|
| Status |
Public on Jul 14, 2022 |
| Title |
beaf_k_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 cells
treatment: dsRNA to BEAF-32
|
| Treatment protocol |
Cells were diluted to 106 ml−1 and 4 μg of dsRNA per 1ml of cells were added. After 2 days the cells were diluted again to 106 ml−1 and 8 μg of dsRNA per 1ml of cells were added. After 2 days, the cells were washed twice with PBS, collected, and used for downstream experiments
|
| Growth protocol |
S2 cells were grown in Schneider’s Drosophila medium supplemented with 10% Fetal Bovine Serum and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
3' RNA-seq library generation was performed based on a previous protocol ( Klein-Brill, A., Joseph-Strauss, D., Appleboim, A. & Friedman, N. Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex. Cell Rep. (2019). doi:10.1016/j.celrep.2018.12.020). In brief, 100ng from each sample was incubated with oligo-dT reverse transcription (RT) primers containing 7bp barcode and 8bp UMI (Unique Molecular Identifier) at 72°C for 3 minutes and moved directly to ice. This was followed by a Reverse transcription reaction (SmartScribe kit Clontech) for 1 hour at 42°C and 70°C for 15 minutes. Next, samples were pooled and purified using SPRI beads X1.2 (Agencourt AMPure XP, Beckman Coulter). The pooled barcoded samples were then tagmented using Tn5 transposase (loaded with oligos Tn5MEDS-A) for 8 min at 55°C Followed by the addition of 0.2% SDS to strip off the Tn5 and SPRI X2 purification was performed. Finally, a PCR was performed with primers containing NGS sequences (KAPA HiFi HotStart ReadyMix, Kapa Biosystems, 12 cycles) and the library was cleaned using 0.8x SPRI beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq reads were aligned by STAR to the full genome sequences of Drosophila Melanogaster (UCSC version dm3)
Reads were counted per annotated gene using ESET (End Sequencing analysis Toolkit)
Genome_build: dm3
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
Jul 14, 2022 |
| Contact name |
Neta Herman |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Hebrew University Of Jerusalem, Migal
|
| Department |
Gentics, Nutrition
|
| Lab |
Shagiv Shifman; Opatovsky Itai
|
| Street address |
Kiryat Shemona
|
| City |
Jerusalem, Kiryat Shemona |
| ZIP/Postal code |
1101202 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE169413 |
The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_S2] |
| GSE169415 |
The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes |
|
| Relations |
| BioSample |
SAMN18437789 |
| SRA |
SRX10417993 |
