|
| Status |
Public on Nov 02, 2022 |
| Title |
TH2_Itgav-KO_1 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: Primary mouse TH2 cells
genotype: av_KO
|
| Growth protocol |
Splenic CD4+ TN cells from Cd4 CreERT2 control or alpha-v conditional knockout mice were flow-purified and cultured in vitro in TH1 or TH2 conditions for 5 days. On day 5, live CD4+ cells were flow-sorted for RNA analyses.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were flow sorted into PBS 50% FCS and RNA was extracted using RNeasy Plus micro kit (Qiagen). After assessment using a Bioanalyser (Agilent), RNA was processed for RNA-sequencing using an Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220,
and bar-coded using Ovation Ultralow Library Systems (Nugen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Samples were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequence data were trimmed to remove adaptors and sequences with a quality score below 30 using Trim Galore (v0.50, Babraham Bioinformatics)
sequences were aligned to the mouse genome (GRCm38) using STAR (v2.6.0a, Spliced Transcripts Alignment to a Reference, Alexander Dobin)
differential expression calculated using DEseq2 (v1.18.1)
Supplementary files format and content: GRCm38
Supplementary files format and content: DEseq2 output file
|
| |
|
| Submission date |
Nov 01, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Alastair Crisp |
| Organization name |
MRC Laboratory of Molecular Biology
|
| Street address |
Francis Crick Avenue
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE179210 |
Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation. |
| GSE217061 |
An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [RNA-seq] |
|
| Relations |
| BioSample |
SAMN31562175 |
| SRA |
SRX18114768 |
