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Sample GSM8263656 Query DataSets for GSM8263656
Status Public on May 14, 2024
Title Drosophila testes, 0h PHS, total lysate, Replicate 1
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: 0 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 1
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
BioSample SAMN41381678
SRA SRX24534773

Supplementary file Size Download File type/resource
GSM8263656_hsTC_bamA_3A15_CS_positions_rmdp_3UTRfb_Sep2019_2_quantify_trim20_merge50.txt.gz 180.6 Kb (ftp)(http) TXT
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Raw data are available in SRA

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