|
| Status |
Public on Oct 18, 2010 |
| Title |
Nuc_untreated_1 |
| Sample type |
SRA |
| |
|
| Source name |
Nuc_untreated
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
|
| Treatment protocol |
For RNAi experiments, S2 cells (DGRC) were harvested 96 hours after addition of dsRNA targeting NELF (NELF-B and NELF-E subunits; NELF-depleted) or β-galactosidase (Mock-treated) as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73.
|
| Growth protocol |
S2(DGRC) cells were grown in M3 media (Sigma) supplemented with bacto-peptone and yeast extract + 10% FBS (GIBCO). S2 cells(Invitrogen) were grown in Schneider's media (GIBCO) supplemented with 10% FBS (GIBCO).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase-digested chromatin from untreated, Mock-treated and NELF-depleted S2 cells was prepared as described in (Gilchrist et. al.,Genes Dev. 2008 Jul 15;22(14):1921-33) except that 200 µl chromatin was digested with 20 units MNase (Worthington) for 45 minutes at 25 degrees C. Following gel purification, mono-nucleosome sized fragments (100-200 bp) were subjected to paired-end sequencing using the Illumina paired-end protocol.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
MNase-digested_chromatin_mononucleosomal_fragments
|
| Data processing |
Paired-end reads were mapped with Bowtie 0.12.3 to the D. melanogaster, Flybase, r5.22 index (Langmead et al., 2009). Biological replicates of untreated samples were in good agreement and were combined, resulting in a data set of 28,494,410 unique read pairs identifying both ends of fragments >=120 bp and =<180 bp in length.
|
| |
|
| Submission date |
Jun 03, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Karen Adelman |
| E-mail(s) |
karen_adelman@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9061 |
| Series (2) |
| GSE20472 |
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation |
| GSE22119 |
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: MNase-seq data |
|
| Relations |
| SRA |
SRX021645 |
| SRA |
SRX021646 |
| SRA |
SRX021647 |
| BioSample |
SAMN00014493 |
