|
| Status |
Public on Aug 30, 2022 |
| Title |
Resident (E11_2) |
| Sample type |
SRA |
| |
|
| Source name |
DN T cells derived from different LNs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: LN
genotype: wild type
treatment: B/6 mice were untreated. For identification of source tissue, cells from different lymph nodes were marked with unique hashtags before pooling.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice were sacrificed and lymph nodes were isolated. Single cell suspnesion was created. Single cell suspensions were staining with antibodies for 30min at 4 degrees and sorted for the desired population using FACS AriaIII.
Single cells were sorted using a FACSAria III (BD Biosciences), before being encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 or v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
Chromium single cell 3´v2 and v3 (10XGenomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CD62L negative, CD44 positive ITCs (multiplexed)
|
| Data processing |
The sequencing data was processed using CellRanger software.
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
|
| |
|
| Submission date |
May 18, 2021 |
| Last update date |
Aug 30, 2022 |
| Contact name |
Antoine-Emmanuel Saliba |
| E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
|
| Phone |
+49-931-31-81341
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2 / D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE174629 |
Lymphatic migration of unconventional T cells promotes site-specific immunity in distinct lymph nodes |
|
| Relations |
| BioSample |
SAMN19242000 |
| SRA |
SRX10920539 |
