|
| Status |
Public on Jun 25, 2019 |
| Title |
H1_Sox2_std_(20171222_MM_HsSc_1208MPM091) |
| Sample type |
SRA |
| |
|
| Source name |
CUT&Run
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: Rb anti-Sox2 Abcam cat# ab92494
cell type: H1 (WA01) human embryonic stem cell line (WiCell)
Stage: 1 day
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT-and-RUN_Standard_protocol.rtf
PMID 25827087
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CUT&RUN for Sox2 in 1 day (H1) cells using Standard CUT&RUN
|
| Data processing |
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --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> (Supplementary file .bed).
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Jun 26, 2019 |
| 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) |
| GSE128499 |
Pioneer factor-nucleosome binding events during differentiation are motif-encoded |
|
| Relations |
| BioSample |
SAMN11163546 |
| SRA |
SRX5539836 |
