|
| Status |
Public on Mar 13, 2023 |
| Title |
8000 Pa, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF10CA1a
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10CA1a
rna: Cytosolic
replicate: 2
stiffness: High stiffness (8000 Pa)
|
| Treatment protocol |
Cells were seeded on 10-cm Petrisoft easycoat dishes (Matrigen, stiffness 500 Pa or 8000 Pa.) conjugated in house with growth factor-reduced Matrigel (0.14 mg/ml, Corning). Cells were plated in growth media containing penicillin/streptomycin and fungizone. Media was changed on day four and RNA was isolated on day 5 after seeding.
|
| Growth protocol |
Cells were maintained in DMEM/F12 (Gibco) media supplemented with 5% horse serum (Gibco), 10 mM HEPES (Gibco) and 0.029 M sodium bicarbonate (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent
Biological triplicate libraries were prepared from each treatment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
After merging mutiple files, paried-end reads were trimmed for nextera adapters using BBmap(version 36.59)
Sequencing reads mapping to ribosomal RNA were removed by matching all sequencing reads to ribosomal RNA sequences from the RefSeq database using BBmap (ver.36.59)
Alignment to GRch38 (with HISAT2 2.1.2) and summarization (Htseq 0.11.4) of the result reads were performed.
After filtering (removing genes with <100 sequencing read counts in all replicates), expression count data were normalized using voom within the limma package.
Differentially expressed genes were identified using DESeq2.
Assembly: GRCh38
Supplementary files format and content: The processed data files include genes, RNA sequencing counts and TMM method normalized expression levels.
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Mar 13, 2023 |
| Contact name |
Ola Larsson |
| E-mail(s) |
ola.larsson@ki.se
|
| Phone |
+46 (0)8 517 73280
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of oncology-pathology
|
| Street address |
CCK, R8:01
|
| City |
Stockholm |
| ZIP/Postal code |
171 76 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE205816 |
Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness [sequencing] |
| GSE205819 |
Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness |
|
| Relations |
| BioSample |
SAMN28961653 |
| SRA |
SRX15665423 |
