|
| Status |
Public on Sep 01, 2017 |
| Title |
Setd2 KO_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: APCmin; Setd2IEC-/-
age: post natal 2 months
tissue: intestine
|
| Treatment protocol |
no treatment
|
| Growth protocol |
All mice were maintained in specific-pathogen-free (SPF) facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Intestines were removed, flash frozen on dry ice and RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd. Transcriptome reads from RNA-Seq experiments were mapped to the reference genome (mm10) by using BWA/Bowtie tool. Genes expression level is quantified by a software package called RSEM.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Setd2 KO
|
| Data processing |
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Use Bowtie2 to map clean reads to reference gene and use BWA to reference genome.
RSEM was used to computed maximum likelihood abundance estimates. FPKM method is used in calculated expression level.
Use NOISeq to screen differentially expressed genes between two groups.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.
|
| |
|
| Submission date |
Mar 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ni Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
|
| Lab |
Laboratory of Tumor Progression and Metastasis
|
| Street address |
320 Yueyang Road, Shanghai, 200025 P.R. China
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE95661 |
Expression data from control and Setd2 IEC-deficient mice intestine [RNA-seq] |
| GSE95664 |
Differential programming of intestinal tissues in SETD2-/- mice |
|
| Relations |
| BioSample |
SAMN06473380 |
| SRA |
SRX2611123 |
