|
| Status |
Public on Jul 14, 2017 |
| Title |
E13.5#1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
age: E13.5
cell type: hepatoblast/hepatocyte
cell marker: DLK+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from about 200,000 DLK+ cells was extracted with the RNeasy Micro Kit (Qiagen, 74004). Poly(A) RNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490).
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB, #E7420) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Bulk-cell_RNA-seq_Read_Count.txt.gz
Bulk-cell_RNA-seq_Pooled_Normalized_TPM.txt.gz
|
| Data processing |
Sequencing reads were mapped to the Mus musculus reference genome (GRCm38/mm10) using TopHat (v2.1.0) with parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2”.
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 reverse -a 30 input_bam gtf”.
Reads of two biological replicates were pooled.
TPM (Transcripts Per Million) was employed to quantify gene expression levels.
TPM data was normalized by size factors calculated on all genes.
Genome_build: mm10
Supplementary_files_format_and_content: 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 |
GPL13112 |
| Series (1) |
| GSE90047 |
A single-cell transcriptomic analysis reveals precise pathways and regulatory mechanisms underlying hepatoblast differentiation |
|
| Relations |
| BioSample |
SAMN06040248 |
| SRA |
SRX2359719 |
