|
| Status |
Public on Feb 04, 2022 |
| Title |
ChrSeq_siLuc_R1 |
| Sample type |
SRA |
| |
|
| Source name |
ChrSeq_siLuc_R1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
antibody: /
sirna: Scramble siRNA
|
| Treatment protocol |
siRNAs were transfected for 72 hours according to Lipofectamine 2000 reagent protocol.
|
| Growth protocol |
HeLa cells were maintained in DMEM with 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were purified from the chromatin fraction. DNA were purified from chromatin IP products.
For Chromatin RNA-seq, libraries were prepared using Illumina's TruSeq Stranded Total RNA library Preparation Kit according to Illumina's instructions. For ChIP-seq and DRIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
Mapped reads were de-duplicated with Picard (ChIP-seq and DRIP-seq)
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples
|
| |
|
| Submission date |
Mar 13, 2020 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Michael Tellier |
| E-mail(s) |
mt477@leicester.ac.uk
|
| Organization name |
University of Leicester
|
| Department |
Department of Molecular and Cell Biology
|
| Lab |
Tellier Lab
|
| Street address |
Lancaster Road
|
| City |
Leicester |
| State/province |
Select State |
| ZIP/Postal code |
LE1 7HB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE146970 |
RNase H2, mutated in Aicardi‐Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation. |
|
| Relations |
| BioSample |
SAMN14376108 |
| SRA |
SRX7910823 |
