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| Status |
Public on Feb 15, 2013 |
| Title |
HeLa siALKB5 RNASeq |
| Sample type |
SRA |
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| Source name |
HeLa cells
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| Organism |
Homo sapiens |
| Characteristics |
passages: 10-15
cell line: HeLa
treatment: siALKB5
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
knock down ALKBH5
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| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 and mm9 whole genome using tophat with -n 2 -g 1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff
Genome_build: hg19,mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Aug 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
zhike lu |
| E-mail(s) |
zhikelu@gmail.com
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| Organization name |
University of Chicago
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| Department |
department of chemistry
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| Street address |
5801 South Ellis Avenue
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE40132 |
ALKBH5 is a New Mammalian RNA Demethylase |
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| Relations |
| SRA |
SRX176914 |
| BioSample |
SAMN01113365 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM986110_HeLa.ALKBH5.gene.txt.gz |
658.7 Kb |
(ftp)(http) |
TXT |
| GSM986110_HeLa.ALKBH5.isoform.txt.gz |
769.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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