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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 23, 2019 |
| Title |
con_2 |
| Sample type |
SRA |
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| Source name |
human colon_con
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SW48 (Human colon adenocarcinoma cell line)
treatment: Control
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| Treatment protocol |
siRNA single treatment (siRNA on day1, day3 and day6, RNA extraction on day8), siDNMT1 combination (siDNMT1 on day1, day3 and day5, TEST siRNA on day7 and day8, RNA extraction on day11) and DAC combination (DAC 50nM on day1, day2 and day3, TEST siRNA on day1 and day2, RNA extraction on day5).
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| Growth protocol |
SW48 were cultured in L-15 medium containd,10% FBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA wasextracted using either Trizol reagent(Life Technologies) or RNeasy (Qiagen). Illumina TruSeq Stranded Total RNA with Ribo-zero Gold kits (RS-122-2301 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 9
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| Data processing |
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat 2.0.9 with these parameters: -p 28 --b2-fast -G /UCSC/hg19/Annotation/Genes/genes.gtf --segment-length 20
Fragments Per Kilobase of exon per Megabase of library size (FPKM) and DE genes were calculated using cuffdiff v 2.1.1 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Oct 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
yasuyuki okamoto |
| E-mail(s) |
tue81852@temple.edu
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| Organization name |
temple university
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| Department |
fels
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| Lab |
ISSA lab
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| Street address |
3307 N. Broad Street
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| City |
Philadelphia |
| State/province |
pa |
| ZIP/Postal code |
19140 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE62804 |
An siRNA screen identifies CHD4 as a target for epigenetic therapy |
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| Relations |
| BioSample |
SAMN03145860 |
| SRA |
SRX746119 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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