|
| Status |
Public on Apr 24, 2024 |
| Title |
Lamina propria, CD4 T cell, TCF7-, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Colon Lamina propria
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon Lamina propria
cell type: CD4 T cell
genotype: GFP- effector T cell
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was purified using the miRNeasy Micro Kit (QIAGEN).
cDNA was reversely transcribed from total RNA with oligo-dT primer, random hexamers with SuperScript™ II Reverse Transcriptase (Invitrogen) and then amplified with IS PCR primers and Kapa HiFi Hotstart Ready Mix (Roche). Then the cDNA library was fragmented and tagged with sequencing adapters using Nextera XT DNA Library Preparation Kit (Illumina), and finally ~500 bp amplicons were got. Quality of library was assessed using the High Sensitivity RNA ScreenTape Kit (Agilent Life Sciences). DNA was quantified using Quant-iT PicoGreen dsDNA Assay Kits (Invitrogen) and purified using AMPure XP beads (Beckman Coulter). Libraries were subjected to 2 × 100-bp paired-end sequencing on an Illumina NovaSeq 6000 (Illumina), generating at least 8 million uniquely mapped reads for each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
LPL_CD4_GFPNeg_2
|
| Data processing |
FASTQ was merged and filtered using fastp (v0.23.3)
Reads were aligned with the STAR aligner (2.7.10b)
Samtools (v1.17) was used to index and sort BAM friles from STAR
QC report was performed with bamCoverage (v3.5.1), and Qualimap (v.2.2.2-dev)
Raw and transcripts per million reads (TPM) counts were taken from STAR’s BAM aligned output.
Assembly: mm10
Supplementary files format and content: bulk_counts.txt.gz raw counts for 6 samples in TAB delimited TXT
Supplementary files format and content: bulk_tpm.txt.gz transcripts per million reads (TPM) counts for 6 samples in TAB delimited TXT
Supplementary files format and content: bulk_metadata.txt.gz metadata for 6 samples in TAB delimited TXT
|
| |
|
| Submission date |
Apr 19, 2024 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Pandurangan Vijayanand |
| E-mail(s) |
vijay@lji.org
|
| Organization name |
La Jolla Institute for Immunology
|
| Department |
Vaccine Discovery
|
| Lab |
Vijayanand Lab
|
| Street address |
9420 Athena Circle
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE235665 |
Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans |
| GSE264463 |
Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans [bulkRNAseq_MouseLPL] |
|
| Relations |
| BioSample |
SAMN41021507 |
| SRA |
SRX24313517 |
