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| Status |
Public on Jul 06, 2024 |
| Title |
shNC-2.mRNA |
| Sample type |
SRA |
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| Source name |
HL7702_shNC
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HL7702
genotype/variation: shNC
tissue source: liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was homogenized from tissues or cells with Trizol reagent.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 |
NextSeq 550 |
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| Description |
shNC HL7702 cells
RNA-20190613-RNA-20190613-NC2_L1
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| Data processing |
bcl2fastq 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 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., 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: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Feb 03, 2021 |
| Last update date |
Jul 06, 2024 |
| Contact name |
RUI Zhou |
| E-mail(s) |
ruizhou@whu.edu.cn
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| Organization name |
Wuhan University
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| Street address |
Donghu Road 185
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| City |
Wuhan |
| ZIP/Postal code |
430071 |
| Country |
China |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE166060 |
High-throughput mRNA-sequence of KSRP knock down cells in HL7702 CELLS |
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| Relations |
| BioSample |
SAMN17767213 |
| SRA |
SRX10011194 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5061053_RNA-20190613-RNA-20190613-NC2_L1_hg38.fwd.bw |
124.1 Mb |
(ftp)(http) |
BW |
| GSM5061053_RNA-20190613-RNA-20190613-NC2_L1_hg38.rev.bw |
138.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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