|
| Status |
Public on May 03, 2024 |
| Title |
COV434, HCB_10X, P33A |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ovary
cell line: small cell carcinoma cell line COV434
group: COV_HCB_10X
genotype: WT
concentration: 10X
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
bcl2fastq (v2.20.0.422) was used to demuliplex the fastq files.
umi_tools extract (v1.0) was then used to extract the barcodes/UMI and add them to the read names in the fastqs
Fastq files were aligned using STAR (v2.7.5b) to the human genome (GRCh38) obtained from Ensembl
The resulted bam files were then deduplicated using umi_tools dedup (v1.0)
Gene counting was then performed using featureCounts (v1.5.1) with Ensembl annotations (Homo_sapiens.GRCh38.101.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for all Samples
|
| |
|
| Submission date |
Jan 08, 2024 |
| Last update date |
May 03, 2024 |
| Contact name |
Tianyi Li |
| E-mail(s) |
tianyi_li1@sina.com
|
| Phone |
+46-739764359
|
| Organization name |
Karolinska Institute
|
| Department |
Clinical Science, Intervention and Technology
|
| Lab |
Damdimopoulou lab
|
| Street address |
Novum plan 5 hiss F, Hälsovägen 7-9
|
| City |
Huddinge |
| ZIP/Postal code |
14186 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE252776 |
Persistent organic pollutants dysregulate energy homeostasis in human ovaries in vitro |
|
| Relations |
| BioSample |
SAMN39299755 |
| SRA |
SRX23141132 |
