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| Status |
Public on Oct 06, 2023 |
| Title |
Heart_40396 |
| Sample type |
SRA |
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| Source name |
fetal heart
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| Organism |
Bos taurus |
| Characteristics |
tissue: fetal heart
fetal weight: 1.659 gr
maternal group: ET_D9
gestational age: 42 days
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Blood and tissues samples were shipped on dry ice to Macrogen Europe (Amsterdam, Netherlands), which performed the RNA extraction, quality control, library preparation, and sequencing. One sample from the heart, one from the gonads, and two from the liver were discarded after quality control because of the rRNA ratio and RIN<7.
Libraries were prepared with Truseq-stranded mRNA for all tissue samples and SMARTer Stranded RNA library for the blood samples, followed by PE100 sequencing with the NovaSeq platform, generating ~30 million raw reads per sample in FASQ format.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Heart_40396
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| Data processing |
The read qualities for each fastq file were accessed with FastQC (V 0.11.9), and low-quality bases and adapters were removed with Trimmomatic.
The sequenced reads were mapped to the bovine reference genome (bosTau 9) with the STAR aligner (V 2.7.0b), generating the genome index with the ARS-UCD1.3 assembly.
Read counts were estimated at the gene level, and the counting was done with featureCounts, part of the Subread software (V 2.0.3).
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file containing raw read counts for each sample.
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| Submission date |
Apr 21, 2023 |
| Last update date |
Oct 06, 2023 |
| Contact name |
Maria Belen Rabaglino |
| E-mail(s) |
m.b.rabaglino@uu.nl
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| Organization name |
Utrecht University
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| Department |
Population Health Science
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| Street address |
Yalelaan 7
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| City |
Utrecht |
| ZIP/Postal code |
3584 CL |
| Country |
Netherlands |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE230294 |
Maternal blood transcriptome reflects fetal maturation at the end of the organogenesis in cattle. |
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| Relations |
| BioSample |
SAMN34293082 |
| SRA |
SRX20051731 |
| 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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