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| Status |
Public on Jan 04, 2021 |
| Title |
DG-S7_S16 |
| Sample type |
SRA |
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| Source name |
Honey bee brain
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| Organism |
Apis mellifera |
| Characteristics |
reproductive status: Reproductive
lineage: L888
genotype (maternal x paternal): Afr x Eur
block: A
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| Growth protocol |
Individuals from reciprocal crosses of Africanized and European honey bees were raised in queenless colonies for ~18 days, allowing time for the workers to activate the ovaries and become reproductively active.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Brains from individual bees were lyophilized and dissected in RNAlater® (Qiagen, Valencia, CA) on dry ice and excess RNAlater® was removed from the samples. RNA was isolated using TRIzol® Reagent (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10.
The transcriptome sequencing reads were aligned to the Amel_4.5 honey bee genome assembly using Hisat2
The data was normalized using a trimmed mean of M-values (TMM) method.
The LIMMA package in R was used to identify significantly differentially expressed genes.
The transcriptome sequencing reads were also aligned to pseudo-parent genomes (reference genome with parental SNPs included, one for paternal and one for maternal) allowing 0 mismatches with Hisat2 to look at parent specific gene expression. This data can be found in PSGE_Sterile_reads.txt and PSGE_Reproductive_reads.txt
Genome_build: Amel4.5
Supplementary_files_format_and_content: PSGE_gene_expression.txt contains the gene expression data for each individual. PSGE_sterile.txt contains read counts for each sterile individual at each parental snp. PSGE_reproductive.txt contains read counts for each reproductive individual at each parental snp.
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| Submission date |
Aug 10, 2020 |
| Last update date |
Jan 04, 2021 |
| Contact name |
David Asher Galbraith |
| E-mail(s) |
dag5031@gmail.com
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| Organization name |
Penn State University
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| Street address |
19a Chemical Ecology Lab
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| City |
University Park |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL19174 |
| Series (1) |
| GSE155984 |
Tissue specific transcription patterns support the kinship theory of intragenomic conflict in honey bees (Apis mellifera) |
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| Relations |
| BioSample |
SAMN15776092 |
| SRA |
SRX8920098 |
| 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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