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| Status |
Public on Sep 06, 2018 |
| Title |
CD4low rep1 |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: CD4lowHLA-G+ T cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA LT V2 Sample Prep Kit(Illumina, Sandiego) was used with 3 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 |
HiSeq X Ten |
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| Data processing |
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg19 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Text generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj and text file with read counts.
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| Submission date |
Sep 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chao Wang |
| E-mail(s) |
tedwang@sjtu.edu.cn
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| Organization name |
Shanghai Jiao Tong University
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| Street address |
1954HuaShan road
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| City |
ShangHai |
| ZIP/Postal code |
200030 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE103537 |
The expression profile of CD4lowHLA-G+ T cells |
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| Relations |
| BioSample |
SAMN07607868 |
| SRA |
SRX3162875 |
| 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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