|
| Status |
Public on Sep 14, 2022 |
| Title |
K562_K27_MulTI_seq_ICELL8_(20210524_MM_Hs_MPM2244K27) |
| Sample type |
SRA |
| |
|
| Source name |
MulTI-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 |
MulTI-Tag was carried out as follows: Nuclei were incubated with pATn5-i5 adapter-primary antibody conjugate complexes and tagmented sequentially, then secondary antibody-pATn5-i7 adapter complexes were bound and tagmented. Tagmented samples were resuspended in 10 mM TAPS with 0.1% SDS, incubated at 58 degrees C for 1 hour, then SDS was neutralized by adding a final concentration of 0.3% Triton X-100. Samples proceeded directly to amplification of tagmented DNA inserts with barcoded primers. See also PMID 32913232 .
MulTI-Tag was carried out using pA-Tn5-adapter-antibody conjugate complexes to integrate barcoded adapters via tagmentation directly to DNA for each antibody target on both sides of the insert, so that the DNA that is released is already a barcoded library.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8
|
| Data processing |
Genome_build: UCSC hg19
A. Bulk MulTI-Tag: 1. We used Bowtie2 2.4.2 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 fragment bed file <chr> <start> <stop>, then used bedtools genomecov 2.28.0 to generate a track in bigwig format (Supplementary file). B. iCell8 system: We used a custom python script to demultiplex and annotate fastq reads, then used custom software to analyse the single cell data. The custom software is available from https://github.com/mpmeers/MeersEtAl_MulTI-Tag.
|
| |
|
| 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 |
SAMN20124814 |
| SRA |
SRX11384887 |
