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| Status |
Public on May 26, 2022 |
| Title |
AdV 2 IEL |
| Sample type |
SRA |
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| Source name |
Small intestine epithelium
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Small intestine epithelium
time: 10 days post treatment
infection status: mAdV-2 infection
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| Extracted molecule |
total RNA |
| Extraction protocol |
For bulk RNAseq: Sorted cells (800 cells) were lysed in a guanidine thiocyanate buffer (TCL buffer, QIAGEN) supplemented with 1% b-mercaptoethanol.
RNA was isolated by solid-phase reversible immobilization bead cleanup using RNAClean XP beads (Agentcourt, A63987), reversibly transcribed, and amplified as described (Trombetta et al., 2014).
Uniquely barcoded libraries were prepared using the Nextera XT kit (Illumina) following the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq500 for a total yield of 400M reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw fastq files were processed by using the mouse transcriptome with the kallisto (v0.46) software (Bray et al., 2016).
Analysis of transcript quantification was performed at the gene level by using the sleuth (v0.30) package for R (Pimentel et al., 2017)
We modeled batch effect and our experimental design using the sleuth_fit function and detected differentially expressed genes between all groups by the likelihood ratio test (LRT). To determine significantly expressed genes between group pairs, we used the wald-test function.
TCRa and TCRb CDR3 sequences were reconstructed in silico using MixCR software (Bolotin et al., 2015) and the extracted sequences were analyzed with the Immunarch package (v0.6.5) for R (10.5281/zenodo.3893991).
Genome_build: Gencode M23 GRCm38
Supplementary_files_format_and_content: tab-delimited tsv files (Kallisto)
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| Submission date |
Feb 09, 2022 |
| Last update date |
May 27, 2022 |
| Contact name |
Roham Parsa |
| E-mail(s) |
Rohamparsa@gmail.com
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| Phone |
2123277521
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| Organization name |
Rockefeller University
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| Lab |
Mucosal Immunology
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| Street address |
1230 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE196417 |
Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection |
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| Relations |
| BioSample |
SAMN25810906 |
| SRA |
SRX14113225 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5880674_abundance1.tsv.gz |
1.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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