|
| Status |
Public on Nov 07, 2017 |
| Title |
EnhancerI_8hrE2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
EnhancerI, 8hr E2
|
| Organism |
Homo sapiens |
| Characteristics |
fusion: SID4x-dCas9-KRAB
guide rnas transfected: pool of 42 gRNAs targeting 10 ERBS
treatment: estradiol, 8 hr 10 nM E2
tissue: Ishikawa endometrial cancer
|
| Treatment protocol |
Cells were treated with E2 at ~72 hours post transfection.
|
| Growth protocol |
Stable lines were grown in estrogen-depleted media for 5-7 days prior to guide RNA transfection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated via direct lysis with Buffer RLT-Plus (Qiagen) with 1% beta-mercaptoethanol (Sigma).
100 ng of each sample was processed using KAPA Stranded mRNA-seq kit (KAPA Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads in fastq format were aligned to hg19 using HISAT2 (Kim et al., 2015) with the following parameters: --dta -t -p 10 --no-unal --rna-strandness R.
HTseq (Anders et al., 2015) was used to generate normalized counts for RefSeq genes.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files have normalized read counts for RefSeq genes for each Sample
|
| |
|
| Submission date |
Jun 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jay Gertz |
| E-mail(s) |
jay.gertz@hci.utah.edu
|
| Organization name |
University of Utah
|
| Street address |
2000 Circle of Hope Dr.
|
| City |
Salt Lake City |
| ZIP/Postal code |
84103 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE99641 |
Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers [RNA-Seq] |
| GSE99906 |
Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers |
|
| Relations |
| BioSample |
SAMN07190349 |
| SRA |
SRX2881514 |
