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| Status |
Public on Sep 04, 2018 |
| Title |
GPY231 Rep2 [RNA] |
| Sample type |
SRA |
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| Source name |
MDA-MB-231
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-231 breast carcinoma cells
treatment: co-culture: Human adipose cells
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| Treatment protocol |
Human adipose cells (5x10^5 cells) were added in Transwell inserts for 36 hours.
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| Growth protocol |
MDA-231 breast carcinoma cells (5x10^4 cells) were seeded in defined medium in the bottom of a 6-well Transwell culture dish and allowed to settle for 24 hours.
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL reagent (Invitrogen) was used to extract total RNA from cells following the manufacturer's protocols.
First, Total RNA was treated with the Epicentre Ribo-Zero kit (cat.#MRZH11124) to remove the all the rRNAs. The remaining RNAs were processed using the TruSeq RNA Sample Prep Kit according to the Illumina protocol. After cDNA synthesis, 6.5 pmol of DNA from each sample were clustered and sequenced on the Illumina HiSeq X-Ten (Illumina) in 150 bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
lncRNA.expression.xls
WT_2
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| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the cleandata were calculated. All the downstream analyses were based on the clean data with high quality.
RNA-sequencing reads were processed using Tophat-Cufflinks（cufflinks-2.2.1） workflows. And FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).Barcodes not matching correct length are filtered out. Besides, the transcript per million (TPM) was used to normalize the expression level of circRNAs.
Genome_build: Human genome version hg38
Supplementary_files_format_and_content: FPKM, TPM
For all generated raw reads, adaptor sequences, low-quality reads, contaminant reads, and reads that were shorter than 18 nt were eliminated and trimmed with the Fastx-Toolkit software. The resulting set of trimmed reads were then mapped against the Homo sapiens of Ensembl (Release 80, http://www.ensembl.org/) using the program SOAP . Subsequently, by the same approach, the perfectly matched reads were screened against miRBase (Release 21, http://www.mirbase.org/) and human non-coding RNA sequence of Ensembl (Release 80, http://www.ensembl.org/) to obtain the annotation of known mature miRNAs and other small non-coding RNAs (allowing two mismatches) To correct for the difference in tag counts between samples, the tag counts were scaled to the copy number of transcripts per million (TPM) based on the total number of tags aligned to known human mature miRNAs in miRBase 21.
Genome_build: miRBase 21
Supplementary_files_format_and_content: FPKM, TPM
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| Submission date |
Sep 03, 2018 |
| Last update date |
Sep 04, 2018 |
| Contact name |
Zhonghua Tao |
| Organization name |
Fudan University Shanghai Cancer Center
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| Street address |
No.270, Dong'an Road, Xuhui.
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE119377 |
Human Adipocytes Regulate Gene Expression in Triple-negative Breast Cancer Assessed by NGS Sequencing |
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| Relations |
| BioSample |
SAMN09948058 |
| SRA |
SRX4634268 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3373921_WT_2.FPKM.txt.gz |
341.7 Kb |
(ftp)(http) |
TXT |
| GSM3373921_WT_2.Gene.tpm.txt.gz |
234.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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