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| Status |
Public on Feb 03, 2022 |
| Title |
SAS cells, shCCT2_3 |
| Sample type |
SRA |
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| Source name |
SAS cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: tongue
cell line: SAS
cell type: Head and neck squamous cell carcinoma (HNSCC)
genotype: CCT2 knockdown
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent. mRNA was enriched with oligo(dT)-attach magnetic beads and fragmented into small pieces, cDNA library was generated using random hexamer-primed reverse transcription followed by second-strand cDNA synthesis and sequenced on an MGI 2000 platform (BGI, Shenzhen, China).
RNA libraries were prepared for sequencing using standard BGI 2000 protocols
instrument model: MGI 2000
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
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| Description |
gene expression_2.txt
The fastq files are no longer available.
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| Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using STAR (v1.5.1)
The read counts were extracted using HTSeq-count （v0.11.3）
Matrix table with raw gene counts for every gene and every sample was generated.
Clean reads after quality control were compared to the reference genome using sequence alignment software, allowing quantification of gene/transcript expression in the sample. At the same time, the whole transcriptome sequencing was analyzed, including the randomness of transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. ReadsRandom.txt.
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| Submission date |
Jan 31, 2022 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Lu Lin |
| E-mail(s) |
lulin8@mail2.sysu.edu.cn
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| Phone |
+86 15986421404
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| Organization name |
sun yat-sen university
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| Street address |
74 zhongshaner road
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| City |
guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL30209 |
| Series (1) |
| GSE195850 |
CCT2 promotes the proliferation and migration of head and neck squamous cell carcinoma via activating PI3K/AKT pathway |
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| Relations |
| BioSample |
SAMN25525273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5852130_shCCT2_3.ReadsRandom.txt.gz |
1.6 Kb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data not provided for this record |
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