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Sample GSM4274235 Query DataSets for GSM4274235
Status Public on Dec 29, 2020
Title BUR_U_1_1
Sample type SRA
 
Source name Bursa
Organism Drosophila melanogaster
Characteristics time relative to matng: Unmated
strain: LHM
age: 3-8 days old
sequencing run: 1
Extracted molecule total RNA
Extraction protocol Females were etherized (unmated, 6hrs, or 24hrs post-mating) and the female reproductive tract (FRT) removed in a drop of 1x PBS. The FRT was then microdissected into 6 discrete tissues. Tissues were rinsed in PBS and transferred directly to Trizol. Pooled tissue collections were homogenized with a pellet pestle and RNA was isolated using a phenol-chloroform extraction with phase-lock gels (ThermoFisher) and an overnight precipitation in isoproponal and 3M sodium acetate with 1.5ul glycogen (LifeTechnologies) at -18 C to maximize RNA recovery. The precipitation was followed by DNAse I (LifeTechnologies) treatment for 30 min at 37 C and a second RNA isolation. RNA was re-suspended in RNase-free H2O
RNA libraries were prepared for sequencing using standard protocols by Beijing Genomics Institute (BGI)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing sequenced reads were cleaned to remove adapter sequences and exclude reads with > 10% unknown bases of > 50% low-quality bases
sequenced reads were aligned to the D. melanogaster reference genome (r6.21) using hisat 2.1.0 with default settings plus the sam option to suppress reads that do not align or represent novel splice sites
read counts per million (CPM) were generated using StringTie
Genome_build: D. melanogaster reference genome (r6.21)
Supplementary_files_format_and_content: tab deliminated text file includes CPM value for each sample
 
Submission date Jan 15, 2020
Last update date Dec 29, 2020
Contact name Caitlin E McDonough
E-mail(s) mcdonouce@gmail.com
Phone 9176207629
Organization name Syracuse University
Department Syracuse University Biology Department
Street address 107 College Place, 114 Life Science Complex
City Syracuse NY
State/province NY
ZIP/Postal code 13210
Country USA
 
Platform ID GPL26560
Series (1)
GSE143759 Spatiotemporal female reproductive tract gene expression in Drosophila melanogaster  
Relations
BioSample SAMN13870087
SRA SRX7569526

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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