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Sample GSM8023905 Query DataSets for GSM8023905
Status Public on May 13, 2024
Title Ctrl_LN_CITE
Sample type SRA
Source name Inguinal lymph node
Organism Mus musculus
Characteristics tissue: Inguinal lymph node
time: 10 week old mice
cell type: Dendritic Cells
genotype: WT
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 (
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
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
BioSample SAMN39487343
SRA SRX23304940

Supplementary file Size Download File type/resource
GSM8023905_cite_ctrl1.barcodes.tsv.gz 21.6 Kb (ftp)(http) TSV
GSM8023905_cite_ctrl1.features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSM8023905_cite_ctrl1.matrix.mtx.gz 37.4 Mb (ftp)(http) MTX
GSM8023905_cite_ctrl2.barcodes.tsv.gz 21.0 Kb (ftp)(http) TSV
GSM8023905_cite_ctrl2.features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSM8023905_cite_ctrl2.matrix.mtx.gz 37.5 Mb (ftp)(http) MTX
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Raw data are available in SRA

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