|
| Status |
Public on Sep 27, 2018 |
| Title |
NT2D1_PRMT6_CT_-RA_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
embryonal carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NT2/D1
cell type: pluripotent embryonal carcinoma cell line
genotype/variation: CRISPR/Cas9 control
atra: -
|
| Treatment protocol |
1 µM all-trans retinoic acid (ATRA) for 3 days.
|
| Growth protocol |
NT2/D1 cells were cultured in DMEMI supplemented with 10% FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using RNA-Mini-Kit (Seqlab, Göttingen, Germany).
Library preparation was done with Illumina TruSeq stranded mRNA Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
CRISPR/Cas9 control NT2/D1 cells.
Processed data file: PRMT6_CT_KO+-ATRA_raw_tagcounts.txt
|
| Data processing |
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using Tophat2.
Exon counts were aggregated for each gene to build a read count table using SubRead function featureCount.
Counts for each gene were normalized by DESeq2 according to instructions by authors.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: PRMT6_CT_KO+-ATRA_raw_tagcounts.txt: Tab-delimited text file includes raw counts for each Sample.
|
| |
|
| Submission date |
Dec 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Uta Maria Bauer |
| E-mail(s) |
bauer@imt.uni-marburg.de
|
| Organization name |
Philipps University Marburg
|
| Department |
Institute of Molecular Biology and Tumor Research
|
| Lab |
AG Bauer
|
| Street address |
Hans-Meerwein-Str. 2
|
| City |
Marburg |
| State/province |
Hessen |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (2) |
| GSE107611 |
Transcriptome analysis of PRMT6 knock-out in NT2/D1 cells |
| GSE107612 |
Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes |
|
| Relations |
| BioSample |
SAMN08120283 |
| SRA |
SRX3437621 |
