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SRX21658848: GSM7765988: CD45+ cells of paracaspase-deficient Malt1 overexpression tumor; Mus musculus; RNA-Seq
3 ILLUMINA (HiSeq X Ten) runs: 359.3M spots, 107.8G bases, 39Gb downloads

External Id: GSM7765988_r1
Submitted by: Tsinghua University
Study: 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.
show Abstracthide Abstract
To invesitigate the additional paracaspase-independent tumor-promoting effect exist for Malt1. We thus collected E0771-Vector control tumor tissue, E0771 wildtype Malt1 (Malt1-WT) overexpression tumor tissue and E0771 paracaspase-deficient Malt1 (Malt1-PD) overexpression tumor tissue, and sorted out immune cells for 10× Genomics single cell RNA-sequencing (scRNA-seq). Overall design: First inject E0771-Vector control,E0771 Malt1-WT overexpression, and E0771 Malt1-PD overexpression cells into the mammary fatty pad of C57B6/J mice to form tumor. We thus collected E0771-Vector control tumor tissue, E0771 Malt1-WT overexpression tumor tissue and E0771 paracaspase-deficient Malt1 (Malt1-PD) overexpression tumor tissue, and sorted out immune cells by FACS for 10× Genomics single cell RNA-sequencing (scRNA-seq).
Sample: CD45+ cells of paracaspase-deficient Malt1 overexpression tumor
SAMN37313411 • SRS18826958 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7765988
Instrument: HiSeq X Ten
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC SINGLE CELL
Selection: cDNA
Layout: PAIRED
Construction 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.
Runs: 3 runs, 359.3M spots, 107.8G bases, 39Gb
Run# of Spots# of BasesSizePublished
SRR2594002793,338,06628G10Gb2024-04-18
SRR2594002815,451,9704.6G1.7Gb2024-04-18
SRR25940029250,495,99475.1G27.4Gb2024-04-18

ID:
29322703

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