|
| Status |
Public on Sep 04, 2019 |
| Title |
K562_LTR2BgRNAs_RNA-3 |
| Sample type |
SRA |
| |
|
| Source name |
Chronic Myelogenous Leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
sgrna: LTR2B
|
| Treatment protocol |
OCI-AML3 and K562 cells were first transduced with lentiviral dCas9-KRAB-mCherry vector and then with a pool of four lentiviruses, each carrying a sgRNA (or an empty control) and a BFP reporter. After 48 hours, cells were sorted for mCherry and BFP expression.
|
| Growth protocol |
OCI-AML3 and K562 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 2mM glutamax and 1% penicillin/streptomycin at 37°C in 5% carbon dioxide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using AllPrep DNA/RNA mini kit.
RNA-Seq libraries were generated from 500-1000 ng of total RNA using the NEBNext rRNA depletion kit and NEBNext ultra II directional RNA library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
gene_expression_vsd.txt
|
| Data processing |
Adaptors and low-quality base calls were trimmed using trim_galore! v0.4.5 with default parameters.
Trimmed reads were mapped to hg38 using HISAT2 v2.0.5 with --no-softclip.
Raw read counts for each gene were generated in Seqmonk with the RNA-seq quantitation pipeline. Normalized gene expression values were calculated with the variance stabilizing transformation in DESeq2.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 200 bp bin size.
Genome_build: hg38
Supplementary_files_format_and_content: Biwig tracks; tab-delimited text file containing normalised gene expression values (log2) for each sample.
|
| |
|
| Submission date |
Sep 03, 2019 |
| Last update date |
Sep 04, 2019 |
| Contact name |
Miguel R Branco |
| E-mail(s) |
[email protected]
|
| Organization name |
Blizard Institute
|
| Street address |
4 Newark Street
|
| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE136763 |
Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia [RNA-Seq] |
| GSE136764 |
Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN12684159 |
| SRA |
SRX6793409 |
