|
| Status |
Public on Sep 27, 2022 |
| Title |
Dm_NP40_MNase_1_(20210920_TB_Dm_4xMnase_NEW_TM2_day1) |
| Sample type |
SRA |
| |
|
| Source name |
MNase-seq
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase-extraction_TB2021.pdf
Library_Preparation_TB2021.pdf
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MNase-seq of Drosophila NP40 day 1
|
| Data processing |
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to the reference sequence for Drosophila melanogaster dm6. 2. We extracted properly paired reads from the alignments with bedtools bamtobed to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz). 3. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).
|
| |
|
| Submission date |
Sep 02, 2022 |
| Last update date |
Sep 29, 2022 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE193224 |
A giant virus genome is densely packaged by stable nucleosomes |
|
| Relations |
| BioSample |
SAMN30648533 |
| SRA |
SRX17408762 |
