|
| Status |
Public on May 18, 2021 |
| Title |
HCT-116_fixed36 |
| Sample type |
SRA |
| |
|
| Source name |
HCT-116 fixed36
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-116
|
| Treatment protocol |
80% methanol was used for cell fixation, fixed cells were stored in -80℃ for one week before further processing
|
| Growth protocol |
Both HepG2 and HCT-116 cell lines were culured with DMEM medium, supplemented with 1% Penicillin-Streptomycin and 10% Fetal Bovine Serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA library was constructed using Smart-seq2 protocl, sequencing library was prepared using Illuminar Nextera DNA Library Prep Kit(Illumina, cat#FC-131-1096), we followed library contruction protocal provided by C1 Fluidigm(Fluidigm)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Index and adapter were trimmed in data downloaded form Basespace
Quality control was done using Fastqc
Alignment and quantification were done by mapping raw reads to GRCh38 using kallisto 0.46.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression/Transcript expression matrix(TPM)
|
| |
|
| Submission date |
May 21, 2020 |
| Last update date |
May 18, 2021 |
| Contact name |
Xinlei Wang |
| E-mail(s) |
xwangda@connect.ust.hk
|
| Organization name |
HKUST
|
| Department |
LIFS
|
| Lab |
Angela Wu Lab
|
| Street address |
Clear Water Bay, Sai Kung,
|
| City |
Hong Kong |
| State/province |
Hong Kong |
| ZIP/Postal code |
999077 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE150993 |
Effect of methanol fixation on single-cell RNA sequencing data |
|
| Relations |
| BioSample |
SAMN14989927 |
| SRA |
SRX8376987 |
