|
| Status |
Public on Jul 12, 2018 |
| Title |
3-4h_AEL_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: W1118
Stage: 3-4hr AEL(after egg laying)
|
| Treatment protocol |
Embyro homogenizied by by Douce all-class tissue grinder, and used lysis buffer to lysis cell.
|
| Growth protocol |
Embryos were collected on grape juice plates with yeast paste from embryo collection cages for 1 hr, and then allowed to develop for 3 and 14 additional hours before being harvested. So the collected embryos are 3-4h and and 14-15h old, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the TRIzol following the manufacturer’s instructions. The quality of the resulting RNA was verified by the relative intensity of rRNA bands using a Agilent 2100 Bioanalyzer, and RNA was quantified using a Nanodrop ND-1000 spectrophotometer
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
mRNA-Seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, aligned to the Drosophila genome (dm3) using Bowtie/Tophat (v1.3.1) with default parameters.
Uniquely mapped reads were assembled into transcripts guided by reference annotation (FlyBase r5.57) with Cufflinks (v1.3.0) to calculate gene expression levels which measured as Fragment Per Kilobase per Million mapped fragments (FPKM).
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited file includes FPKM values for each gene
|
| |
|
| Submission date |
Jul 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Hu |
| E-mail(s) |
hujian5241@126.com
|
| Organization name |
Tongji University
|
| Street address |
1239,Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE101328 |
Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[RNA-Seq] |
| GSE101330 |
Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos |
|
| Relations |
| BioSample |
SAMN07346909 |
| SRA |
SRX2998873 |
