|
| Status |
Public on Aug 21, 2023 |
| Title |
HBF/TERT88 rep 1 [P4802_111] |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
cell line: HBF/TERT88
genotype: WT
|
| Growth protocol |
All cell lines were cultivated at 37°C in a 5% CO2humidified environment in growth media. Details can be found at https://doi.org/10.1126/science.aal3321.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the cells using the RNeasy kit (Qiagen).
Samples with high-quality total RNA (i.e., RIN > 8) were used as input material for library construction with Illumina TruSeq Stranded mRNA reagents.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequences were mapped to the human reference genome GRCh38 and further quantified using the Kallisto (v0.46.2).
Transcript abundances were aggregated into gene level as transcripts per million (TPM) by tximport (v1.22.0)
Only protein-coding genes and transcripts were included for downstream analysis, resulting in 20,090 genes analyzed.
Assembly: GRCh38.p13 (Ensembl build 103.38)
Supplementary files format and content: A tab separated text file containing gene expression TPM for each sample.
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Han Jin |
| Organization name |
Maastricht University
|
| Street address |
P. Debyelaan 25
|
| City |
Maastricht |
| ZIP/Postal code |
6229 HX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE240542 |
RNA-sequencing of 69 cell lines in the Human Protein Atlas database |
|
| Relations |
| BioSample |
SAMN36935054 |
| SRA |
SRX21329294 |
