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| Status |
Public on Jan 15, 2023 |
| Title |
Wild type replicate 5 |
| Sample type |
SRA |
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| Source name |
Esophagus
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| Organism |
Mus musculus |
| Characteristics |
tissue: Esophagus
strain: 129SvE
genotype: wild type
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Esophagi were snap frozen with liquid nitrogen and stored at ‐80°C until RNA isolation. Total RNA was isolated from the inner esophagi of WT or R1 mice (Direct‐zol RNA miniprep Plus; Zymo Research Corp., Irvine CA). PolyA selected mRNA libraries were generated using the Illumina TruSeq Stranded Library protocol, and mRNA samples were pooled and sequenced on a HiSeq2500.
PolyA selected mRNA libraries were generated using the Illumina TruSeq Stranded Library protocol, and mRNA samples were pooled and sequenced on a HiSeq2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
WT_2929
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| Data processing |
Raw fastq files were trimmed for quality and adapter contamination using Cutadapt v2.10
Trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3
Gene-level expression quantification was performed using RSEM v1.3.0
Differential expression analysis was performed using the R package limma with voom normalization
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and fpkm
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| Submission date |
Jan 15, 2022 |
| Last update date |
Jan 15, 2023 |
| Contact name |
Karen Laky |
| E-mail(s) |
klaky@niaid.nih.gov
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| Phone |
301 961-5419
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| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
FARS
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE193756 |
TGFbR signaling in squamous epithelial cells plays a fundamental role in controlling tissue specific allergic inflammation |
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| Relations |
| BioSample |
SAMN25025961 |
| SRA |
SRX13799322 |
| 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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