 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 15, 2024 |
| Title |
WT,day2,rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo,NC14
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Embryo,NC14
genotype: H2B-EGFP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryo was staged to proper NC13 to Nc14 before they were placed on 1.5mL microcentrifuge tube caps (3 embryos per sample). Embryos were macerated in 10ul TRIzol™ using sterile an 18 gauge needle. RNA was isolated using Chloroform and phasemaker tubes as described in Bogart, K. and Andrews, J.
RNA libraries were made using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's recommended protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
To quantify transcript abundances from RNA-seq data we used the pseudoaligner Kallisto. Reads were aligned to the Drosophila melanogaster BDGP6.28 cDNA reference using a pre-built kallisto index (Bray et al., 2016). Data was normalized by eliminating transcripts with no reads in more than half of the samples from each condition and then using EdgeR to perform the ‘Trimmed Mean of M-values’ method to correct for compositional differences between libraries. Clear differences between the WT and ZF5 transcript abundances were observed via Principal Component Analysis (Fig S3). To determine differentially expressed genes, the ‘voom’ method from the ‘Limma’ package in R was applied to the log-transformed counts per million (CPM) data. After fitting linear models to the transformed gene expression data using the lmFit function, we applied the empirical Bayes (eBayes) method to the model fits. Subsequently, we extracted the top DEGs from the eBayes-fitted models. We adjusted for multiple testing to control the false discovery rate using the Benjamini-Hochberg (BH) method. Genes were classified as differentially expressed if they had logFC greater than 1.5 and an adj. p-value less than 0.05.
Assembly: DM6
Supplementary files format and content: .csv files have gene names and counts per million
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
Jul 12, 2024 |
| Contact name |
Mustafa Mir |
| E-mail(s) |
MIRM@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Street address |
3501 Civic Center Boulevard, CTRB 9030
|
| City |
philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE263997 |
A fine kinetic balance of interactions directs transcription factor hubs to genes [RNA-Seq] |
| GSE264096 |
A fine kinetic balance of interactions directs transcription factor hubs to genes |
|
| Relations |
| BioSample |
SAMN40976786 |
| SRA |
SRX24269201 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8208539_H2B_GFPwt2_3_1.csv.gz |
123.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
