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| Status |
Public on Aug 20, 2018 |
| Title |
frt82_w_3 |
| Sample type |
SRA |
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| Source name |
3rd instar wing disc
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain/genotype: w11- 18(+);p{ ry+ hs-neor FRT}82D p{w+}90E/+
developmental stage: 3rd instar
tissue: wing disc
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| Treatment protocol |
third-instar larvae were harvested 24±2h before puparium formation
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| Growth protocol |
eggs laid in 4h cohorts were raised at 25°C on yeast-glucose medium supplemented with 20μg/ml tetracycline to minimize potential differences in microbiome between genotypes.
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| Extracted molecule |
total RNA |
| Extraction protocol |
from each genotype, ~50 wing discs were dissected into Trizol reagent (25 discs into 250μL) and frozen at -80°C. Following thawing and centrifugation (12000g 15 min 4°C), the aqueous phase was precipitated with an equal volume of isopropanol (10 min room temperature). The pellet was recovered by centrifugation (12000g 15 min 4°C), washed with RNAse-free 75% ethanol twice, and air dried (5-10 min room temperature) after removing the remaining ethanol with a filtered RNAse-free pipette tip. Samples were resuspended in RNAse-free water, analyzed by nanodrop spectroscopy and Bioanalyzer and satisfactory samples stored at -80°C
library was constructed by Beijing Genomics Institute. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The library is sequenced using Illumina HiSeqTM 2000
Then raw reads is subjected to quality control (QC)
After QC, raw reads are filtered into clean reads for alignment to the reference sequences.
Genome_build: dm6
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample; Excel files for different expression between wildtype (frt82_w) and two types of Rp+/- (M67_w and M95_w), as well as RpS3+/- Xrp1+/- (M2-73_M95)
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| Submission date |
Apr 09, 2018 |
| Last update date |
Feb 21, 2019 |
| Contact name |
Nicholas Baker |
| E-mail(s) |
[email protected]
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| Phone |
7184302854
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| Organization name |
albert einstein college of medicine
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| Department |
genetics
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| Street address |
1300 Morris Park Avenue
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| City |
bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE112864 |
RNA-seq analysis to assess transcriptional effects of Rp mutations in wing imaginal discs and their dependence on Xrp1 |
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| Relations |
| BioSample |
SAMN08897502 |
| SRA |
SRX3908181 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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