|
| Status |
Public on Dec 29, 2015 |
| Title |
Mushroom body neuroblast replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mushroom body
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: neuroblast
age: 50hr after larva hatch
num_cells (number of cells in the sample): 101
ercc_mix (1 or 2): 1
ercc_5 (10^-5 dilution of ercc in ul): 1
|
| Growth protocol |
Newly hatched Fly larvae were first synchronized with maxiumum 2 hour age difference and then grew at 25C until dissection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
30 fly larvae brain tissues were dissected at defined ages, digested with a mixture of pronase(1mg/ml) and dispase (1mg/ml) for 30 min at 25C, washed, triturated and 10 GFP labeled cells were sorted with a robotic sorter and stored at -80C in XB buffer from PicoPure kit (life technologies, KIT0204). Total RNA from around 100 pooled cells was extracted using PicoPure kit.
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were assigned to genes using HTSeq v0.6.1p1 with parameter -s no -m intersection-nonempty and using iIllumina UCSC/dm3 annotation. FPKM for a gene was calculated by dividing assigned count by the sum of lengths of all exons belonging to the gene and then by total number of reads in million.
Genome_build: dm3
Supplementary_files_format_and_content: tab deliminated files include TPM values, raw count values
|
| |
|
| Submission date |
Jul 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ken Sugino |
| Organization name |
Janelia Research Campus
|
| Lab |
NeuroSeq
|
| Street address |
19700 Helix Dr
|
| City |
Ashburn |
| State/province |
VA |
| ZIP/Postal code |
20147 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE71104 |
Transcriptomes of lineage-specific Drosophila neuroblasts profiled via genetic targeting and robotic sorting |
|
| Relations |
| Reanalyzed by |
GSM3276048 |
| BioSample |
SAMN03890819 |
| SRA |
SRX1101047 |
