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Sample GSM1937997 Query DataSets for GSM1937997
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
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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