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| Status |
Public on Jun 08, 2020 |
| Title |
CB_HGFs |
| Sample type |
SRA |
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| Source name |
CD34+ human cord blood-derived cells
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| Organism |
Homo sapiens |
| Characteristics |
modulating agent: DMSO
time point: 96hr
cell type: hUCB CD34+ cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Takara, Japan) following the manufacturer's procedure. The libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated
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 |
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: Homo_sapiens.GRCh38.91.chr
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 |
Jun 07, 2020 |
| Last update date |
Jun 08, 2020 |
| Contact name |
ying chen |
| E-mail(s) |
[email protected]
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| Organization name |
Union Hospital，Tongji Medical College, Huazhong University of Science and Technology
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| Department |
Institute of Hematology
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| Street address |
1277 Jiefang Avenue, Wuhan, Hubei Province
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| City |
Wuhan |
| ZIP/Postal code |
430022 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE151964 |
Transcriptome data of uncultured and HGFs along with 0.1% DMSO or LY plus Rapa or SR1-treated hUCB CD34+ cells |
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| Relations |
| BioSample |
SAMN15160182 |
| SRA |
SRX8489895 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4594410_CB_HGFs.txt.gz |
275.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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