|
| Status |
Public on Dec 12, 2018 |
| Title |
Mixture_Sample_3 |
| Sample type |
SRA |
| |
|
| Source name |
Mixture_Sample_3
|
| Organism |
Homo sapiens |
| Characteristics |
origin: cell line
sample name: Mixture_3
tumor-mcf7 proportions: 85
cafs-hs_343.t proportions: 3
normal_breast-hmecs-htert proportions: 9
lymphocytes-namalwa proportions: 3
treatment: control
|
| Treatment protocol |
No treatment
|
| Growth protocol |
MCF7 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS). Namalwa cells were a gift from Dr. Sandeep Dave, Duke University, and were cultured in RPMI medium supplemented with 10% FBS. Hs343T and hTERT-HME1 (ATCC) were cultured in HuMEC Ready medium (Thermo Fisher Scientific).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy kit
TruSeq RNA sample preparation kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
all_samples_per_gene_counts.txt
|
| Data processing |
Generation of FASTQ files performed using Illumina bcl2fastq2
FASTQ files from each sequencing run concatenated into single file per library
Adapter sequence trimmed using cutadapt 1.12
Trimmed reads aligned using STAR version 2.5.2b to GRCh38 assembly
Counts per gene determined using featureCounts version 1.5.1 based on Ensembl release 90 GRCh38 annotations
Coverage tracks generated using genomeCoverageBed (bedtools v2.25.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig (.bw) containing raw read coverage; tab-delimited text (.txt) containing raw read counts per gene for all samples
|
| |
|
| Submission date |
Dec 11, 2018 |
| Last update date |
Dec 14, 2018 |
| Contact name |
Kai Kang |
| E-mail(s) |
[email protected]
|
| Organization name |
MIT
|
| Department |
CSAIL
|
| Street address |
32 Vassar Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE123604 |
A novel computational complete deconvolution method using RNA-seq data |
|
| Relations |
| BioSample |
SAMN10579031 |
| SRA |
SRX5124485 |
