|
| Status |
Public on May 14, 2024 |
| Title |
Drosophila testes, 48h PHS, Polysome fraction '4+ ribosomes', Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila testes
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Drosophila testes
genotype: bam-/-;hsBam
treatment: 30 min 37C heat shock
time: 48 hours
|
| Treatment protocol |
Pupae were heat shocked by placing bottles in 37C water bath for 30 mins and returned to 25C incubator
|
| Growth protocol |
Progeny of fly crosses were grown at 22C in bottles containing standard molasses media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For Polysome profiling, RNA was isolated by acid phenol-chloroform extraction and fractions were combined based on the absorbance profiles at A260 nm to create 6 groups: free, 40S, 60S, 80S, 2-3 ribosomes and 4+ ribosomes
RNA libraries for RNA-seq were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
biological replicate 2
|
| Data processing |
Sequence reads were mapped to dm6 using BOWTIE version 0.12.8 with a value of e = 5000 to allow for expected mismatches in the poly-A tail not encoded in the genome
Custom perl script written to identify sequencing reads that contain polyA sequences that were not genomically encoded
Reads within annotated 3'UTRs (with 500bp extension) were assigned to the nearest upstream CDS end as defined by Flybase
Assembly: dm6
Supplementary files format and content: tab-delimited text files containing in column: 1) location of CDS end, 2) gene symbol, 3) associated cleavage site location and count (location and count separated by *, and multiple cleavage sites are separate by |)
|
| |
|
| Submission date |
May 13, 2024 |
| Last update date |
May 14, 2024 |
| Contact name |
Cameron W Berry |
| Organization name |
Stanford University
|
| Department |
Developmental Biology
|
| Lab |
Margaret Fuller
|
| Street address |
279 W. Campus Drive, B300
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE267303 |
Developmentally regulated alternate 3’ end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage |
|
| Relations |
| BioSample |
SAMN41381637 |
| SRA |
SRX24534814 |
