|
| 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 |
