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| Status |
Public on Apr 18, 2024 |
| Title |
CD45+ cells of wildtype Malt1 overexpression tumor |
| Sample type |
SRA |
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| Source name |
tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
cell type: immune cell
treatment: Wildtype Malt1 overexpression
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspensions isolated from tumors developed from E0771-Vector control tumor tissue, E0771 Malt1-WT overexpression tumor tissue and E0771 paracaspase-deficient Malt1 (Malt1-PD) overexpression tumor tissue. About 10000 CD45+ live cells were sorted from tumors of each strain by BD FACS Aria ii. Reverse transcription, cDNA amplification and library preparation were performed using the Chromium Single Cell V(D)J Reagent Kits (10x Genomics, includes Cat# PN-1000006, Cat# PN-1000020, Cat# PN-1000009, and Cat # PN-120262) according to manufacturer’s protocol. Pair-end 150 bp sequencing was performed on Illumina HiSeq X Ten platform by Novogene Co.,Ltd. Single cell sequence data was pre-processed with Cell Ranger 3.0.2 (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, CD45+ cells in each group were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
FASTQ reads of 10× scRNA sequencing data were processed with GRCh38 reference genome using Cell Ranger (version 3.1, 10× Genomics). Downstream analyses of scRNA-seq data were performed in Seurat package version 3.2.0.(https://www.cell.com/cell/fulltext/S0092-8674(19)30559-8). Low quality cells were excluded from downstream analyses based on %mitochondrial reads <10, features per cell >500. All functions were run with default parameters. Identification of cell types is determined by the expression of the immune cell marker gene.
Assembly: hg38
Supplementary files format and content: single-cell RNA-seq expression counts files and matrix files
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| Submission date |
Sep 07, 2023 |
| Last update date |
Apr 18, 2024 |
| Contact name |
Hanqiu Zheng |
| E-mail(s) |
hanzheng@tsinghua.edu.cn
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| Organization name |
Tsinghua university
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| Street address |
Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE242554 |
Gene expression profile at single cell level of CD45+ immune cells from E0771-Vector control tumor tissue, E0771 wildtype Malt1 overexpression tumor tissue and E0771 paracaspase-deficient Malt1 overexpression tumor tissue. |
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| Relations |
| BioSample |
SAMN37313412 |
| SRA |
SRX21658847 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7765987_Malt1_WT_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM7765987_Malt1_WT_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7765987_Malt1_WT_matrix.mtx.gz |
160.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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