|
| Status |
Public on Jul 22, 2024 |
| Title |
BamGal4_2 |
| Sample type |
SRA |
| |
|
| Source name |
Testes
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Testes
genotype: bamGal4
|
| Treatment protocol |
150 pairs of testes per sample were dissected in PBS in a glass cyclops dish in batches of 50 pairs. Testes were transferred to a 1.7 ml tube with PBS using forceps. PBS was removed and the sample snap-frozen in liquid nitrogen. Samples were kept at −80°C until the next step.
|
| Growth protocol |
Crosses were maintained for 3 days at 25C, the adult flies removed and the progeny moved to 29C until dissection time.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was extracted using the kit: RNeasy Plus Mini Kit from QIAGEN
Library was constructed using the kit: NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760S) using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490S).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters and low-quality bases were trimmed with trimGalore: trim_galore –quality 20 –stringency 1 –length 30 –paired_end –clip_R1 3 $Input1 $Input2 –output_dir trim_PE/
Reads were mapped to the Drosophila melanogaster genome build dm6 using STAR. Reads that fell within gene regions were counted with STAR using Ensembl annotation BDGP6.28. star_pass1: STAR –runThreadN 4 –runMode alignReads –genomeDir $star_index –alignSJoverhangMin 10 –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –readFilesIn $Input1_trimmed $Input2_trimmed –outFileNamePrefix $pass1_prefix –outSAMtype None. star_pass2: STAR –runThreadN 4 –runMode alignReads –quantMode GeneCounts –genomeDir $star_index –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –sjdbFileChr- StartEnd $junction –readFilesIn $Input1_trimmed $Input2_trimmed –out- SAMtype BAM SortedByCoordinate –limitBAMsortRAM 10000000000 –outFileNamePrefix $pass2_prefix.
Samtools was used to create .bw files for visualization: bamCoverage -b $Input -o $Output –binSize 1 –normalizeUsing CPM -p 4
Assembly: Ensembl annotation BDGP6.28
Supplementary files format and content: STAR output: ReadsPerGene
Supplementary files format and content: bamCoverage output: bw fliles for visualization
|
| |
|
| Submission date |
Jul 18, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Lorenzo Gallicchio |
| E-mail(s) |
lgallicc@stanford.edu, gallicchiolorenzo@gmail.com
|
| Organization name |
Stanford University
|
| Department |
developmental Biology
|
| Lab |
Fuller
|
| Street address |
Campus Drive W
|
| City |
Stanford |
| State/province |
california |
| ZIP/Postal code |
94033 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE272581 |
A developmental mechanism to Regulate Alternative Polyadenylation in an Adult Stem Cell Lineage [RNA-seq] |
|
| Relations |
| BioSample |
SAMN42589601 |
| SRA |
SRX25379913 |
