|
| Status |
Public on Aug 12, 2019 |
| Title |
NTC_K4-1 |
| Sample type |
SRA |
| |
|
| Source name |
HEL
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human erythroleukemia (HEL) cells
cell line: HEL
genotype variation: NTC
|
| Growth protocol |
Cells were cultured in RPMI+10% FBS at 37C 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was MNase digested in vivo and the fragments precipitated from the supernatant per the CUT&RUN protocol (PMID: 29651053)
Libraries were prepared for sequencing using standard Illumina protocols as recommended in the CUT&RUN protocol (PMID: 29651053)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
NTC CRISPR CUT&RUN sample
|
| Data processing |
Library strategy: CUT&RUN
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and employed a paired-end, 50 base read length (PE50) sequencing strategy.
Raw fastq files were aligned with Bowtie to genome (hg19) and spike in genome(sacCer3), spike in calibration was performed Picard was used to remove duplicate reads , aligned framents were extracted from bam file to a bed file, Bed file was used to call peaks following protocol described at https://github.com/Henikoff/Cut-and-Run/
Genome_build: hg19
Supplementary_files_format_and_content: called peaks are submitted as processed data file
|
| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Sonali Arora |
| E-mail(s) |
[email protected]
|
| Organization name |
FHCRC
|
| Street address |
1100 Fairview Ave N,
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE106124 |
N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis |
| GSE117314 |
N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis [CUT&RUN] |
|
| Relations |
| BioSample |
SAMN09689889 |
| SRA |
SRX4404708 |
