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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 12, 2018 |
| Title |
Brd7oe_DGE |
| Sample type |
SRA |
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| Source name |
embryonic kidney cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human embryonic kidney cell line transformed with adenovirus 5 DNA
tissue: kidney
genotype: BRD7 overexpression
cell line: HEK293
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| Treatment protocol |
Overexpression of BRD7 gene
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| Growth protocol |
HEK293 cells were grown in DMEM media containing 10% FBS
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was used for mRNA purification using oligo-dT magnetic beads adsorption, and then oligo-dT was used to guide reverse transcription to synthesize double-stranded cDNA.The generation of 5' ends of tags was recognized by endonuclease NlaIII, which recognizes and cuts off the CATG sites on cDNA.Then, cDNA fragments with 3' ends were purified by magnetic beads precipitation, and Illumina adapter 1 was added to their 5' ends. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, the 21 bp unique tags with adaptor 1 were purified and ligated to the adaptor 2 to form a cDNA tag library. These adapter-ligated cDNA tags were enriched after 15 cycles of linear PCR amplification. The resulting fragments were purified by PAGE gel electrophoresis. The tag library was then verified using Agilent 2100 and ABI StepOnePlus Real-Time PCR System, and sequenced using the Illumina HiSeq 2000 system according to the manufacturer’s protocols.
Single read - Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw sequences were transformed into clean tags by data-processing steps using bio-perl scripts, then about 0.22 and 0.24 million non-redundant tags with high qualities were contained in treated and control groups, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: Each txt file contains a table with data matrix seperated by tabs. The table header descriptions are: Tag (tag sequence), CopyNumber (copy number of tags) and TPM (Transcript Per Million)
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| Submission date |
Feb 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xiong |
| E-mail(s) |
xiongwei@csu.edu.cn
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| Organization name |
Central South University
|
| Department |
Cancer Research Institute
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| Street address |
110 Xiangya Road
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410078 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE65975 |
Gene expression profiling of HEK293 in control and BRD7 overexpression cells (DGE) |
| GSE65981 |
BRD7 overexpression cells |
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| Relations |
| BioSample |
SAMN03351751 |
| SRA |
SRX883304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1611873_HEK293_BRD7oe_TagCopyNumber.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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