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| Status |
Public on Jun 22, 2019 |
| Title |
Ctrl siRNA2 |
| Sample type |
SRA |
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| Source name |
Ctrl siRNA2
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human hepatic stellate cell
cell line: LX-2
sirna: sicontrol
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| Extracted molecule |
total RNA |
| Extraction protocol |
LX2 cells were transfected with siControl or siLIX1L, and subsequently cultured for 48h. The total RNA was harvested using Trizol reagent.
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 |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al. 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: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Jun 21, 2019 |
| Last update date |
Jun 23, 2019 |
| Contact name |
xiaoyun zhu |
| E-mail(s) |
[email protected]
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| Phone |
15951718368
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| Organization name |
China Pharmaceutical University
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| Street address |
江苏省南京市中国药科大学
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| City |
南京 |
| State/province |
10 |
| ZIP/Postal code |
211198 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE133121 |
LIX1L stabilization of CCL20 promotes fibrosis |
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| Relations |
| BioSample |
SAMN12102261 |
| SRA |
SRX6100718 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3900429_con2.txt.gz |
149.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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