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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 06, 2023 |
| Title |
D18-182156 |
| Sample type |
SRA |
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| Source name |
Non-tumoral thymus
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| Organism |
Mus musculus |
| Characteristics |
tissue: Normal Thymus_DN3
genotype: RERT2-Cdc20(D/AAA)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from primary cells or tumors, using the RNeasy Plus Mini Kit (Qiagen) and sequenced on an Illumina HiSeq2000. At least 5000 cells were sorted directly in lysis buffer for specifc T cell progenitor populations in the thymus while at least 5 million cells have used for RNA isolation form thymic lymphomas. Unless otherwise indicated samples from tumors were isolated without sorting specific polulations.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNASeq180717_gene_counts.txt
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| Data processing |
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, sample contamination estimation, intergenic reads percentile calculation, intronic reads percentile calculation, UTR reads percentile calculation, gene coding reads percentile calculation, and rRNA contamination estimation. Besides, sense to antisense reads ratio was calculated to indicate strand specificity. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against GRCm38/mm10 reference for mouse sequences using STAR/2.5.3a
Gene expression was quantitated using RSEM v. 1.3.0
Gene set enrichment analyses was performed by GSEA 2-2.0.13 basing on normalized expression values
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt file. Each gene per row and each sample per column(raw counts from RSEM)
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| Submission date |
May 06, 2021 |
| Last update date |
Jun 06, 2023 |
| Contact name |
Dunaduan Ma |
| E-mail(s) |
maduanduan8@gmail.com
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| Organization name |
MIT
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| Department |
Koch Institute
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| Lab |
Bioinformatics Core
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| Street address |
77 Massachusetts Ave
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| City |
Cambridge |
| State/province |
Ma |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE174012 |
Bulk RNA sequencing from sorted thymic populations and tumors from control Cdc20(+/D) and aneuploid Cdc20(D/AAA)mice |
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| Relations |
| BioSample |
SAMN19057323 |
| SRA |
SRX10810056 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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