Representative examples of the four major patterns of clonal evolution inTP53-sAML patients: bi-allelic mutations (b), hemizygous mutations (c), parallel evolution (d) andJAK2negative bi-allelic evolution (e). The numbers in parenthesis indicate the number of patients in each category...
Reads in the R2 FASTQ files were pre-processed so that the sequences to the left and right of the lineage barcodes (BC) were trimmed. Lineage barcodes shorter than 37 bp were discarded. Cell barcodes (Cell) were extracted from the corresponding Seurat object of the dataset to generate a...
Fastq files from the 2 lanes were concatenated to make a single R1 and R2 file per library. Fastq files were processed using the Trailmaker data analysis platform using the mTSC custom transcriptome for the alignment step. Each sample was filtered to exclude low quality cells (UMIs/cell, Mitoc...
run-trust4 -f hg38_bcrtcr.fa --ref human_IMGT+C.fa -u path_to_10X_fastqs/*_R2_*.fastq.gz --barcode path_to_10X_fastqs/*_R1_*.fastq.gz --readFormat bc:0:15 --barcodeWhitelist cellranger_folder/cellranger-cs/VERSION/lib/python/cellranger/barcodes/737K-august-2016.txt [other ...
(KLF1andAHSP) and haemostasis (ITGA2BandSERPINE2; Fig.2a,b). Of note, genes involved in response to reactive oxygen species (ROS;FOXO3,SOD1,DUSP1,JUNandFOS) were upregulated in HSC/MPPs in the Ts21 fetal liver compared with the bone marrow (Fig.2a,b), and not differentially ...
Publicly available raw FASTQ files (n = 32) from Zhao et al. [20] underwent quality assessment using FastQC v.0.12.1 (https://github.com/s-andrews/FastQC) with default parameters. Adapters and low-quality bases were trimmed from the reads using TrimGalore v.0.6.10 (https://github....
.gz Sample3_R2_file.fastq.gz > Combined_R2_file.fastq.gz cat Sample1_I1_file.fastq.gz Sample2_I1_file.fastq.gz Sample3_I1_file.fastq.gz > Combined_I1_file.fastq.gz cat Sample1_I2_file.fastq.gz Sample2_I2_file.fastq.gz Sample3_I2_file.fastq.gz > Combined_I2_file.fastq....
The raw FASTQ files are only provided for mouse due to human patient privacy concerns. Additional Resources Analysis and visualization of scRNA-seq datasets from both human and mouse can be also performed at http://crcleukocyte.cancer-pku.cn/. Acknowledgments We thank Y.S. Li for sample ...
Reads were preliminarily filtered and processed using the Cell Ranger Single-Cell Software Suite (release 5.0.1) with default and recommended parameters. After the demultiplex raw data were generated using Illumina sequencers, the FASTQ files were aligned to the reference genome ofOvis aries. Only ...
The fastq files for single-cell and bulk RNA-seq are available. The data can be obtained from the National Genomics Data Center (PRJCA016521). The spatiotemporal expression patterns in the de-etiolating atlases are available at http://182.92.183.62:4576/ or http://www.pku-iaas.edu.cn/li...