|
| Status |
Public on May 10, 2020 |
| Title |
BAP170_RNAseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 Cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
dsrna: BAP170
|
| Treatment protocol |
Growing S2 cells were diluted to 10e6 cells/mL in serum free media containing dsRNA complementary to the target transcript at final concentration 10 µg/mL. After 45 min at 25 °C, serum-containing media was added to a final serum concentration of 10%. After 2.5 days, cells were passaged 1:2 and more ds RNA was added to maintain the concentration. After a total of 5 days, flasks were harvested and pooled. Two independent knockdown replicates were performed for each target.
|
| Growth protocol |
Drosophila S2 cells were maintained in M3+BPYE medium supplemented with 10% FBS at 25 °C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For 3'RNA-seq, we counted and aliquoted 10e6 cells and added a fixed amount of ERCC polyadenylated spike-in RNA. We then isolated total RNA using TRIzol, followed by ethanol precipitation. RNA was removed using RNase-free DNase I.
Libraries were constructed from 325 ng total RNA using the QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen) with the UMI add-on kit per manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
5R
processed data file: BAP170_RNAseq_pooled_normalized_fwd.bw
processed data file: BAP170_RNAseq_pooled_normalized_rev.bw
|
| Data processing |
Reads were trimmed of adapter and polyA sequences and UMIs were extracted using fastp v0.20.0.
Reads were aligned to a combined dm6/ERCC genome using STAR v2.7.0f_0328.
Alignments were PCR-deduplicated using umi_tools dedup v1.0.0.
bigWig strand-specific coverage tracks were generated from the 5' ends of alignments (so each read is only counted once in the signal tracks) using deepTools bamCoverage v3.1.3.
Genome_build: dm6
Supplementary_files_format_and_content: For each sample, there are strand-specific raw signal bigWig tracks of read 5' end positions. There are also replicate-pooled, spike-in normalized bigWig coverage tracks of read 5' end positions.
|
| |
|
| Submission date |
Apr 24, 2020 |
| Last update date |
May 10, 2020 |
| Contact name |
Julius Judd |
| E-mail(s) |
[email protected]
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
John Lis
|
| Street address |
417 Biotechnology Bldg; 215 Tower Road
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE149337 |
Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription [RNA-seq] |
| GSE149339 |
Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription |
|
| Relations |
| BioSample |
SAMN14693011 |
| SRA |
SRX8174045 |
