|
| Status |
Public on Dec 31, 2016 |
| Title |
avervaged_onefifth_MCF10A_ERCC_spiked_1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF10A cell line + ERCC spike-in
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
sample type: pool-and-split averaged 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 |
SAMN05601476 |
| SRA |
SRX2036981 |
