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| Status |
Public on Nov 10, 2023 |
| Title |
eyeRNA_nocteRNAi2 |
| Sample type |
SRA |
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| Source name |
eye discs
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: eye discs
genotype: ey-GAL4, UAS-nocte-RNAi
treatment: flies maintained at 25oC, eye discs with mouth hooks were dissected from late L3 larvae.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted byTRizol following the product manual. For Ribo-seq, total RNA was digested with Mnase S7 and run using 15% TBE-urea gel, followed by cutting the 28 nt RNA fragments.
Library was constructed by standard Illumina protocol. Ribo-seq library was generated by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
For RNA-seq of polyA RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function. Bam files and bed files are used to get bedgraph and raw counts. Raw counts are normalized to get RNA expression levels.
For RNA-seq of total RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index. Sorted bam files are used to generate bigwig graph and get raw counts in CDS regions by Htseq. Raw counts are normalized to get RNA expression levels.
For Ribo-seq fastq files, adaptors are removed by fastx_clipper, ribosomal RNA sequences are removed by bowtie2. Following steps are the same to the analysis of RNA-seq of total RNA samples.
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| Submission date |
May 12, 2023 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Weidong Wang |
| E-mail(s) |
wangw@grc.nia.nih.gov
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| Phone |
4104548418
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| Organization name |
National Institute of Aging
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| Lab |
LGG
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| Street address |
251 Bayview Blvd BRC, Suite 100 Rm10B014
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platform ID |
GPL30203 |
| Series (1) |
| GSE232395 |
Study Nocte's functions in transcription and translation in Drosophila eye discs |
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| Relations |
| BioSample |
SAMN35061561 |
| SRA |
SRX20309582 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7329885_eyeRNA_nocteRNAi2.bedGraph.gz |
6.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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