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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 02, 2021 |
| Title |
S2R+ GFP-replicate3 |
| Sample type |
SRA |
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| Source name |
RNAs polyA enriched from Drosophila S2R+ cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: embryonic cells
overexpression: overexpressing nlsGFP
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted from four independent replicates from Drosophila S2R+ cells expressing GFPnls, myc-UbxWT, or myc-UbxN51A (Gal4-UAS, actin promoter) using Qiagen RNA extraction kit (RNeasy). RNA quality was assessed using BioAnalyzer 2100TM (Agilent Technologies).
Material handling and mRNA-Seq directional libraries were performed with the Deep-Sequencing facility in Heidelberg (Cell Networks), using the true-seq illumina standard protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA-Seq analysis was performed by using genome 6 (dm6). The quality of the RNA-Seq reads was quantified via FastQC. Trimming was performed with java script "Trimmomatic 0.36"(Bolger et al., 2014), for the removal of the adapter (TruSeq-SE sequencing adapter), with the following command line: java -jar /path_to_java_script/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 <file.txt> <outputfile.txt> ILLUMINACLIP:TruSeq-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The reads were aligned using STAR (genome generated: STAR --runThreadN 14 --runMode genomeGenerate --genomeFastaFiles Drosophila_melanogaster.BDGP6.dna.toplevel.fa --sjdbGTFfile Drosophila_melanogaster.BDGP6.86.gtf --genomeSAindexNbases 12; running STAR: STAR --runThreadN 14 --genomeDir /STAR/GenomeDir/ --readFilesIn /STAR/<file> --outSAMtype BAM Unsorted) (Dobin et al., 2013). Aligned reads were counted by HTSeq (htseq-count -f bam -r pos -m union -s no -t exon accepted_hits.bam Drosophila_melanogaster.BDGP6.86.gtf > count.txt) for further analysis in DESeq (Anders et al., 2015).
For the analysis in Junction-Seq the aligned reads were counted and the genome flattened with QoRTs by using the available java scripts (counting: java -jar /path/QoRTs.jar QC --singleEnded --minMAPQ 75 --nameSorted sorted.bam Drosophila_melanogaster.BDGP6.86.gtf rawCts/file; flattened: java -jar /path/QoRTs.jar makeFlatGff --stranded Drosophila_melanogaster.BDGP6.86.gtf annoFiles/JunctionSeq.flat.gff.gz) (Hartley and Mullikin, 2015). Differential expression analysis was performed with DESeq2 under standard conditions (Love et al., 2014). Different exon usage and the identification of splicing variants was identified by using the R tool Junction-Seq under standard conditions (Hartley and Mullikin, 2016). All data results were further processed in Excel and False Discovery Rate (FDR) was established at FDR 0.1.
Genome_build: Drosophila_melanogaster.BDGP6.86.gtf
Supplementary_files_format_and_content: Tables with raw gene counts for every gene and each sample
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| Submission date |
Apr 06, 2021 |
| Last update date |
Dec 02, 2021 |
| Contact name |
Julie Carnesecchi |
| E-mail(s) |
julie.carnesecchi@gmail.com
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| Organization name |
ENS Lyon
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| Department |
IGFL
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| Street address |
32, 34, avenue Tony Garnier
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| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE171547 |
The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II |
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| Relations |
| BioSample |
SAMN18631079 |
| SRA |
SRX10519536 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5226907_unsorted_GFP4_count.txt.gz |
68.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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