|
| Status |
Public on May 20, 2022 |
| Title |
RNA_wing_nub1_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
L3 imaginal disc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Wing imaginal disc
genotype: yw;nub[1]
|
| Growth protocol |
Drosophila larvae were raised on standard cornmeal food and kept at 25 degrees untill the wandering 3rd instar stage before harvesting of imaginal discs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.
RNA-seq library constructed using NEBnext Ultra II directional RNA library prep kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads taken from multiplexed Next-seq run were trimmed using the standard Basespace flowthrough (Bcl2Fastq) on pre-defined indices
RNA-seq raw count files generated by Rsubread FeatureCounts. GTF file; dm6.ensGene.gtf.gz, ignoreDup = FALSE, countMultiMappingReads = FALSE, GTF.featureType = "exon"
Bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq).
For ATAC Bowtie2 was used to map reads to Drosophila melanogaster genome (dm6) using default parameters with paired-end options (ATAC-seq).
For RNA-seq HISAT2 was used to map reads to the Drosophila melanogaster genome (dm6) with default parameters
Assembly: dm6
Supplementary files format and content: bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq) or RPKM (ChIP-seq)
|
| |
|
| Submission date |
May 17, 2022 |
| Last update date |
May 20, 2022 |
| Contact name |
Ryan Loker |
| E-mail(s) |
[email protected]
|
| Phone |
(212) 305-2111
|
| Organization name |
Columbia University
|
| Street address |
3227 Broadway
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE203208 |
Genomic characterization of nub[1] wing tissue |
|
| Relations |
| BioSample |
SAMN28495146 |
| SRA |
SRX15312096 |
