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| Status |
Public on Feb 07, 2020 |
| Title |
mTECs_Chd4cKO_1_RNA-seq |
| Sample type |
SRA |
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| Source name |
mTECs
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6x129P2
genotype/variation: Chd4cKO
cell type: TECs
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from sorted mTECs is extracted by Maxwell® 16 Automated Purification System (Promega).
Library for sequencing was synthesized using SMART-seq v4 Ultra Low Input RNA Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
mTECs_Chd4cKO_1
mTECs from Chd4 flox/flox Foxn1-Cre mice
processed data file: RNA_seq_data_summary.txt
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| Data processing |
Data was trimmed and mapped to reference Mus musculus (mm10) genome by using CLC genomics Workbench v.9.0 (CLC).
RPKM was calculated by using CLC genomics Workbench v.9.0 (CLC).
log(RPKM) was calculated and DEGs were detected from total exon reads by using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNA_seq_data_summary.txt
Supplementary_files_format_and_content: Aire_KO_RNA_seq.csv, Chd4_cKO_RNA_seq.csv, Fezf2_KO_RNA_seq.csv
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| Submission date |
Feb 06, 2020 |
| Last update date |
Mar 11, 2020 |
| Contact name |
Yoshihiko Tomofuji |
| Organization name |
University of Tokyo
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| Department |
Immunology
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| Lab |
Takanayagi's lab
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| Street address |
hongo 7-3-1
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| City |
bunkyo |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8654 |
| Country |
Japan |
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| Platform ID |
GPL18635 |
| Series (2) |
| GSE144877 |
RNA-seq analysis on mTECs from Fezf2KO, AireKO and Chd4cKO mice |
| GSE144880 |
RNA-seq, ChIP-seq, and ATAC-seq analyses of mTECs |
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| Relations |
| BioSample |
SAMN14051819 |
| SRA |
SRX7691559 |
| 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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