|
Status |
Public on Dec 31, 2016 |
Title |
MCF10A_sc_6 |
Sample type |
SRA |
|
|
Source name |
MCF10A cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: MCF10A sample type: single cell
|
Growth protocol |
HEK293T cells were grown in DMEM/High Glucose medium (ThermoFisher Scientific) with 10% FBS (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies). Cells were passed every 2-3 days. MCF10A cells were grown in DMEM/F12 medium with 5% Horse Serum, 20ng/ml EGF, 100ng/ml Cholera Toxin, 10ug/ml Insulin, 500ng/ml Hydrocortisone, and 1% Penicillin Streptomycin.
|
Extracted molecule |
total RNA |
Extraction protocol |
cDNA libraries were prepared for sequencing using standard Illumina Truseq protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
The raw sequencing data was trimmed using skewer package. The reads were mapped to the transcriptome using TOPHAT A Python program using HT-seq package was written to analyze the barcode information Genome_build: Hg19 Supplementary_files_format_and_content: dat files include the read count and barcode count for exon-based and intron-based analyses
|
|
|
Submission date |
Aug 21, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Kuanwei Sheng |
E-mail(s) |
sheng@bcm.edu
|
Organization name |
Baylor College of Medicine
|
Department |
Molecular and Human Genetics
|
Lab |
Zong Lab
|
Street address |
ONE BAYLOR PALAZA
|
City |
HOUSTON |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE78968 |
Effective Detection of Variation in Single Cell Transcriptome using MATQ-seq |
|
Relations |
BioSample |
SAMN05601483 |
SRA |
SRX2036974 |