|
| Status |
Public on Dec 24, 2014 |
| Title |
S2 repB_1hr |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: hemocyte-like cell line S2
treatment: heat-killed Salmonella typhimurium stimulation
time: 1hr
|
| Treatment protocol |
Heat killed S. typhimurium was added to S2 cells at a final concentration of 107 cells/ml. S2 cells were harvested at 0, 30 minutes, 1 hour, and 4 hours after stimulation at 3 × 107 S2 cells each time point, formaldehyde crosslinked and digested with 40U/ml MNase.
|
| Growth protocol |
S2 cells were maintained at 28oC in Schneider's Drosophila medium (Invitrogen), supplemented with 10% heat inactivated fetal bovine serum (Life Technologies).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase-digested DNA samples were resolved on 2% agarose gel. DNA band containing mononucleosomal DNA (<=200bps) was excised and purified by the freeze-squeeze method.
Libraries of mononucleosomal DNA were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), starting with 30ng of mononucleosomal DNA for each reaction. The samples were end-prepared, adaptor-ligated and indexed (NEB #E7335S/L, NEB #E7500S/L) according to the manufacturer’s instructions, followed by purification with AMPure XP beads (Beckman Coulter, Inc. #A63881) without size selection. The quantity and quality of the library were checked with Qubit 2.0 Fluorometer (Life Sciences) and Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were quantified using KAPA Library Quantification (KK824). Resulting libraries were plated using the Illumina cBot and run on the Illumina HiSeq 2500 platform configured for 50 bp paired-end reads.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina adapters were clipped from the 3' ends of reads with cutadapt 1.7.
MNase-seq reads were aligned to the Drosophila reference genome UCSC.dm3 using bowtie2 2.1.0
Bed files correspond to inferred fragment coordinates based on concordant mate-pair alignments to the dm3 reference assembly
Genome_build: UCSC.dm3
Supplementary_files_format_and_content: bed files include genome-wide nucleosome positions for each sample
|
| |
|
| Submission date |
Dec 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonathan H Dennis |
| E-mail(s) |
dennis@bio.fsu.edu
|
| Organization name |
Florida State Unversity
|
| Department |
Biological Science
|
| Lab |
Jonathan Dennis lab
|
| Street address |
319 Stadium Dr
|
| City |
Tallahassee |
| State/province |
FL |
| ZIP/Postal code |
32306 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE64507 |
Drosophila melanogaster S2 cells nucleosome occupancy data after simulation by heat killed Salmonella typhimurium |
|
| Relations |
| BioSample |
SAMN03273150 |
| SRA |
SRX823997 |
| Named Annotation |
GSM1572835_STB1.bed.gz |
