U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX7500997: GSM4250617: Worker_ATAC_Rep2; Monomorium pharaonis; ATAC-seq
1 BGISEQ (BGISEQ-500) run: 365.6M spots, 18.3G bases, 8.9Gb downloads

Submitted by: NCBI (GEO)
Study: The chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain
show Abstracthide Abstract
The emergence of eusociality is one of the major transitions in evolution. There have been several investigations into the reasons for shaping caste differentiation and social behavior of eusocial insects, such as ants and honeybees. However, the molecular mechanisms governing the sociality of these insects remain obscure. In this study, we profiled the transcriptome and chromatin accessibility of brain tissues in all castes: queens, males, gynes and workers in Monomorium pharaonis which is a typical caste-dependent eusocial insect. We created a comprehensive dataset including 16 RNA-seq and 16 ATAC-seq profiles from 4 biological replicates. We also demonstrated strong reproducibility of the datasets and identified specific genes and open chromatin regions in the genome that may be associated with caste differentiation. Overall, our data will be a valuable resource for further study of the mechanisms underlying eusocial insect behavior, particularly the role of the brain in the control of eusociality. Overall design: We have profiled caste-dependent transcriptomes in the brain of Monomorium pharaonis, which is a typical eusocial insect, and the colony consists of four adult castes: queens, males, gynes and workers. We analyzed the gene expression by producing RNA-seq and ATAC-seq profiles of four castes brain. 16 samples from 4 biological replicates were processed and sequenced.
Sample: Worker_ATAC_Rep2
SAMN13721883 • SRS5942425 • All experiments • All runs
Library:
Instrument: BGISEQ-500
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Whole-brain RNA was extracted immediately after dissection with RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol and eluted in 10 μl nuclease-free water (Ambion). Total amounts of RNA were quantified using an Invitrogen Qubit RNA High Sensitivity assay.In brief, brains were dissected and then washed twice with 500 μl ice-cold PBS. After centrifugation at 500 x g for 5 min, the brain samples were lysed with 50 μl lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). We used an optimized Smart-seq2 method for RNA-seq library construction.The supernatant was discarded and replaced with a 50 μl transposition reaction mix containing 10 mM TAPS-NaOH (pH 8.5), 5 mM MgCl2, 10% DMF, 2.5 μl of in-house Tn5 transposase (0.8 U/μl) and NF-water for ATAC-seq.
Experiment attributes:
GEO Accession: GSM4250617
Links:
Runs: 1 run, 365.6M spots, 18.3G bases, 8.9Gb
Run# of Spots# of BasesSizePublished
SRR10827623365,563,20218.3G8.9Gb2020-01-05

ID:
9797355

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...