|
| Status |
Public on Mar 21, 2018 |
| Title |
HCT116-siCse1l-RNA.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
siCse1l treated HCT116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
parental cell line: HCT116 cell line
cell line: HCT116-siCse1l
cell type: somatic cell line
genotype/variation: siCse1l treated HCT116 cells
tissue: colon cancer
developmental stage: adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
According to standard protocols provided by Illumina Kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Basecalls performed by BGI, Shenzhen.
Data were filtered using samtools to remove potential PCR duplicates
MeDIP sequencing reads were mapped to the Human genome (hg19) using Bowtie2.
Sequencing qualities were evaluated with FASTQC software and then the reads were aligned to hg19 genome sequences with a maximum of 2 mismatches allowed. Only the uniquely mapped reads were kept, and duplicate reads were removed. Mapped reads were extended to the average fragment sizes. Genome profile files were generated with IGV tools and linearly normalized to the same depth of 10 million reads.
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: hg19
Supplementary_files_format_and_content: The transcription levels (RPKM) were quantified with Cufflinks (v2.0.2) software. Bigwig files were generated with IGV tools followed by UCSC utilities.
|
| |
|
| Submission date |
Mar 20, 2018 |
| Last update date |
Mar 21, 2018 |
| Contact name |
Zhuqiang Zhang |
| E-mail(s) |
zhangzhuqiang@ibp.ac.cn
|
| Organization name |
Institute of Biophysics, CAS
|
| Street address |
15 Datun Road, Chaoyang District.
|
| City |
Beijing |
| State/province |
--- |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE96852 |
The roles of CSE1L in epigenetic silencing |
|
| Relations |
| BioSample |
SAMN08742983 |
| SRA |
SRX3823831 |
