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| Status |
Public on Oct 08, 2021 |
| Title |
SF3B1 H698D-mut strain2 rep3 |
| Sample type |
SRA |
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| Source name |
Sf3b1H698D_5d_adults
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain background: w1118
developmental stage: 5d_adults
genotype: Sf3b1H698D
tissue: Whole Body
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs from larvae were isolated by TRIzol (Ambion) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, cDNAs were reverse transcribed using RevertAid Reverse Transcriptase (Thermo) and amplified by Ex-Taq (TaKaRa).A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
D-2_3
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| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapped to dm6 whole genome using hisat2(v2.1.0) with defeault parameters. Reference genome and gene model annotation files were downloaded from FlyBase r6.16.
FeatureCounts(v1.6.3) was used to count the reads numbers mapped to each gene.
The abundance of each gene was calculated by stringtie(v2.0).
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include gene abundance values for each Sample .
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| Submission date |
Mar 28, 2021 |
| Last update date |
Oct 09, 2021 |
| Contact name |
Zhan Ding |
| E-mail(s) |
dingzhan@cemps.ac.cn
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| Organization name |
CAS Center for Excellence in Molecular Plant Science
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| Street address |
FengLin 300
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL23702 |
| Series (1) |
| GSE171002 |
Two oppositely-chargedsf3b1 mutations cause defective development, impaired immune response, and aberrant selection of intronic branch sites in Drosophila |
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| Relations |
| BioSample |
SAMN18521696 |
| SRA |
SRX10462707 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5215957_D_2_3.geneAbund.txt.gz |
424.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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