|
| Status |
Public on Mar 14, 2018 |
| Title |
E13.5KL_5_03 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
embryonic day: E13.5
cell type: dorsal pancreas; E13.5 Pdx1-Cre; Jmjd3 fl/fl ; Ngn3-low
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA synthesis was performed following the Smart-seq2 method described by Picelli et al. 0.1 ul ERCC spike-in RNA (1:1,000,000 dilution, Life, 4456740) was added to the 4 ul lysis buffer in single cell RNA-seq.
2.5 ng of cDNA was used to conduct library using “TruePrep DNA Library Prep Kit” (Vazyme, TD502).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Single-cell_RNA-seq_Gene_Read_Count.txt.gz
Single-cell_RNA-seq_Gene_RPKM.txt.gz
|
| Data processing |
The sequencing reads were aligned to the Mus musculus genome (mm10) using TopHat (v2.1.0) with the parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
Reads aligned to genes were counted using HTSeq (v0.6.0) with the parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
Gene expression levels were quantified as reads per kilobase of the longest transcript per million mapped reads (RPKM).
genome build: mm10
processed data files format and content: values tab-delimited text files include read count and RPKM values for each sample
|
| |
|
| Submission date |
Jan 02, 2018 |
| Last update date |
Mar 14, 2018 |
| 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) |
| GSE84324 |
Dynamics of chromatin marks and the role of JMJD3 during pancreatic endocrine cell fate commitment |
|
| Relations |
| BioSample |
SAMN08285246 |
| SRA |
SRX3527013 |
