|
| Status |
Public on Jul 14, 2017 |
| Title |
E13.5E_2_03 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
embryonic day: E13.5
culture time: NA
treatment: NA
sorting: P2 gate, EpCAM+
putative cell type: hepatoblast/hepatocyte
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After FACS sorting, single cells were manually picked up under the microscope with a mouth pipette and transferred into 4 μl of cell lysis buffer containing 0.05 μl of a 1:300,000 dilution of ERCC Spike-in RNA (Life Technologies, 4456740). The cDNA was synthesized, amplified (18 cycles) using the Smart-seq2 protocol, and purified using VAHTS DNA Clean Beads XP beads (Vazyme, N411-03).
Two nanograms of cDNA were used to prepare the sequencing libraries using the TruePrep DNA Library Prep Kit (Vazyme, TD502) with 0.4 × of the standard reaction volume. PCR amplifications were conducted in 8 cycles. Purification and size-based selection of PCR products were performed to obtain libraries with a peak size of 350 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Single-cell_RNA-seq_in_vivo_Read_Count.txt.gz
Single-cell_RNA-seq_in_vivo_Normalized_TPM.txt.gz
|
| Data processing |
Sequencing reads were mapped to the Mus musculus reference genome (GRCm38/mm10) and the 92 ERCC spike-in sequences using TopHat (v2.1.0) with parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
HTSeq (v0.6.0) was used to count the number of reads mapped to each gene with parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
TPM (Transcripts Per Million) was employed to quantify gene expression levels.
genome build: mm10
values tab-delimited text files include read count and TPM values for each sample
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cheng-ran Xu |
| Organization name |
Peking University
|
| Department |
School of Basic Medical Sciences
|
| Street address |
NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA
|
| City |
Beijing |
| State/province |
- |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE90047 |
A single-cell transcriptomic analysis reveals precise pathways and regulatory mechanisms underlying hepatoblast differentiation |
|
| Relations |
| BioSample |
SAMN06039948 |
| SRA |
SRX2359937 |
