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| Status |
Public on Sep 13, 2024 |
| Title |
dunnart face P0 rep3 |
| Sample type |
SRA |
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| Source name |
face
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| Organism |
Sminthopsis crassicaudata |
| Characteristics |
tissue: face
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| Extracted molecule |
total RNA |
| Extraction protocol |
The reads for three replicates were generated from facial prominences of P0 dunnart pouch young. Each replicate is a pool of two pouch young
Libraries were prepared using the Illumina stranded mRNA kit and were sequenced to a depth >=50M read pairs (i.e. 25M F + 25M R) in 2x100bp format.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The raw reads were first trimmed using trimmomatic v0.39 (Bolger et al., 2014) [ILLUMINACLIP:2:30:10 SLIDINGWINDOW:5:15 MINLEN:50 AVGQUAL:20]. Reads were mapped with hisat2 v2.21 (Zhang et al., 2021) [--fr --no-mixed --no-discordant] and alignments were filtered using samtools view (Li et al., 2009) [-f 1 -F 2316]. Finally the count table was generated using featureCounts from the Subread package v2.0.1 (Liao et al., 2013) [-s 2 -p -t exon --minOverlap 10].
Assembly: Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fasta
Supplementary files format and content: featureCounts
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| Submission date |
Sep 06, 2024 |
| Last update date |
Sep 15, 2024 |
| Contact name |
Laura E Cook |
| E-mail(s) |
[email protected]
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| Organization name |
Lawrence Berkeley National Laboratory
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| Department |
Biosciences
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| Lab |
MFGL
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| Street address |
1 Cyclotron Road
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| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL34873 |
| Series (1) |
| GSE188990 |
Gene regulatory dynamics during craniofacial development in a carnivorous marsupial |
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| Relations |
| BioSample |
SAMN43527290 |
| SRA |
SRX26083394 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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