|
| Status |
Public on May 02, 2019 |
| Title |
E8_75_Isl1_wt_RNA_seq_rep2 |
| 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 |
SAMN10911793 |
| SRA |
SRX5360311 |
