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Sample GSM3373929

Query DataSets for GSM3373929

Status

Public on Sep 04, 2018

Title

WT231 Rep1 [miRNA]

Sample type

SRA

Source name

MDA-MB-231

Organism

Homo sapiens

Characteristics

cell line: MDA-231 breast carcinoma cells
treatment: None

Treatment protocol

Human adipose cells (5x10^5 cells) were added in Transwell inserts for 36 hours.

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.

Extracted molecule

total RNA

Extraction protocol

TRIZOL reagent (Invitrogen) was used to extract total RNA from cells following the manufacturer's protocols.
For small RNA librarires, 18-30 nt RNAs were isolated from total RNA of dissected ovaries using 15% polyacrylamide gels and libraries were constructed using the Illumina TruSeq smallRNA Library Kit. And the libraries were sequenced with an Illumina HiSeq2500 in 50-bp single-end fashion.

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2500

Description

all_miRNA_exp.xls
YD_1

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

Submission date

Sep 03, 2018

Last update date

Sep 04, 2018

Contact name

Zhonghua Tao

Organization name

Fudan University Shanghai Cancer Center

Street address

No.270, Dong'an Road, Xuhui.

City

Shanghai