|
| Status |
Public on Jul 01, 2017 |
| Title |
RNA Kc GFP RNAi 9 days [Sample 110] |
| Sample type |
SRA |
| |
|
| Source name |
Kc cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Kc
gender: female
treatment: GFP RNAi 9 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from 4 million cells using RNeasy mini columns (Qiagen) and 2.5 μg of RNA was used for polyA selection. Libraries were prepared using New England Biolabs reagents according to protocols (E7490, E6150, E7525, E6111, E7442, E7335 and (Peleg et al., 2016)).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
PolyA RNA
|
| Data processing |
RNA-seq alignment was performed using Tophat2 (2.0.5) against the reference genome (BDGP 5.74). Bedgraph files were generated using genomeCoverageBed (Bedtools) with –split parameter.
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.
|
| |
|
| Submission date |
Jan 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Schauer |
| E-mail(s) |
[email protected]
|
| Organization name |
Helmholtz Zentrum München
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Street address |
Feodor-Lynen-Straße 21
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19951 |
| Series (1) |
| GSE94115 |
The Drosophila Dosage Compensation Complex activates target genes via chromosome looping within the active compartment |
|
| Relations |
| Reanalyzed by |
GSM3282756 |
| BioSample |
SAMN06274332 |
| SRA |
SRX2520656 |
