|
| Status |
Public on Mar 23, 2014 |
| Title |
Cell T0_CT_B08 |
| Sample type |
SRA |
| |
|
| Source name |
Myoblast_Cell T0_CT_B
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Skeletal Muscle Myoblasts (HSMM)
hour post serum-switch: 0
debris: FALSE
control well: FALSE
cells in well: 1
library protocol: Single-cell
|
| Treatment protocol |
HSMM cells were differentiated for the via switch to 2% HS aMEM (Lifetech).
|
| Growth protocol |
Human Skeletal Muscle Myoblasts (HSMM) derived from quadricep biopsy (Lonza, catalog #CC-2580, lot #257130) were expanded in 10% FBS SkGM-2 (Lonza). All procedures have been performed using HSMM within P10 from explant.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For single-cell mRNA sequencing, dissociated cells were captured and processed with the C1™ Single-Cell Auto Prep System (Fluidigm) following manufacturer’s protocol 100-5950. Starting with a suspension of cells at a concentration of approximately 250 cells/µL, up to 96 single cells are captured in each C1 microfluidic device.
[TruSeq] - HSMM in either growth or differentiation medium were dissociated, washed and resuspended in complete media containing 0.1U/ul of RNaseOUT (Lifetech). Each time point was collected in three independent biological replicates for regular mRNA sequencing while for single cell mRNA sequencing the independent replicates were pooled in equal amounts. For bulk RNA-Seq libraries, total RNA was extracted with Trizol and mRNA libraries were produced starting from 100ng of total RNA using the TruSeq mRNA-Seq library kit (Illumina) according to manufacturer’s instructions.
[Single Cell] - After imaging with a microscope to identify which sites have captured a single cell, processing of the cells occurs within the C1 instrument to perform the steps of cell lysis, cDNA synthesis with reverse transcriptase, and PCR amplification of each cDNA library. The cDNA synthesis and PCR use reagents from the SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing (Clontech 634936). The SMARTer chemistry utilizes a strand-switching mechanism so that both the 1st and 2nd strands of cDNA are synthesized in a single reaction. Following harvest from the C1 microfluidic device, each cDNA library is subjected to tagmentation (simultaneous fragmentation and tagging with sequencing adapters) using the Nextera XT DNA Sample Preparation Kit (Illumina FC-131-1096) as described in Fluidigm protocol 100-5950. PCR amplification of the tagmented cDNA uses Index Primers from the Nextera XT DNA Sample Preparation Index Kit (Illumina FC-131-1002). Following PCR, the cDNA libraries from individual cells are pooled and purified using AMPure® XP beads (Agencourt Bioscience Corp A63880) as described in Fluidigm protocol 100-5950.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
T0_CT_B08
|
| Data processing |
Reads were mapped with TopHat 2.0.9 and Bowtie 2.0.6. TopHat was provided with GENCODE version 17
Mapped reads were analyzed with Cuffdiff 2.2 to generate normalized per-cell expression profiles.
Cells were pseudo-temporally ordered with Monocle
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression matrix; fpkm_matrix.txt for Cell* samples and truseq_fpkm_matrix.txt for *Bulk RNA-Seq samples
|
| |
|
| Submission date |
Nov 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Cole Trapnell |
| E-mail(s) |
cole@broadinstitute.org
|
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology
|
| Lab |
John Rinn
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE52529 |
Pseudo-temporal ordering of individual cells reveals regulators of differentiation |
|
| Relations |
| BioSample |
SAMN02413248 |
| SRA |
SRX379619 |
