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GEO help: Mouse over screen elements for information. |
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Status |
Public on Dec 01, 2023 |
Title |
GOF E15.5 WT_3 |
Sample type |
SRA |
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Source name |
Heart ventricles
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Organism |
Mus musculus |
Characteristics |
tissue: Heart ventricles genotype: WT
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Extracted molecule |
polyA RNA |
Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen) Total RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher) Libraries were sequenced on a HiSeq4000 (Illumina) to generate 60 bases single reads.FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
WT_3
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Data processing |
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina). Sequencing adapter contaminations were removed with cutadapt, discarding those reads that were shorter than 30 nt after trimming. Resulting reads were aligned against the GRCm38.91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level. Assembly: GRCm38.91 Supplementary files format and content: Ensembl gene and transcript IDs, and RSEM-estimated raw counts for 53,465 annotated genes, in each sample.
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Submission date |
Oct 24, 2022 |
Last update date |
Dec 01, 2023 |
Contact name |
Jose Luis de la Pompa |
E-mail(s) |
jlpompa@cnic.es
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Phone |
+34620936633
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Organization name |
Centro Nacional de Investigaciones Cardiovasculares (CNIC)
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Lab |
Intercellular Signaling in Cardiovascular Development & Disease
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Street address |
Melchor Fernández Almagro 3
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City |
Madrid |
State/province |
MADRID |
ZIP/Postal code |
28029 |
Country |
Spain |
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Platform ID |
GPL21103 |
Series (2) |
GSE216467 |
Characterization of the effect of overexpressing the Nrg-1 (neuregulin-1) gene, using the cardiac driver line Nkx2.5-Cre, in E (embryonic day) 15.5 heart venticles |
GSE216471 |
Role of Nrg-1 in the development of heart ventricular chamber in mice. |
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Relations |
BioSample |
SAMN31430894 |
SRA |
SRX18006977 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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