|
| Status |
Public on Sep 05, 2018 |
| Title |
nosGAL4>UAS-TKV |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Ovary
rna source: Total
strain/genotype: NosGAL4>UAS-TKV
|
| Treatment protocol |
Flies were fattened with yeast a day before dissection and kept at 25C.
|
| Growth protocol |
Crosses and control flies were grown at 25C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
ovaries were dissected in 1XPBS. After dissection, all the PBS was aspirated and 100 μl of Trizol reagent was added to the tissue. The tissue was homogenized. 900 μl of Trizol was added, mixed and incubated at RT for 3 minutes. After incubation, 200 μl of Chloroform was added to each sample and mixed vigorously and incubated at RT for 5 minutes. The samples were then centrifuged at 13,000 rpm for 20 minutes at 4C. The aqueous layer was then transferred to a new centrifuge tube. 2 volumes of 100% ethanol, 10% volume 3 M sodium acetate and 0.5 ul of glycol blue was added to the samples and incubated at -20C for 1 hour. The samples were then centrifuged at 13,000 rpm for 20 minutes at 4C. The pellet was then washed with 75% ethanol, air-dried and re-suspended in RNase free H2O. For efficient re-suspension of the isolated nucleic acid, the sample was incubated at 50C for 10 minutes. The concentration of the isolated RNA was determined using a Nanodrop. 10μg of nucleic acid was then taken and subjected to a DNase treatment using the TURBO DNA-free Kit by Life Technologies (AM1907). poly(A)+ RNA was isolated by double selection with poly-dT beads, using the Turbo DNase treated samples, which is then followed by first- and second-strand synthesis. Sequencing libraries were prepared using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit (Bioo Scientific). Samples were single-end sequenced on a NextSeq 500.
Bioo Scientific Manufactures protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment was performed with HISAT2 2.0.5.2 using spliced alignment
Bam files were sorted withSortSam by coordinate order 2.7.1.1
Raw counts were generated with featureCounts 1.4.6.p5
BigWig file was generated with bamCoverage 2.5.0
Genome_build: DMEL Release 6.01
Supplementary_files_format_and_content: BigWig file was generated with bamCoverage 2.5.0
|
| |
|
| Submission date |
Sep 04, 2018 |
| Last update date |
Sep 05, 2018 |
| Contact name |
Prashanth Rangan |
| E-mail(s) |
ranganlabualbany@gmail.com
|
| Phone |
5184423485
|
| Organization name |
RNA Institute
|
| Department |
Biological Sciences
|
| Lab |
Rangan Lab
|
| Street address |
1400 Washington
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12222 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE119457 |
Sequential regulation of maternal mRNAs through a conserved cis-acting element in their 3’UTRs [II] |
| GSE119458 |
Sequential regulation of maternal mRNAs through a conserved cis-acting element in their 3'UTRs |
|
| Relations |
| BioSample |
SAMN09953983 |
| SRA |
SRX4639461 |
