 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 01, 2016 |
| Title |
control |
| Sample type |
SRA |
| |
|
| Source name |
human embryonic kidney
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
transfection: X-TremeGENE 9
hours after transfection: 48 hours
|
| Treatment protocol |
Cells were transfected with a total of 1 ug plasmid DNA using X-tremeGENE 9. Total RNA were extracted from the FACS-sorted BFP positive cells 48 hours after transfection
|
| Growth protocol |
HEK293T cells were cultured in DMEM medium, 10%FBS, 1%P/S, 1%GlutaMAX. 37 celsius degrees, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus Mini kit (QIAGEN)
After DNase I treatment, mRNA were isolated by magnetic beads with Oligo (dT). Mixed with the fragmentation buffer, mRNA were fragmented into short fragments. cDNA was synthesized using the mRNA fragments as templates, resolved with EB buffer for end reparation and ligated with adapters. After size selected and purified by agarose gel electrophoresis, cDNA with sizes about 240 bp were selected for PCR amplification (12 cycles) and library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Torrent Suite Software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, and short reads (length < 30nt) were filtered out. Then clean reads were mapped to the hg19 UCSC RefSeq using tmap 3.4.1 with parameters mapall -a 2 -n 8 -v -Y -u -o 1 stage1 map4.
Gene level expression was performed by transforming uniquely mapped transcript reads to TPM (transcript per million).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Nov 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yonglun Luo |
| E-mail(s) |
alun@biomed.au.dk
|
| Phone |
0045-22411944
|
| Organization name |
Aarhus University
|
| Street address |
Wilhelm Meyers Allé 4
|
| City |
aarhus |
| ZIP/Postal code |
8000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE74935 |
Inhibition of uPA expression by CRISPR-dCas9 DNA methyltransferases |
|
| Relations |
| BioSample |
SAMN04261752 |
| SRA |
SRX1427722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1937997_HEKpUC19.Gene.tpm.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
