|
| Status |
Public on Oct 18, 2018 |
| Title |
mTEC_hi_3 |
| Sample type |
SRA |
| |
|
| Source name |
mature medullary thymic epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: thymus
age: 5-8 weeks
cell type: mTEChi
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
KAPA RNA Stranded PolyA
TriZol + RNeasy mini Kit (Qiagen, #74106)
see SAMPLES section
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
abundance_mTEC_hi_C57BL6_GRCm38.87.tsv
|
| Data processing |
Basecalls performed using CASAVA-1.8.2 for HiSEQ 2000 data and bcl2fastq version 2.19 for NextSeq 500 data
Sequenced reads were trimmed for sequencing adapters and low quality extremities using Trimmomatic version 0.35
Expression values were estimated using kallisto version 0.43.1 for each sample with replicates pooled into one sample
Genome_build: GRCm38 using transcript annotations from Ensembl 87
Supplementary_files_format_and_content: Tab-delimited files where columns are described in the header and are standard kallisto output: Ensembl transcript identifier, transcript length, eff_length, estimated counts, TPM values.
|
| |
|
| Submission date |
Feb 25, 2018 |
| Last update date |
Oct 18, 2018 |
| Contact name |
Krystel Vincent |
| E-mail(s) |
krystel.vincent.1@gmail.com
|
| Organization name |
Institute for Research in Immunology and Cancer
|
| Lab |
Immunobiology - Claude Perreault
|
| Street address |
2950, chemin de la Polytechnique, Marcelle-Coutu Pavilion
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3T 1J4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE111092 |
Non-coding regions are the main source of tumor-specific antigens [mouse] |
| GSE113992 |
Non-coding regions are the main source of tumor-specific antigens |
|
| Relations |
| BioSample |
SAMN08605979 |
| SRA |
SRX3741363 |
