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Sample GSM5047303 Query DataSets for GSM5047303
Status Public on Jan 28, 2021
Title KL rep2
Sample type SRA
Source name Tumor sections of Tumor bearing lungs
Organism Mus musculus
Characteristics tissue: lungs
strain: C57BL/6
genotype: KrasLSL-G12D/+ Lkb2fl/fl
Extracted molecule total RNA
Extraction protocol Single-cell suspension were isolated from tumor-bearing KL mice using micro-dissection after 10 weeks of Ad-cre induction. And cells were prepared as described above. Single-cell RNA-seq libraries were prepared with Chromium Single cell 3’Reagent v3.0 Kits according to the manufacturer’s protocol. Single-cell suspensions were loaded on the Chromium Single Cell Controller Instrument (10×Genomics) to generate single cell gel beads in emulsions (GEMs). Briefly, 105 single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. About 15000-20000 cells were added to each channel with a targeted cell recovery estimate of 5000 cells (4400 and 2780 for 2 KL mice, respectively). After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform (HiSeq X Ten), and 151 bp paired-end reads were generated.
single cell RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description RNA from single cell using 10x genomics
Data processing Illumina Hiseq X Ten platform for sequencing with 151-bp paired-end reads strategy (Novogene)
Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev)
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.2.0) with default parameters
Genome_build: Mus_musculus_Ensemble_94
Supplementary_files_format_and_content: matrix.mtx with counts for every gene across two mice
Submission date Jan 27, 2021
Last update date Jan 29, 2021
Contact name 鹏 - 王
Phone +8613071211141
Organization name 武汉大学
Street address 169 Donghu nan road,Wucang District
City Wuhan
State/province 湖北省
ZIP/Postal code 430071
Country China
Platform ID GPL21273
Series (1)
GSE165641 10X genomics single cell RNA sequencing of tumor sections from tumor bearing KrasG12D/+Lkb1fl/fl(KL) mice after Ad-cre injection for 10 weeks
BioSample SAMN17609712
SRA SRX9961784

Supplementary file Size Download File type/resource
GSM5047303_KL2_count.tar.gz 87.0 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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