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| Status |
Public on May 26, 2022 |
| Title |
PBS3 LP |
| Sample type |
SRA |
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| Source name |
Small intestine lamina propria
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Small intestine lamina propria
time: 10 days post treatment
infection status: PBS control
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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.
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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 |
SAMN25810895 |
| SRA |
SRX14113236 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5880685_abundance12.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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