|
| Status |
Public on Jul 15, 2021 |
| Title |
PRO-seq_del-cIDR_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cultured THP-1 cells
|
| Treatment protocol |
Media with 100 ng/ml of doxycycline was added
|
| Growth protocol |
For THP-1 cell transduction, 1 × 106 THP-1 cells were transduced with 500 μl of 30-fold concentrated lentivirus through spin-inoculation at 25°C at 2200 rpm for 2 hours each for 3 times with 24 hours interval, and were cultured with 500 μg/ml of G418 (Invivogen) for selection for 12-14 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For Chip-seq, genomic DNA were pulled down by antibodies. For RNA-seq, RNA was extracted with Qiagen miRNA-ease RNA extraction kit. HICHIP DNA was collected with Arima HICHIP kit.
For ChIP-seq and HICHIP, library preparation using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. For RNA-seq, NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used for library prepapration.
Library quality was assessed by Tapstation and Qubit concentration measurement.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
library strategy: Pro-seq
RNA-seq reads were aligned to the human genome assembly GRCH38/hg38 or mouse genome assembly GRCm38/mm10 using STAR. RNA-seq counts were annotated using RSEM. Differentially expressed genes were calculated using DESeq2.
ChIP-seq and PRO-seq sequence reads were aligned to the human genome assembly GRCH38/hg38 using BWA. Sam files were converted into bam files using Samtools. MACS2 was used to call peaks under the FDR threshold of 0.01.
H3K4me3/H3K27ac HiChIP data were performed with MAPS.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Peak file, loop bedpe or gene count
|
| |
|
| Submission date |
Jun 13, 2021 |
| Last update date |
Jul 15, 2021 |
| Contact name |
Bi Shi |
| E-mail(s) |
bs6yk@virginia.edu
|
| Phone |
2056433665
|
| Organization name |
University of Virginia
|
| Department |
Department of Biochemistry and Molecular Genetics
|
| Lab |
Jiang Lab
|
| Street address |
1340 JPA Pinn Hall Room 6017
|
| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE149420 |
UTX condensation underlies its tumor suppressive activity |
|
| Relations |
| BioSample |
SAMN19692548 |
| SRA |
SRX11136853 |
