|
Status |
Public on Jan 04, 2020 |
Title |
Worker_ATAC_Rep4 |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Monomorium pharaonis |
Characteristics |
cell type: Brain cells caste: worker
|
Treatment protocol |
Ants were put on ice to reduce activity and then brains were dissected23 and transferred into 1.5 ml centrifuge tubes with phosphate-buffered saline (PBS, Gibco). Washed the brains twice with 500 μl ice-cold PBS.
|
Growth protocol |
Ants were kept under a constant temperature of 25 °C and 50% humidity and fed with mealworm.
|
Extracted molecule |
genomic DNA |
Extraction 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.
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
BGISEQ-500 |
|
|
Description |
Peak_Readcounts_matrix.xls
|
Data processing |
RNA-seq total reads were aligned to the Monomorium pharaonis ASM326058v2 genome using hisat2.ATAC-seq total reads were aligned to the Monomorium pharaonis ASM326058v2 genome using Bowtie2. The read counts per gene of each sample were calculated with featureCounts; ATAC-seq readcount per peak of each sample were calculated with bedtools. The differentially expressed genes (DEGs) between castes were identified by DESeq2;The differentially accessible regions (DARs) between castes were identified by DESeq2. Genome_build: ASM326058v2 Supplementary_files_format_and_content: tab-delimited Excel files include read counts for each sample
|
|
|
Submission date |
Jan 03, 2020 |
Last update date |
Jan 04, 2020 |
Contact name |
CNSA CNGB |
Organization name |
BGI
|
Street address |
BGI
|
City |
shenzhen |
ZIP/Postal code |
518083 |
Country |
China |
|
|
Platform ID |
GPL27969 |
Series (1) |
GSE143056 |
The chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain |
|
Relations |
BioSample |
SAMN13721881 |
SRA |
SRX7500999 |