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| Status |
Public on May 06, 2023 |
| Title |
RNAseq_EryPro_KDCon_72_Rep2 |
| Sample type |
SRA |
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| Source name |
Cord Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Cord Blood
cell line: Erythroid progenitor
cell type: Erythroid progenitor
genotype: pooled
treatment: siCon, 72h
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA-seq was performed with Single Cell Full Length mRNA-Amplification Kit (Vazyme, Cat. # N712) which is based on SMART-seq2 method.
In brief, two hundred cells were lysed, and reverse transcription was conducted, then 11 cycles of PCR were used to amplify transcriptome library. Quality of whole transcriptome libraries was validated using a D5000 DNA Chip run on a Bioanalyzer 4150 system (Agilent), followed by library preparation using the TruePrep DNA Library Prep Kit (Vazyme, Cat. # TD503) and custom index primers according to the manufacturer’s instructions. The final libraries were quantified using a VAHTS Library Quantification Kit (Vazyme, Cat. # NQ101) and a D1000 High Sensitivity DNA chip run on a Bioanalyzer 4250 system (Agilent). Two biological replicates per condition were sequenced in a Novaseq 6000 (S4, PE150, Illumina) by Novogene (Beijing).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
SMART-seq2
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| Data processing |
The bulk RNA-seq data were checked the quality by FastQC (version 0.11.7, https://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
Data were aligned to the hg19 reference genome using RNA STAR.
The expression level of each gene was calculated by FeatureCounts then reads counts were normalized to TPM (transcription per million)
Genes with TPM > 0 are considered as expressed genes. DESeq2 was used to calculate the differential expression genes, and fold change > 2 & FDR < 0.05 will be consider significantly different. Gene set enrichment analysis for gene ontology biological processes were performed by using clusterProfiler R package.
Assembly: hg19
Supplementary files format and content: RAW reads counts, export by FeatureCount: RNA_All_Sample_Counts.FC.txt
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| Submission date |
Oct 04, 2022 |
| Last update date |
May 06, 2023 |
| Contact name |
Dong Li |
| E-mail(s) |
lidongpaul@gmail.com
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| Organization name |
Peking University
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| Department |
College of Life Science
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| Lab |
Hsiang-Ying (Sherry) Lee
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| Street address |
No.5 Yiheyuan Road, Haidian District,
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE214809 |
Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [RNA-seq] |
| GSE214811 |
Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis |
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| Relations |
| BioSample |
SAMN31029462 |
| SRA |
SRX17718599 |
| 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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