|
| Status |
Public on Jan 20, 2017 |
| Title |
Tj-Gal4_RNAseq1 |
| Sample type |
SRA |
| |
|
| Source name |
fly testis
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Tj-Gal4
developmental stage: adult
age: 5 days old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
[ChIP-seq] Sonication of fly testes was performed. Then sonicated chromatin was incubated with GFP antibody.
[ChIP-seq] Libraries were generated using reagents provided in the Illumina TruSeq ChIP Sample Preparation Kit (IP-202-1012).
[RNA-seq] Total RNA was purified following the manufacturer’s instruction of PicoPure RNA isolation kit (KIT0204, Life technologies)
[RNA-seq] libraries were generated using reagents provided in Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7 default
Bowtie aligner (version 0.12.7) following configuration (-a --phred33-quals -n 2 -e 70 -l 28 -m 1 --best –strata)
non-redundant reads are filtered through;SAMtools software suite was utilized to convert between related read formats to BAM
edgeR R package TMM normalization
MACS2.0 peakcall default settings
Genome_build: flybase d_melanogaster r5.43
Supplementary_files_format_and_content: bedgraph generated by 500bp interval inhouse software; raw_count_per_gene_RNAseq.txt is summarized by inhouse software; RPKM is calculated by edgeR
|
| |
|
| Submission date |
Jan 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
The Joihns Hopkins University
|
| Department |
Biology
|
| Lab |
Chen
|
| Street address |
3400 N Charles St
|
| City |
baltimore |
| State/province |
MD |
| ZIP/Postal code |
21218 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE93828 |
E(Pc) ChIP-seq experiment in fruitfly testis somatic gonadal cells and RNA-seq experiment in fruitfly testis |
|
| Relations |
| Reanalyzed by |
GSM3282730 |
| BioSample |
SAMN06241870 |
| SRA |
SRX2504297 |
