|
| Status |
Public on Jan 01, 2024 |
| Title |
mouse_adult_mTEC_Insm1-mutant_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
medullary thymic epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: medullary thymic epithelial cells
genotype: Insm1-mutant
strain: CD1
developmental stage: adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For E18.5 embryoes, six to nine thymi of each genotype (wildtype and Insm1 mutant) were collected and mTECs were isolated from the pool of two to three thymi with the same genotype using UEA1 coupled Dynabeads. Total RNAs were isolated using TRIZOL reagents. For adult mice, mTEC was isolated from each of the thymus using UEA1 coupled Dynabeads.
According to NEBNextRUltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA).
Three sequencing libraries for each genotype were generated
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
mouse_adult_RNAseq_gene_read_count.tsv.gz
mouse_adult_RNAseq_gene_FPKM.tsv.gz
|
| Data processing |
All RNAseq fastq files were aligned to mouse genome (mm10) using STAR with parameter --outFilterMismatchNmax 2.
Bam files were sorted by read ID using samtools, and read number were counted using HTSeq-count with parameter -s reverse and annotation Mus_musculus.GRCm38.79.
Fragments per kilobase of exon model per million mapped reads (FPKM) were calculated according to its definition. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript was counted and normalized by the length of the meta-transcript and by the total number of mapped reads. Only protein-coding and lincRNA genes were considered.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene read counts and RPKM values for all samples
|
| |
|
| Submission date |
Jan 09, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Shiqi Jia |
| E-mail(s) |
shiqijia@jnu.edu.cn
|
| Organization name |
Jinan University
|
| Street address |
Huangpu Avenue West 613
|
| City |
Guangzhou |
| ZIP/Postal code |
510613 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE193927 |
Insm1 regulates the expression of thymic tissue-restricted antigens and the immune tolerance [RNA-seq] |
| GSE193929 |
Insm1 regulates the expression of thymic tissue-restricted antigens and the immune tolerance |
|
| Relations |
| BioSample |
SAMN32644425 |
| SRA |
SRX18981156 |
