|
| Status |
Public on Jun 30, 2023 |
| Title |
S8_TSC3_DN-MAML1_Dox [BD01008] |
| Sample type |
SRA |
| |
|
| Source name |
placenta
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta
cell line: TSC3
cell type: trophoblast stem cells
genotype: DN-MAML1
treatment: doxycycline treated (6 days)
|
| Treatment protocol |
DN-MAML1 overexpression was induced by adding 1 µg/mL doxycycline for 6 consecutive days to the cell culture medium.
|
| Growth protocol |
TSCs were cultivated in DMEM/F12 supplemented with 1x B-27, 1x Insulin-Transferrin-Selenium-Ethanolamine, 1 µM A83-01, 50 ng/mL recombinant human epidermal growth factor, 2 µM CHIR99021 and 5 µM Y27632.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
Sequencing libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Pooled libraries were sequenced in 1x75bp single-read sequencing mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BD01008
Dietrich_12samples_raw_gene_counts_GeneSymbols_GeneTypes.tsv
|
| Data processing |
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (V2.19.1.403) inclusive trimming of the sequence adapters.
Reads were aligned to the human reference genome version GRCh38 using STAR aligner version 2.6.1a.
Raw reads pere gene were counted by STAR.
Read counts were normalized and vst-transformed using DESeq2 version 1.22.2.
TPM were generated by RSEM.
Assembly: GRCh38
Supplementary files format and content: raw counts of sequencing reads
|
| |
|
| Submission date |
May 22, 2023 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Bianca Dietrich |
| Organization name |
Medical University of Vienna
|
| Street address |
Waehringer Guertel 18-20
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE233140 |
Next Generation Sequencing of human trophoblast stem cells expressing a doxycycline-inducible dominant-negative MAML1 construct. |
|
| Relations |
| BioSample |
SAMN35306639 |
| SRA |
SRX20465597 |
