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| Status |
Public on Oct 09, 2020 |
| Title |
RNA-seq_KAT7-rep2 |
| Sample type |
SRA |
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| Source name |
CRISPR Screening
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| Organism |
Homo sapiens |
| Characteristics |
genotype: KAT7 Over-expressed
cell type: H9 hMSCs
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| Growth protocol |
MSCs were maintained in MEM-α medium (invitrogen) with 10% fetal bovine serum (FBS, Gemcell), 1% penicillin/streptomycin (Gibco), 10 ng/ml bFGF (JPC). Media was added and the cultured cells were expanded onto additional plates to keep cells at an appropriate culture density.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, total RNA was extracted by TRIzol (Invitrogen) at passage 4 post infection.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Raw RNA-seq sequencing data were firstly removed adaptors and low-quality bases, and then the clean reads were mapped to the UCSC human hg19 reference genome using Tophat (version: 2.0.12) with default parameters. Reads counts were calculated with HTSeq, and gene expression levels are quantified with RPKM (reads per kilobase million).
Genome_build: UCSC human reference genome hg19 and UCSC drosophila reference genome dm6
Supplementary_files_format_and_content: RNA_expression.txt files include the read counts and RPKM of RefSeq genes
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| Submission date |
Dec 20, 2018 |
| Last update date |
Oct 11, 2020 |
| Contact name |
Yuxuan Zheng |
| Organization name |
Fudan University
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| Street address |
825 Zhangheng Rd.
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| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE124197 |
A Genome-wide CRISPR-Based Screen Identifies KAT7 as a Senescence Driver |
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| Relations |
| BioSample |
SAMN10620714 |
| SRA |
SRX5170667 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3523719_KAT7-rep2_RNA_expression.txt.gz |
217.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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