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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 29, 2021 |
| Title |
S-S1 |
| Sample type |
SRA |
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| Source name |
Human corneal stromal cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: CSCs in the S model
culture time: 7 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 |
Illumina NovaSeq 6000 |
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| Description |
S-S1_S174
processed data file: S_count.txt
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. 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.
Genome_build: GRCg6A, hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jun 28, 2021 |
| Last update date |
Jun 29, 2021 |
| Contact name |
Zekai Cui |
| E-mail(s) |
cuizk7@gmail.com
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| Organization name |
Aier Eye Institute
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| Street address |
18th floor, the New Century Building, #198, Furong Middle Road
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410015 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE179020 |
DRG-CSC co-culture tissue engineered model, CSCs monoculture model and DRG monoculture model |
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| Relations |
| SRA |
SRX11242880 |
| BioSample |
SAMN19945980 |
| 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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