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| Status |
Public on Jul 27, 2019 |
| Title |
KIAA1429-rep1-RIP |
| Sample type |
SRA |
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| Source name |
HCC cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCCLM3
intervention: KIAA1429 RNA immunoprecipitation
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina) 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 |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using BOWTIE software (V2.1.0).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *-RIP.txt: Tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Jul 26, 2019 |
| Last update date |
Jul 27, 2019 |
| Contact name |
Tian Lan |
| E-mail(s) |
[email protected]
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| Organization name |
West China Hospital
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| Department |
Department of Liver Surgery & Liver Transplantation
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| Lab |
Laboratory of Liver Surgery
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| Street address |
No. 37 of Guoxue Lane
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE134978 |
Genome-wide identification of transcripts associated with KIAA1429 by RIP-seq |
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| Relations |
| BioSample |
SAMN12384691 |
| SRA |
SRX6602405 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3983047_KIAA1429-rep1-RIP.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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