Khamis 2015, Honey bee brain transcriptome from nurses and forager bees.


Genes expression analysis with CAGEscan technique of 2 different kinds of Apis Mellifera bees, nurse and foragers, with 8 biological replicas each.



From A. mellifera (Apr 2011 Amel_4.5/amel5).

Transcription Profiling data:

Filename Description Feature GEO-ID
1 SRR1582004_ACAGAT.sga Brain|CAGE|Nurse|Rep 1 CAGE GSM1568470
2 SRR1582004_ATCGTG.sga Brain|CAGE|Nurse|Rep 2 CAGE GSM1568470
3 SRR1582004_CACGAT.sga Brain|CAGE|Nurse|Rep 3 CAGE GSM1568470
4 SRR1582004_CACTGA.sga Brain|CAGE|Nurse|Rep 4 CAGE GSM1568470
5 SRR1582004_CTGACG.sga Brain|CAGE|Nurse|Rep 5 CAGE GSM1568470
6 SRR1582004_GAGTGA.sga Brain|CAGE|Nurse|Rep 6 CAGE GSM1568470
7 SRR1582004_GTATAC.sga Brain|CAGE|Nurse|Rep 7 CAGE GSM1568470
8 SRR1582004_TCGAGC.sga Brain|CAGE|Nurse|Rep 8 CAGE GSM1568470
9 SRR1582203_ACAGAT.sga Brain|CAGE|Forager|Rep 1 CAGE GSM1568471
10 SRR1582203_ATCGTG.sga Brain|CAGE|Forager|Rep 2 CAGE GSM1568471
11 SRR1582203_CACGAT.sga Brain|CAGE|Forager|Rep 3 CAGE GSM1568471
12 SRR1582203_CACTGA.sga Brain|CAGE|Forager|Rep 4 CAGE GSM1568471
13 SRR1582203_CTGACG.sga Brain|CAGE|Forager|Rep 5 CAGE GSM1568471
14 SRR1582203_GAGTGA.sga Brain|CAGE|Forager|Rep 6 CAGE GSM1568471
15 SRR1582203_GTATAC.sga Brain|CAGE|Forager|Rep 7 CAGE GSM1568471
16 SRR1582203_TCGAGC.sga Brain|CAGE|Forager|Rep 8 CAGE GSM1568471

Merged samples:

Each biological replica was extracted form the ame sequencing run as described in the Techniacal Notes.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0). Following manuscript protocol, paired-end reads were grouped according to 8 different barcodes into the biological replicas. Subsequently, reads were trimmed of the 21 bp long adapter at the 5' end and mapped to the genome using Bowtie2 v2.2.9. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using (ChIP-Seq v. 1.5.2).


Last update: 1 Oct 2018