|
| Status |
Public on Sep 17, 2016 |
| Title |
lacz 2 for mlf KD |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila S2 cells, lacZ KD
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
genotype/variation: lacZ KD
|
| Treatment protocol |
Drosophila S2 cells were grown in Schneider's medium supplemented with 10% fetal bovine serum to a density of 3-6 x10^6 cells/ml. Cells were diluted to 1x10^6 cells/ml in serum-free media and incubated with 10 μg dsRNA per 1 x10^6 cells for 45 min at 25°C. An equal volume of Schneider's media containing 10% serum was added to the cells and the cells were grown for 4 days at 25°C before collection for ChIP, RNA, and/or protein isolation. dsRNA against lacZ was used as a control for all RNAi experiments.
|
| Growth protocol |
Drosophila S2 cells were grown in Schneider's medium supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from S2 cells treated with either dsRNA against lacZ, mlf, bag2, or dnaj-1 using TRIzol (Invitrogen). Two separate biological experiments were performed for each RNA-seq analysis.
RNA-seq libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
lacz2_mlf
PolyA RNA
|
| Data processing |
Base-calling and bcl to fastq generation was done with CASAVA 1.8.2 from Illumina.
RNA-seq was aligned to genome dm3 from UCSC using tophat 2.0.10 with arguments --solexa-quals --segment-mismatches 1 -x 1 -g 1 --no-coverage-search. ChIP-seq was aligned to dm3 using bowtie2 2.1.0 with -k 1.
bigWig tracks were generated in R 3.0.2 by dividing by the total number of alignments and multiplying by 1e6 (rpm).
Peaks were called using macs2 (2.0.10.20120913).
Differentially expressed genes were called with edgeR 3.4.2.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: bigWig tracks with rpm-normalized coverages.
|
| |
|
| Submission date |
Sep 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE87022 |
Myeloid Leukemia Factor acts in a chaperone complex to regulate transcription factor stability and gene expression |
|
| Relations |
| Reanalyzed by |
GSM3282016 |
| BioSample |
SAMN05784494 |
| SRA |
SRX2172432 |
