|
| Status |
Public on Apr 12, 2021 |
| Title |
K27me3_H4DE_r2_(20190910_K27me3_H4DE_r2) |
| Sample type |
SRA |
| |
|
| Source name |
CUT&TAG
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: H3K27me3, Cell Signaling Technology, Cat# 9733; Lot# 8
cell type: hESC to Endoderm (Day 4, Rep 2)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
scCnT_protocol.pdf
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
scCUT&Tag (iCell8) for native nuclei from a directed differentiation time-coarse of H1 hESC to Endoderm
|
| Data processing |
Genome_build: UCSC HG38
A. iCell8 system: 1. We used a custom python script to demultiplex and annotate fastq reads in the following format: Antibody_CellType_Rep_Cell#, e.g K27me3_K562_r1_54. 2. 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 HG38 of Homo sapiens genomic sequence obtained from UCSC. 3. We extracted properly paired reads from Homo sapiens alignments to generate a fragment bed files <chr> <start> <stop> <barcode> <duplicateCount>. Custom software to analyse these files is available from https://github.com/Henikoff/scCUT-Tag. B. 10X system: Cell Ranger ATAC v1.1 from 10X company with default parameters was used to do the demultiplexing, alignment to HG38 and read quantification.
|
| |
|
| Submission date |
Sep 14, 2020 |
| Last update date |
Apr 13, 2021 |
| 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) |
| GSE157910 |
Single-cell analysis of chromatin silencing programs in development and tumor progression |
|
| Relations |
| BioSample |
SAMN16129341 |
| SRA |
SRX9120166 |
