|
| Status |
Public on Feb 11, 2022 |
| Title |
EBdCas9+dox_1 |
| Sample type |
SRA |
| |
|
| Source name |
EBdCAS9-WTC-11
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: hiPSCS
treatment: dox
|
| Growth protocol |
cells were grown in mTeSR1 stem cell media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol (Life Technologies) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Reads were aligned using Hisat2(Kim et al., 2019) version 2.1.0, to version hg38 of the human genome with EBdCas9 sequence added.
Differentially expressed genes were identified with DESeq2
RNA-seq read counts were generated with featureCounts using Ensembl GRCH38 gene annotations
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited file of gene-level transcript per million (TPM) for each sample.
|
| |
|
| Submission date |
Sep 27, 2021 |
| Last update date |
Feb 11, 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 |
GPL30173 |
| Series (2) |
| GSE155022 |
dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [bulk RNA-seq] |
| GSE195555 |
dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region |
|
| Relations |
| BioSample |
SAMN21854787 |
| SRA |
SRX12369241 |
