|
Status |
Public on Feb 11, 2022 |
Title |
SL_HsSc_g1K4me3 |
Sample type |
SRA |
|
|
Source name |
hiPSC WTC #11
|
Organism |
Homo sapiens |
Characteristics |
cell type: hiPSC WTC #11 antibody: anti-CTCF Millipore 07-729
|
Extracted molecule |
genomic DNA |
Extraction protocol |
PMID 29651053 PMID 25827087
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
AutoCUT&RUN
|
Data processing |
Library strategy: AutoCUT&RUN Genome_build: Masked UCSC dm6 1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We used bowtie 2.2.5 with options "--local --very-sensitive-local --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to masked UCSC dm6. 3. We extracted properly paired reads from the marked alignments to both genomes. 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to D.melanogaster) to create a normalized yeast track file (Supplementary file .bedgraph.gz). Genome_build: Genome_build: UCSC hg19
|
|
|
Submission date |
Jan 27, 2022 |
Last update date |
Feb 13, 2022 |
Contact name |
Hannele Ruohola-Baker |
E-mail(s) |
hannele@u.washington.edu
|
Organization name |
Institute for Stem Cell and Regenerative Medicine
|
Street address |
850 Republican Street
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98109 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (2) |
GSE195553 |
dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [AutoCUT&RUN] |
GSE195555 |
dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region |
|
Relations |
BioSample |
SAMN25336145 |
SRA |
SRX13948370 |