|
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
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|
|
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 |