|
| Status |
Public on Jul 17, 2022 |
| Title |
K562_Ser5_CUTnTag_comb_(190716_MM_Hs_MPM1074Ser5) |
| Sample type |
SRA |
| |
|
| Source name |
CUT&Tag
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: PolIIS5P Abcam ab5408 Lot GR3264297-2
cell type: K562 human immortalised myelogenous leukemia cell line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
bench-top-cut-amp-tag-bcuhiwt6.pdf
PMID 25827087
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PolIIS5P-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled
|
| Data processing |
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (hg19). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments. 3. We used bedtools genomecov to make a normalized count bedgraph 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. 4. We used Kent_tools bedGraphToBigWig to convert the bedgraph file to bigwig format (Supplementary file .bw).
|
| |
|
| Submission date |
Jul 14, 2022 |
| Last update date |
Nov 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 |
GPL16791 |
| Series (1) |
| GSE179756 |
Multifactorial chromatin regulatory landscapes at single cell resolution |
|
| Relations |
| BioSample |
SAMN29758525 |
| SRA |
SRX17595764 |
| SRA |
SRX16249448 |
