|
| Status |
Public on Jun 05, 2023 |
| Title |
AM285_C |
| Sample type |
SRA |
| |
|
| Source name |
Colorectal Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HCT116 cell line
treatment: ASO control
replicate: 2
molecule subtype: Nascent Strands (ssDNA converted to dsDNA)
|
| Treatment protocol |
ASO transfection with lipofectamine 2000
|
| Growth protocol |
HCT116 cells were grown in RPMI medium at 37ºC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Phenol:chlorophorm
Based on Blecher-Gonen et al. 2013
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Short Nascent Strand_ASO control_Replicate 2
|
| Data processing |
Quality control of sequenced reads was performed using FastQC (Babraham Institute) and MultiQC
Reads were aligned to the Homo sapiens genome (hg19 build) (Ensembl v75) using Bowtie2 (v.2.3.4.2)
Picard (v.2.18.17) (Broad Institute) was used to remove duplicate reads.
Peaks were called using MACS2 (v. 2.1.0.20151222) (threshold q=0.1) and EPIC2 (v. 0.0.40) (threshold FDR=0.1)
Bigwig files were generated with deepTools (v.3.2.0)
Assembly: hg19
Supplementary files format and content: bigWig files
Supplementary files format and content: peak bed files
Library strategy: SNSseq
|
| |
|
| Submission date |
Jun 23, 2022 |
| Last update date |
Jun 05, 2023 |
| Contact name |
Maite Huarte |
| E-mail(s) |
maitehuarte@unav.es
|
| Organization name |
CIMA
|
| Street address |
c/ Avd Pio XII, 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE173452 |
ORC1 binds to cis-transcribed RNAs for efficient activation of human origins |
| GSE206833 |
ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [SNSseq_ASO] |
|
| Relations |
| BioSample |
SAMN29270197 |
| SRA |
SRX15857347 |
