|
| Status |
Public on Mar 02, 2018 |
| Title |
RNA.CARM1-KO |
| Sample type |
SRA |
| |
|
| Source name |
A1847 cell line, CARM1 CRISPR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A1847
genotype/variation: CARM1 knockout
|
| Treatment protocol |
pLentiCRISPR-CARM1 was constructed by inserting the CARM1 guide RNA (gRNA; 5′-AGCACGGAAAATCTACGCGG-3′). pLentiCRISPR v2 (Addgene) was digested and dephosphorylated with BsmBI restriction enzyme (Fermentas) for 30 min at 37°C. The digested plasmid was run on a 1% agarose gel, cut out, and purified using the Wizard SV Gel and PCR Clean Up kit (Promega). The oligonucleotides were phosphorylated using T4 PNK (M0201S) with T4 Ligation Buffer (New England Biolabs, Inc.). Samples were annealed in a thermocycler at 37°C for 30 min and then at 95°C for 5 min and then were ramped down to 25°C at 5°C/min. Annealed oligonucleotides were diluted 1:200 in RNase/DNase-free water. Ligation of the annealed oligonucleotide and digested pLentiCRISPR v2 plasmid was performed using Quick Ligase (New England Biolabs, Inc.)
|
| Growth protocol |
A1847 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C supplied with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol (Invitrogen) and subsequently cleaned and DNase-treated using RNeasy columns (Qiagen).
Libraries for RNA-seq were prepared with ScriptSeq complete Gold kit (Epicentre) and subjected to a 75 bp paired-end sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq in CARM1 KO cells
|
| Data processing |
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
edgeR was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
[email protected]
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE95644 |
CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity [RNA-Seq] |
| GSE95645 |
CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity |
|
| Relations |
| BioSample |
SAMN06471151 |
| SRA |
SRX2610702 |
