|
| Status |
Public on Nov 13, 2020 |
| Title |
K562_H3K4me2_dmf_p-w_(20201012_SH_Hs_K4me2E_dmf_1004) |
| Sample type |
SRA |
| |
|
| Source name |
CUT&TAG-direct
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: H3K4me2 Epicypher cat# 13-0027
cell type: K562 human immortalised myelogenous leukemia cell line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUTnTag-direct_v2_Protocols.io.pdf
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 |
CUTAC Post-wash for K4me2 20 min dmf in K562 cells at home
|
| 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 the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens 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 (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).
|
| |
|
| Submission date |
Nov 05, 2020 |
| Last update date |
Nov 13, 2020 |
| 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) |
| GSE158327 |
Efficient transcription-coupled chromatin accessibility mapping in situ |
|
| Relations |
| BioSample |
SAMN16675657 |
| SRA |
SRX9443949 |
