|
| Status |
Public on Jul 26, 2021 |
| Title |
X1-800K_input |
| Sample type |
SRA |
| |
|
| Source name |
X1 cells, S2 cells
|
| Organisms |
Drosophila melanogaster; Schmidtea mediterranea |
| Characteristics |
cell type: S. mediterannea stem cells (X1 cells)
cell type: Drosophila S2 cells
|
| Growth protocol |
X1 planarian stem cells were isolated using a well-established protocol in the field in which animals were dissociated into a single cel suspension, stained with Hoechst 33342, then sorted by FACS; the X1 gate is set in comparison to the profile of Hoechst stained cells from lethally iradiated worms, in which no dividing stem cells remain.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
chromatin was solubilized to mononucleosomes with Micrococcal nuclease and histone-DNA particles were precipitated with antibody.
DNAseq libraries were made using an optimized protocol with reagents from the Illumina TruSeq RNA kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ files were aligned to dd_Smes_g4 using bowtie2 under default parameters.
Peaks were called with MACS2 under default parameters.
Genome_build: dd_Smes_g4
Supplementary_files_format_and_content: BED files representing reproducible peak locations
|
| |
|
| Submission date |
Jul 21, 2021 |
| Last update date |
Jul 26, 2021 |
| Contact name |
Elizabeth Duncan |
| E-mail(s) |
Elizabeth.duncan@uky.edu
|
| Organization name |
University of Kentucky
|
| Department |
Biology
|
| Street address |
675 Rose St
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40506 |
| Country |
USA |
| |
|
| Platform ID |
GPL30416 |
| Series (1) |
| GSE180591 |
Set1 targets gene with essential identity and tumor suppressing functions in planarian stem cells. Mnase-ChIP was used to validate a wide histone H3K4me3 peak width signature. |
|
| Relations |
| BioSample |
SAMN20343470 |
| SRA |
SRX11516353 |
