|
| Status |
Public on Sep 14, 2022 |
| Title |
K562_K27_CUTnTag_indiv_(20190716_MM_Hs_MPM1069) |
| Sample type |
SRA |
| |
|
| Source name |
CUT&Tag
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: H3K27me3 Cell Signaling Technology CST9733 Lot 16; cell type: K562 human immortalised myelogenous leukemia cell line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CUT&Tag for H3K27me3 in K562 cells, individually profiled
|
| Data processing |
Genome_build: UCSC hg19
1. We used Bowtie2 2.4.1 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 hg19 Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from the alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19_fragments.bed.gz). 3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (137567484) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).
|
| |
|
| Submission date |
Jul 08, 2021 |
| Last update date |
Sep 17, 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 |
GPL16791 |
| Series (1) |
| GSE179756 |
Multifactorial chromatin regulatory landscapes at single cell resolution |
|
| Relations |
| BioSample |
SAMN20124766 |
| SRA |
SRX11384863 |
