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Sample GSM6070096 Query DataSets for GSM6070096
Status Public on Apr 30, 2022
Title medullary thymic epithelial cells, immature, donor 214 [pt214_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: 6 days
donor sex: female
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
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
BioSample SAMN27918986
SRA SRX15018777

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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