|
| Status |
Public on Nov 20, 2016 |
| Title |
NSC.RNA |
| Sample type |
SRA |
| |
|
| Source name |
Neural stem cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Sca-Gal4/cyo;UAS-3xFLAG-blrp-mCherry-RanGap
tissue: Neural stem cells
Stage: 5–7h after egg laying (AEL)
molecule subtype: total nuclear RNA
|
| Treatment protocol |
Nuclei mixture were harvested by homogenizing the whole cross-linked Drosophila embryo, and nuclei of interest were isolated by anti-Flag M2 magnetic beads affinity purification.
|
| Growth protocol |
Embryos were collected on grape juice plates with yeast paste from embryo collection cages for 2 hr, and then allowed to develop for 3 and 10 additional hours before being harvested. So the collected embryos are 5–7h and and 12–14h old, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei RNA was harvested used the RNeasy micro kit (Qiagen, cat. no. 74004). Contaminating genomic DNA was removed from the RNA by treating with the Turbo DNA-free kit(Ambion, cat. no. AM1907M).
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 r5.43) with Cuffdiff (v1.3.0) to calculate gene expression levels which measured as Fragment Per Kilobase per Million mapped fragments (FPKM) and identify differentially expressed genes with FDR < 0.05.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene
|
| |
|
| Submission date |
Apr 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Youqiong Ye |
| E-mail(s) |
[email protected]
|
| Phone |
+8613661565591
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
280 Chongqing south road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE80456 |
Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos [RNA-seq] |
| GSE80458 |
Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos |
|
| Relations |
| Reanalyzed by |
GSM3278908 |
| BioSample |
SAMN04870926 |
| SRA |
SRX1715666 |
