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Experiment information
Accession CRX347405
Organism Mus musculus
Title AKI72h
BioProject PRJCA008567
BioSample SAMC628420
Platform Illumina HiSeq X Ten
Library
Library name Construction protocol Strategy Source Selection Layout
Sequencing data from 10X genomics was processed with CellRanger software package (version 2.1.0) with default mapping arguments. For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 human transcriptome (UCSC) using Hisat2 (version 2.10). Uniquely mapped reads were counted by HTSeq package83 and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene RNA-Seq TRANSCRIPTOMIC PCR PAIRED
Processing Planned read length (bp) for mate 1: 150
Planned read length (bp) for mate 2: 150
Insert size (bp): 400
Release date2022-03-15
Run
Run accession Run data file information
File nameFile size (MB)
CRR401412 CRR401412_f1.fastq.gz
CRR401412_r2.fastq.gz 		4,725.37
3,882.01
CRR401413 CRR401413_f1.fastq.gz
CRR401413_r2.fastq.gz 		4,583.69
3,722.32
CRR401414 CRR401414_f1.fastq.gz
CRR401414_r2.fastq.gz 		4,743.1
3,856.47
CRR401415 CRR401415_f1.fastq.gz
CRR401415_r2.fastq.gz 		4,717.32
3,868.79
CRR401416 CRR401416_f1.fastq.gz
CRR401416_r2.fastq.gz 		3,787.87
3,060.13
CRR401417 CRR401417_f1.fastq.gz
CRR401417_r2.fastq.gz 		3,697.49
2,959.35
CRR401418 CRR401418_f1.fastq.gz
CRR401418_r2.fastq.gz 		3,775.81
3,025.25
CRR401419 CRR401419_f1.fastq.gz
CRR401419_r2.fastq.gz 		3,762.8
3,041
CRR401420 CRR401420_f1.fastq.gz
CRR401420_r2.fastq.gz 		4,755.48
3,862.54
CRR401421 CRR401421_f1.fastq.gz
CRR401421_r2.fastq.gz 		4,628.77
3,720.9
CRR401422 CRR401422_f1.fastq.gz
CRR401422_r2.fastq.gz 		4,750.11
3,822.24
CRR401423 CRR401423_f1.fastq.gz
CRR401423_r2.fastq.gz 		4,728.47
3,837.86
CRR401424 CRR401424_f1.fastq.gz
CRR401424_r2.fastq.gz 		3,966.59
3,249.63
CRR401425 CRR401425_f1.fastq.gz
CRR401425_r2.fastq.gz 		3,858.13
3,125.6
CRR401426 CRR401426_f1.fastq.gz
CRR401426_r2.fastq.gz 		3,981.14
3,229.48
CRR401427 CRR401427_f1.fastq.gz
CRR401427_r2.fastq.gz 		3,959.19
3,239.04
SubmitterMin Zhang (mzhangcool@yeah.net)
Organizationthe Fifth Medical Center of PLA General Hospital
Date submitted2022-03-07
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