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Sample GSM6252826 Query DataSets for GSM6252826
Status Public on Apr 28, 2023
Title Tumor, Control, mRNA-derived cDNA
Sample type SRA
 
Source name Tumor
Organism Mus musculus
Characteristics tissue: Tumor
cell type: CD11b+ myeloid cells
library type: mRNA
antibodies/tags: none
treatment: Control
Treatment protocol MC38 tumors were received irradition (20 Gy, one dose), three days after IR, cells were collected
Growth protocol CD45+CD11b+Ly6Chi were sorted from MC38 tumors or blood of MC38 tumor-bearing mice
Extracted molecule polyA RNA
Extraction protocol first use totalseq B for hashtagging, then use a Takara iCell 8 and a MissionBio Tapestri
The libraries were performed using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1
CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
RRW-01-barcodes.tsv.gz
RRW-01-features.tsv.gz
RRW-01-matrix.mtx.gz
Data processing The demultiplexing, barcoded processing and gene counting were made using 10X Genomics Cell Ranger (v6.0.1).
Further processing was done with Seurat (v4.0.6) (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
 
Submission date Jun 17, 2022
Last update date Apr 28, 2023
Contact name Xiaoyang Dou
E-mail(s) xiaoyang.dou@sibcb.ac.cn
Organization name Center for Excellence in Molecular Cell Science, CAS
Street address 320 Yue Yang Road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL24247
Series (2)
GSE206381 YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [CITE-Seq]
GSE206387 YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells
Relations
BioSample SAMN29180201
SRA SRX15783098

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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