7 protocols
AccessionNameType
P-MTAB-20762
normalization
We utilised the program Deseq written for the statistical package R by , to compare the expression profiles of tags across samples. Count data was normalised within the program for within and between library variation.
P-MTAB-20761
alignment_and_count
All tags were mapped to the Nasonia Vitripennis genome obtained from ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Nvitripennis/fasta/Nvit_1.0/linearized_sequence/ using MAQ 0.6.8, allowing for a 2bp mismatch between the tag and the reference. A mapping quality score of 30, incorporating sequence quality and ability of the tag to map to one unique site in the transcriptome, was used to identify tags that align uniquely to reference sequence. Further, the tags that didnot map to the genome were extracted and aligned to transcripts available at ftp://ftp.nasoniagenome.hgsc.bcm.tmc.edu/_annotation/_official_gene_set/. Also, the tags that did not map to either genome or available transcripts were extracted and clustered togather. The tags were counted against the genome and transcript coordinate for each samples. We utilised the program Deseq written for the statistical package R by , to compare the expression profiles of tags across samples. Count data was normalised within the program for within and between library variation.
P-MTAB-20760
high_throughput_sequencing
Sequence tag preparation was performed with Digital Gene Expression Tag Profile Kit (Illumina), according to the manufacturer's instructions
P-MTAB-20757
behavioral_stimulus
Virgin females were exposed to virgin males and allowed to fully complete all aspects of courtship and copulation. Females were held for a period of 30 minutes or 4-hours post-mating in individual tubes in a 25 degree incubator
P-MTAB-20759
rna_extraction
RNA was extracted from samples using Quiagen's RNAeasy kit
P-MTAB-20758
tissue_seperation
Female heads and bodies were seperated in RNAlater-ice prior to RNA extraction
P-MTAB-20756
control
Virgin females were used as controls and were held alongside 30 minute mated female samples without exposure to males