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| Status |
Public on May 11, 2017 |
| Title |
PB-Tcf1 |
| Sample type |
SRA |
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| Source name |
HES2 human embryonic stem cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: embryo
expression: PB-Tcf1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. BGISEQ-500 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 |
BGISEQ-500 |
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| Description |
PB-VS-PB_Tcf1.GeneDiffExp.xls.xls
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| Data processing |
Integrative Genomcs Viewer 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
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from BGI company. 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 of BGI.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
May 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
shoudong ye |
| Organization name |
Anhui University
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| Department |
Cell Biology
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| Street address |
No 111, Jiu Long Road
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| City |
Hefei |
| ZIP/Postal code |
230601 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE98720 |
RNA-seq Analysis of Tcf1-regulated Genes in Human ESCs |
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| Relations |
| BioSample |
SAMN06921259 |
| SRA |
SRX2793426 |
| 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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