|
| Status |
Public on May 13, 2024 |
| Title |
TDLN_CITE |
| Sample type |
SRA |
| |
|
| Source name |
Inguinal lymph node of tumor bearing mouse
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Inguinal lymph node of tumor bearing mouse
time: 4 weeks following 4-hydroxy-tamxifen tumor induction
cell type: Dendritic Cells
genotype: BRafCA, PtenloxP, Tyr::CreERT2
strain: C57BL/6
|
| Growth protocol |
B6.Cg-Tg(Tyr-cre/ERT2)13BosBraftm1MmcmPtentm1Hwu/BosJ mice from Jackson Lab were induced with 4HT on the back of the mice . Tumor were allowed to for 4 weeks at which point the inguinal TDLN or tumor was collected.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lymph nodes were digested in collagenase and Dnase and tumor was digested using collagenase DNase and Hyaluronidase. DCs were collected by FACS sorting for Lin- Cd11c+ MHCIIhi cells. During the antibody staining process CITEseq oligo tagged antibodies were incubated along with the fluorescence conjugated antibodoies for cell sorting. For cell hashing, an n=2 was used with DCs sorted from two independent mice and labeled with either Totalseq-B0301 Hashtag 1 or TotalseqB0302 Hashtag2.
Libraries were constructed using 10x Genomics default protocols following the Chromium 3' v3.1. A separate antibody CITEseq barcode library was created using the 10x Genomics feature barcoding primer set.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics Next Gem Single Cell 3' Gene Expression
|
| Data processing |
Sequencing was demultiplexed, the barcodes were identified and the genes were counted using the CellRanger 6.0.1 pipeline and cell ranger multi was used to resolve cell hashtags (https://www.10xgenomics.com/support/software/cell-ranger/release-notes/cr-release-notes)
Assembly: mm10
Supplementary files format and content: tab seperated values and matrix files
|
| |
|
| Submission date |
Jan 18, 2024 |
| Last update date |
May 13, 2024 |
| Contact name |
Brent Hanks |
| E-mail(s) |
brent.hanks@duke.edu
|
| Organization name |
Duke University
|
| Department |
Medicine
|
| Street address |
308 Research Dr
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE253586 |
A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression [CITEseq] |
| GSE253593 |
A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression |
|
| Relations |
| BioSample |
SAMN39487342 |
| SRA |
SRX23304941 |
