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| Status |
Public on Feb 11, 2022 |
| Title |
EBdCas9-Dox |
| Sample type |
SRA |
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| Source name |
WTC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC WTC
construct: EBdCas9
chip antibody: H3K27me3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were dissociated using versene, washed once in cold PBS and counted. Approximately 6x10^6 cells were fixed and chromatin was PIXUL sonicated as described above. H3K27me3 (Active Motif Ab) Matrix-ChIP’ed DNA was purified using phenol-chloroform extraction and ChIP-seq libraries were prepared (Next Gen DNA Library Kit, Active Motif, Cat# 53216, 53264).
Libraries were sequenced on NextSeq2000 in single end run and approximately 45 million raw reads were obtained for each sample.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
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| Data processing |
ChIP-seq reads were trimmed and aligned to hg19 using bowtie2. Reads were normalized via RPKM and aggregate read signal for all coding genes was calculated in a 5k window centered at the TSS, using deepTools. Significance by first calculating average signal in 5k window for all TSS’, then comparing means across conditions via t-test.
Genome_build: Genome_build: UCSC hg19
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| Submission date |
Jan 27, 2022 |
| Last update date |
Feb 13, 2022 |
| Contact name |
Hannele Ruohola-Baker |
| E-mail(s) |
hannele@u.washington.edu
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| Organization name |
Institute for Stem Cell and Regenerative Medicine
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| Street address |
850 Republican Street
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE195552 |
dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [ChIP-seq] |
| GSE195555 |
dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region |
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| Relations |
| BioSample |
SAMN25336139 |
| SRA |
SRX13948759 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5840472_EBdCas9-Dox.bw |
114.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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