|
| Status |
Public on Aug 03, 2021 |
| Title |
immature_mTEC_WT3 |
| Sample type |
SRA |
| |
|
| Source name |
immature mTEC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 4-6 weeks
Sex: female
genotype: wildtype
tissue: thymus
cell type: immature medullary thymic epithelial cells (mTEC)
facs phenotype: CD45- EpCAM+ Ly51- UEA+ CD80- CD86-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thymi were dissected from mice, enriched for CD45- cells (AutoMACS) and 10,000 cells sorted by FACS (CD80-CD86- immature versus CD80+CD86+ mature mTEC). RNA was extracted using QUIAGEN RNeasy micro plus kit.
Libraries were prepared using the cDNA-PCR kit (SQK-PCS108) from Oxford Nanopore Technologies.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
RNA from 1 individual mouse
immature_mtec_transcripts.counts.gz
|
| Data processing |
Basecalling was performed using Albacore (v2.3.1) and reads were trimmed using Porechop (v0.2.3)
Fastqs from 3 replicates were merged and mapped using Minimap2 (-ax splice, v2.14-r883)
Counts were quantified using featureCounts (-L option, v1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: [*mtec_transcripts.counts.txt] tab-delimited files including transcript counts from the combined mature and immature samples
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Stephen Sansom |
| E-mail(s) |
[email protected]
|
| Organization name |
Kennedy Institute of Rheumatology
|
| Department |
NDORMS
|
| Lab |
Sansom
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7FY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24973 |
| Series (2) |
| GSE145914 |
Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells [mTEC_ONT_RNAseq] |
| GSE145931 |
Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells |
|
| Relations |
| BioSample |
SAMN14206929 |
| SRA |
SRX7800605 |
