|
| Status |
Public on Apr 30, 2022 |
| Title |
medullary thymic epithelial cells, immature, donor 226 [pt226_lo_RNAseq] |
| Sample type |
SRA |
| |
|
| Source name |
thymus
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: thymus
cell type: medullary thymic epithelial cells
phenotype: MHCII low
donor age: 9 months
donor sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mTECs were sorted as CD45-, CDR2-, EPCAM+ cells and MHCII (HLA-DR) was used to separate immature mTEClo and mature mTEChi cell populations
RNA from sorted mTEChi and mTEClo populations was extracted using the High Pure RNA Isolation Kit (Roche)
The libraries were prepared manually using the NEBNext® Ultra ™ Directional RNA Library Prep Kit according to the manufacturer’s instruction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ens_gene: Ensembl gene; target_id: Transcript ID; ext_gene: Gene name; pval: the Wald test pvalue (sleuth output); qval: the p-value adjusted for multiple test correction (sleuth output); b: beta value, which is the log fold changes between conditions (sleuth output); se_b: standard error of the beta value (sleuth output); mean_obs: the mean expression (log) of the transcript across all samples (sleuth output); var_obs: the biological variance of the expression (sleuth output); tech_var: the technical variance of expression (sleuth output); sigma_sq: raw estimator of the variance once the technical variance has been removed (sleuth output); smooth_sigma_sq: the smooth regression fit for the shrinkage estimation (sleuth output); final_sigma_sq: max(sigma_sq, smooth_sigma_sq) (sleuth output);length: transcript length (kallisto output); $pt_tpm: Sample transcript expression (kallisto output)
|
| Data processing |
Quality control was conducted using FastQC (v0.11.8)
Reads were filtered with fastp (v0.11.8) for minimum phred quality (-q 25) of at most 10% unqualified bases (-u 10), a minimum length of 50bp (-l 50), at least 30% complexity (-y) and polyX tail trimming (-x)
Differential gene expression: Filtered reads were pseudo-aligned and quantified using Kallisto (v0.4.6) with 100 bootstrap samples
Differential gene expression: Sleuth (v0.30.0) was used for differential expression analysis between mTEChi and mTEClo samples, adjusting for patient effect in the reduced and full model. Transcripts with q-value ≤ 0.05 were considered differentially expressed
Raw reads were processed with bamboozle (Ziegenheim, Nature Communications, 2021) to remove genetic variation that could help de-identify samples ie any genetic variant was replaced with the corresponding reference genome variant
Assembly: GRCh38/Gencode annotation (release 33)
Supplementary files format and content: comma-separated value files including transcripts per million for each sample and differential expression statistics
|
| |
|
| Submission date |
Apr 27, 2022 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Hannah Verena Meyer |
| E-mail(s) |
hmeyer@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE201719 |
Transcriptome diversity in human medullary thymic epithelial cells - RNAseq |
| GSE201720 |
Transcriptome diversity in human medullary thymic epithelial cells |
|
| Relations |
| BioSample |
SAMN27918982 |
| SRA |
SRX15018781 |
