|
| Status |
Public on Feb 11, 2022 |
| Title |
JS_HsSc_0927_JFS540 |
| 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 |
SAMN25336144 |
| SRA |
SRX13948371 |
