|
Status |
Public on Dec 22, 2015 |
Title |
L1210_35 scRNA-seq |
Sample type |
SRA |
|
|
Source name |
Single L1210 cells grown for multiple generations on-chip
|
Organism |
Mus musculus |
Characteristics |
cell type: L1210 lymphocytic leukemia (ATCC CCL-219) strain: DBA subline 212 hours since division: 4.6761 sister: L1210_24 cousin 1: L1210_1 cousin 2: L1210_13 doublet?: No
|
Treatment protocol |
The CD8+ T cells were activated with 5 μg/mL plate-bound anti-mouse CD3 (clone: 145-2C11, BioLegend catalog number 100314) and 2 μg/mL of anti-mouse CD28 (clone: 37.51, BioLegend catalog number 102112) in solution for 30h prior to loading in to the device.
|
Growth protocol |
L1210 cells were cultured in the device in RPMI 1640 (Gibco) with 10% FBS and 1% penicillin-streptomycin solution (Gibco). CD8+ T cells were cultured in the device in RPMI 1640 (Gibco) with 10% FBS, 55μM 2-mercaptoethanol (Gibco), 1% penicillin-streptomycin solution (Gibco) and 100 U/mL IL2 (PeproTech) after 30h activation in vitro (see below).
|
Extracted molecule |
total RNA |
Extraction protocol |
Single cells were flushed from the device with 5 ul of PBS directly in to 5 ul of 2X TCL lysis buffer (Qiagen) resulting in a total volume of 10 ul of single-cell lysate. These samples were immediately frozen on dry ice and subsequently stored at -80°C prior to library preperation and sequencing. Libraries were constructed using the Smart-Seq2 protocol for single cells.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
L1210 scRNA-seq
|
Data processing |
Illumina bcl2fastq2.15.0.4 was used to generat .fastq files from .bcl files. tophat2 was used to align the scRNA-seq data rsem-1.2.3 generated an expression matrix in transcripts per million. mm10 ucsc genomestudio Genome_build: mm10 Supplementary_files_format_and_content: RSEM transcripts per million matrix with genes as rows and samples as columns.
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|
|
Submission date |
Nov 12, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Robert Kimmerling |
E-mail(s) |
rjkimmer@mit.edu
|
Phone |
6318793159
|
Organization name |
MIT
|
Department |
Biological Engineering
|
Lab |
Manalis
|
Street address |
32 Vassar St., 76-221
|
City |
Cambridge |
State/province |
Massachusetts |
ZIP/Postal code |
02139 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE74923 |
A microfluidic platform enabling single cell RNA-seq of multigenerational lineages |
|
Relations |
BioSample |
SAMN04261875 |
SRA |
SRX1427195 |