|
| Status |
Public on Jun 05, 2018 |
| Title |
e14.5 EP 5 |
| Sample type |
SRA |
| |
|
| Source name |
e14.5 endocrine progenitor (Ngn3-eGFP+ cell) from Ngn3-eGFP mouse
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: e14.5
tissue: Endocrine progenitors
strain: Ngn3-eGFP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After flow sorting, Ngn3-eGFP+ cells were collected in RPMI medium. We used mouth pipette to pick single cells into PCR tubes with MATQ-seq lysis buffer (Sheng et al., 2017).
MATQ-seq was then performed to amplify the whole transcriptome of single cells. After second strand synthesis, the input and yield of each sample was quantified by qPCR. Highly degraded samples or samples with multiple cells were discarded. After PCR amplification, we performed library preparation and data analysis according to the previous publication (Sheng et al., 2017). Duplex specific Nuclease was used to remove the majority of ribosomal cDNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
single e14.5 mouse EPs
e14_5
|
| Data processing |
First MATQ-seq amplification primers are trimmed off the reads using Skewer.
Extra 14 based are further trimmed to remove the UMI sequence and extra bases from the reads.
The trimmed reads are then mapped using STAR algorithm.
The uniquely mapped reads are assigned to the genes using HTseq-count.
Based the assigned reads, the UMI for unique amplicons are retrieved and counted for each gene.
The amplicons per million amplicons (APM), similar to reads per million reads (RPM) are calculated and used to quantify the gene expression in single cells. For detailed procedures, please refer to Sheng et al. (2016).
Genome_build: mm9
Supplementary_files_format_and_content: text file with APM
|
| |
|
| Submission date |
Jun 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Malgorzata Borowiak |
| E-mail(s) |
borowiak@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE100620 |
High-Resolution temporal profiling of developing pancreas uncovers the mechanisms of endocrine cell fate determination [MATQ-seq] |
| GSE100622 |
High-Resolution temporal profiling of developing pancreas uncovers the mechanisms of endocrine cell fate determination |
|
| Relations |
| BioSample |
SAMN07290942 |
| SRA |
SRX2965700 |
