|
| Status |
Public on Oct 20, 2013 |
| Title |
Single Cell C1 Microfluidics 29 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cdna synthesis method: Clontech SMARTer
library construction method: Nextera (transposon)
cell line: HCT116
|
| Treatment protocol |
N/A
|
| Growth protocol |
standard cell culture protocol according to instructions from ATCC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
standard cell lysis to extract RNA, followed by either kit specific mRNA priming or polyT bead extraction of mRNA. Microfluidic preparation sample cells were lysed within the microfluidic device.
Most were prepared using Illumina Nextera kit per illumina's protocols; some prepared using NEBNext kit per protocol instructions. Samples prepared using each are identified above in "overall design", in the sample descriptions, and in the associated manuscript
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
remove adapter sequences using cutadapt-1.2.1
trim base quality and remove low complexity reads using prinseq-lite-0.20.3
alignment using bowtie-0.12.9 if single end, using bowtie2-2.1.0 if paired end, and tophat-2.0.8 against hg19
FPKM values computed using cufflinks-2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: R dataframe format; one combined file for all samples. Contains tophat/cufflinks generated FPKM values.
Supplementary_files_format_and_content: pcr_cts.txt: tab-delimited text file that includes the qPCR data.
|
| |
|
| Submission date |
Sep 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Angela Ruohao Wu |
| E-mail(s) |
angelawu@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Bioengineering
|
| Lab |
Quake
|
| Street address |
318 Campus Drive, Clark Center E300
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE51254 |
Quantitative assessment of single-cell RNA sequencing methods |
|
| Relations |
| BioSample |
SAMN02366491 |
| SRA |
SRX360989 |
