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| Status |
Public on Apr 01, 2021 |
| Title |
MDA-MB-231 untreated replicate 1 |
| Sample type |
SRA |
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| Source name |
Breast carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: No treatment
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| Treatment protocol |
50IU of IFNγ
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| Growth protocol |
MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% Penicillin/streptomycin and L-glutamine (2 mM) (Gibco) at 37°C with 5% CO2. Total RNA was extracted from 1x10^5 MDA-MB-231 cells in three biological replicates of IFNγ treated and untreated conditions using RNeasy mini kit (Qiagen).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy mini kit to extract the RNA and QC on nanodrop to determine concentration.
Library construct was done by BGI (Paired-end, 30 million bp with 1% ERCC spike in control).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
NonStrandedCounts-withNames.txt
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| Data processing |
BGI normalised the sequence fastaq data to the 1% ERCC spike in control
raw fastq files were processed from alignment to raw count files using RNAsik software on Massive 3 that wrapped aroudn the following tools/packages: STAR 2.5.2b, qualimap v2.2.1, BigDataScript 0.99999g, bwa v0.7.15, samtools v1.4.1, RNAsik-pipe 1.5.0, subread/1.5.2, bedtools2 v2.25.0, python v3.6.2, picard v2.18.0, multiqc v1.4, gcc v4.9.3, fastqc v0.11.5 and java v8u144
Raw count files were filltered and QC using the following steps… :
removal of 0 counts, prinicple component analysis (outliers were removed if >3SD), removal of genes were the average <10 counts across the samples.
filtered counts were normalised using EdgeR TMM
Genome_build: GRCh37 homo sapian
Supplementary_files_format_and_content: raw count file created using RNAsik pipeline (.txt)
Supplementary_files_format_and_content: Differential gene expression of all genes that passed filltering (.csv)
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| Submission date |
Dec 11, 2020 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Gabriel Goncalves |
| E-mail(s) |
[email protected]
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| Phone |
0432700015
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| Organization name |
Monash University
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| Street address |
15 Innovation walk
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| City |
Clayton |
| State/province |
VICTORIA |
| ZIP/Postal code |
3168 |
| Country |
Australia |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE163067 |
IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing and diversifying antigen processing and presentation |
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| Relations |
| BioSample |
SAMN17061496 |
| SRA |
SRX9674606 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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