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Sample GSM2689402 Query DataSets for GSM2689402
Status Public on Jun 05, 2018
Title e14.5 EP 2
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_2
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 SAMN07290540
SRA SRX2965697

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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