples, 100 ng of total RNAs was used for library preparation and sequenced on NextSeq500 (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description E8_75_Isl1_wt_RNA_seq.bw
E8_75_Isl1_KO_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 GPL17021
Series (2)
GSE80383 Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate
GSE126406 Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [Isl1_E8_75_RNA_seq]
Relations
BioSample SAMN10911791
SRA SRX5360313

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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