|
| Status |
Public on Oct 30, 2019 |
| Title |
9M.cTEC.3 |
| Sample type |
SRA |
| |
|
| Source name |
cTEC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57 B6 (CD45.2)
genotype: WT
tissue: Thymus
cell type: cTEC
sorting profile: DAPI- EpCAM+ CD45- Ly51+ UEA-1-
batch: 3
|
| Growth protocol |
samples were isolated by cell sorting from thymus single cell suspensions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy plus micro kit (Qiagen)
mRNA sequencing libraries were prepared using the SMARTer Ultra Low Input RNA Kit v3 (Clontech) and Nextera XT DNA library preparation kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling by RTA 1.18.64, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 1.8.4, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq fastq reads were aligned to mouse genome (mm10) using STAR (v. 2.5.2b) on 2-pass mode with mouse gencode (release 12) gtf
Genes were subsequently counted using Rsubread and further normalized using limma-voom with quantile normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Genes were subsequently counted using Rsubread and further normalized using limma-voom with quantile normalization and Combat for batch removal.
|
| |
|
| Submission date |
Apr 02, 2019 |
| Last update date |
Oct 30, 2019 |
| Contact name |
Margaret C Cam |
| E-mail(s) |
maggie.cam@nih.gov
|
| Phone |
240-760-7179
|
| Organization name |
NIH
|
| Street address |
Bldg 37/3041C
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE129192 |
Characterization of Fetal Specific Transcriptional Programs in Thymic Epithelial Cells Identifies Myc as a Critical Determinant of Thymus Size [bulk RNA-Seq] |
| GSE131368 |
Characterization of Fetal Specific Transcriptional Programs in Thymic Epithelial Cells Identifies Myc as a Critical Determinant of Thymus Size |
|
| Relations |
| BioSample |
SAMN11316774 |
| SRA |
SRX5624249 |
