|
| Status |
Public on Mar 03, 2015 |
| Title |
IMR90 MNase-seq |
| Sample type |
SRA |
| |
|
| Source name |
IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: IMR90 fetal lung fibroblasts
cell line: IMR90
|
| Growth protocol |
IMR90 were grown in DMEM medium, 10% FCS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin isolation was performed under native conditions. MNase treatment was performed with 5 U at 37°C for 30 min per 1 million cells and the mononucleosomal band was extracted from2% agarose gel.
Library preparation was performed using Illumina Genomic DNA Sample Preparation Guide starting with 2 μg of mononucleosomal fraction DNA.
Single End Genomic Adapter Oligo Mix was used and the library was amplified for 10 cycles.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the human genome (hg18) with bowtie (v0.12.8) using the parameters "-m 1 -best -strata" retaining only the uniquely mapping reads
The wig files represent single nucleotide genome coverages of the 5' ends of the reads.
Two wig files are provided, each containing either alignments from the plus or the minus strand
Genome_build: hg18
|
| |
|
| Submission date |
Mar 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dimos Gaidatzis |
| E-mail(s) |
d.gaidatzis@fmi.ch
|
| Organization name |
Friedrich Miescher Institute
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44985 |
Nucleosome positioning in the IMR90 cell line |
|
| Relations |
| SRA |
SRX247410 |
| BioSample |
SAMN01942139 |
