|
| Status |
Public on Oct 12, 2012 |
| Title |
6-8hr Midline Sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic CNS-midline cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: CNS midline
time-point: 6-8 hours After Egg Laying
genotype: w1118 ; 3.7sim-GAL4 ; UAS-mCD8.GFP
|
| Treatment protocol |
Staged embryos were dissociated into single cells. GFP-positive CNS-midline cells and GFP-negative non-midline cells were FACS sorted on an iCyt/Sony Reflection cell sorter.
|
| Growth protocol |
Embryos were harvested and aged at 25 degrees C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Minikit
Poly(A) mRNA was purified using the Poly(A) Purist Mag kit from Ambion and cDNA was generated using Invitrogen's SuperScript III Reverse Transcriptase. cDNA library prep followed the protocol from "Preparing Samples for Sequencing Genomic DNA/Chip-Seq v2.5" provided by the UNC High-Throughput Sequencing Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Alignments to Drosophila melanogaster genome build 5 were performed with Bowtie(v0.12.7) and TopHat(v1.3.1.OSX_x86_64) with the following non-default parameters: -i 20 -I 142000 -g 1 --solexa1.3-quals
Mapped reads were associated with D. melanogaster reference annontation r5.39 using Cufflinks(v1.0.3.OSX_x86_64) with a Mask file to eliminate mapping of reads to rRNA, tRNA, snRNA, snoRNA, snmRNA, and ribosomal protein genes
Genome_build: FlyBase Build 5
Supplementary_files_format_and_content: The genes.fpkm_tracking files were generated from Cufflinks.
|
| |
|
| Submission date |
Oct 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Crews |
| E-mail(s) |
steve_crews@unc.edu
|
| Organization name |
UNC Chapel Hill
|
| Department |
Biochemistry and Biophysics
|
| Street address |
133 N. Medical Dr
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE41510 |
Transcriptome analysis of Drosophila CNS midline cells reveals diverse peptidergic properties and a role for castor in neuronal differentiation |
|
| Relations |
| Reanalyzed by |
GSM3281664 |
| SRA |
SRX193615 |
| BioSample |
SAMN01761193 |
