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Experiment information
Accession CRX347404
Organism Mus musculus
Title AKI48h
BioProject PRJCA008567
BioSample SAMC628419
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)
CRR401396 CRR401396_f1.fq.gz
CRR401396_r2.fq.gz 		3,425.84
2,905.19
CRR401397 CRR401397_f1.fq.gz
CRR401397_r2.fq.gz 		3,479.58
2,958.15
CRR401398 CRR401398_f1.fq.gz
CRR401398_r2.fq.gz 		3,476.92
2,961.64
CRR401399 CRR401399_f1.fq.gz
CRR401399_r2.fq.gz 		3,462.23
2,940.06
CRR401400 CRR401400_f1.fq.gz
CRR401400_r2.fq.gz 		3,515.2
3,046.3
CRR401401 CRR401401_f1.fq.gz
CRR401401_r2.fq.gz 		3,483.34
3,013.9
CRR401402 CRR401402_f1.fq.gz
CRR401402_r2.fq.gz 		3,541.65
3,074.38
CRR401403 CRR401403_f1.fq.gz
CRR401403_r2.fq.gz 		3,542.62
3,082.06
CRR401404 CRR401404_f1.fq.gz
CRR401404_r2.fq.gz 		3,494.09
2,927.88
CRR401405 CRR401405_f1.fq.gz
CRR401405_r2.fq.gz 		3,468.64
2,899.61
CRR401406 CRR401406_f1.fq.gz
CRR401406_r2.fq.gz 		3,495.93
2,925.48
CRR401407 CRR401407_f1.fq.gz
CRR401407_r2.fq.gz 		3,434.28
2,868.08
CRR401408 CRR401408_f1.fq.gz
CRR401408_r2.fq.gz 		2,695.49
2,279.18
CRR401409 CRR401409_f1.fq.gz
CRR401409_r2.fq.gz 		2,678.25
2,261.95
CRR401410 CRR401410_f1.fq.gz
CRR401410_r2.fq.gz 		2,707.38
2,290.94
CRR401411 CRR401411_f1.fq.gz
CRR401411_r2.fq.gz 		2,714.15
2,301.65
SubmitterMin Zhang (mzhangcool@yeah.net)
Organizationthe Fifth Medical Center of PLA General Hospital
Date submitted2022-03-07
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Experiments(3)