|
| Status |
Public on Mar 14, 2018 |
| Title |
E13.5 Ngn3-low #1 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
embryonic day: E13.5
cell type: dorsal pancreas; Ngn3-low
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated from about 4-6 X 10e4 sorted cells by RNeasy Micro Kit (Qiagen, 74004). mRNA was purified from ~200 ng of total RNA by “NEBNext Poly(A) mRNA Magnetic Isolation Module” (NEB #E7490).
Libraries were prepared using” NEBNext Ultr Directional RNA Library Prep Kit for Illumina” (NEB #E7420) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_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_fastq1 input_fastq2”.
Reads aligned to genes were counted using HTSeq (v0.6.0) with the parameters “htseq-count -f bam -r pos -s reverse -a 30 input_bam gtf”.
Reads of two biological replicates were pooled.
Gene expression levels were quantified as reads per kilobase of the longest transcript per million mapped reads (RPKM).
The normalization of RPKM was performed by size factors which were calculated by function “estimateSizeFactorsForMatrix” of R package DESeq (v1.20.0).
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 |
Jul 12, 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) |
| GSE84324 |
Dynamics of chromatin marks and the role of JMJD3 during pancreatic endocrine cell fate commitment |
|
| Relations |
| BioSample |
SAMN05385884 |
| SRA |
SRX1941069 |
