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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 17, 2019 |
| Title |
K562_sh-lncRNA-IIRX_3 |
| Sample type |
SRA |
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| Source name |
K562_sh-LncRNA-IIRX
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
sh-rna: sh-lncRNA-IIRX
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from three independent groups of K562 cells expressing shRNA targeting lncRNA-IIRX and control cells, using TRIzol reagent (Invitrogen, Carlsbad, CA).
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 4000 |
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| Description |
pSIH_up37_5_2_2_CGGAAT_L008
RPKM-pSIH.up37.5.2.2
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| Data processing |
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v0.32, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie 2 v2.1.0 with parameters default
Reads Per Kilo bases per Million reads (RPKM, Mortazavi et al., 2008) were calculated, and then analyzed using samtools v0.1.19 (Li et al., 2009).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.
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| Submission date |
Sep 22, 2018 |
| Last update date |
Apr 17, 2019 |
| Contact name |
Xuefei Wang |
| E-mail(s) |
wangxf09sk@126.com
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| Phone |
18810357854
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| Organization name |
nstitute of Microbiology, Chinese Academy of Sciences (CAS)
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| Lab |
1. CAS Key Laboratory of Pathogenic Microbiology and Immunology
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| Street address |
NO.1 West Beichen Road, Chaoyang District, Beijing 100101, China
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE120337 |
Genomic expression analysis of K562 cells expressing shRNA targeting lncRNA-IIRX and control cells |
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| Relations |
| BioSample |
SAMN10104746 |
| SRA |
SRX4729776 |
| 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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