logo
  1. Home
  2. Browse
  3. CRA006298
  4. CRX347403
Experiment information
Accession CRX347403
Organism Mus musculus
Title AKI24h
BioProject PRJCA008567
BioSample SAMC628418
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)
CRR401380 CRR401380_f1.fastq.gz
CRR401380_r2.fastq.gz 		3,336.76
2,689.15
CRR401381 CRR401381_f1.fastq.gz
CRR401381_r2.fastq.gz 		3,253.08
2,596.05
CRR401382 CRR401382_f1.fastq.gz
CRR401382_r2.fastq.gz 		3,312.63
2,644.75
CRR401383 CRR401383_f1.fastq.gz
CRR401383_r2.fastq.gz 		3,307.29
2,662.51
CRR401384 CRR401384_f1.fastq.gz
CRR401384_r2.fastq.gz 		4,375.78
3,513.23
CRR401385 CRR401385_f1.fastq.gz
CRR401385_r2.fastq.gz 		4,250.62
3,381.63
CRR401386 CRR401386_f1.fastq.gz
CRR401386_r2.fastq.gz 		4,371.14
3,477.93
CRR401387 CRR401387_f1.fastq.gz
CRR401387_r2.fastq.gz 		4,355.88
3,494.84
CRR401388 CRR401388_f1.fastq.gz
CRR401388_r2.fastq.gz 		3,581.26
2,943.64
CRR401389 CRR401389_f1.fastq.gz
CRR401389_r2.fastq.gz 		3,484.89
2,828.83
CRR401390 CRR401390_f1.fastq.gz
CRR401390_r2.fastq.gz 		3,564.71
2,896.23
CRR401391 CRR401391_f1.fastq.gz
CRR401391_r2.fastq.gz 		3,557.14
2,913
CRR401392 CRR401392_f1.fastq.gz
CRR401392_r2.fastq.gz 		3,834.03
3,102.03
CRR401393 CRR401393_f1.fastq.gz
CRR401393_r2.fastq.gz 		3,712.11
2,972.81
CRR401394 CRR401394_f1.fastq.gz
CRR401394_r2.fastq.gz 		3,829.32
3,067.42
CRR401395 CRR401395_f1.fastq.gz
CRR401395_r2.fastq.gz 		3,817.75
3,083.43
SubmitterMin Zhang (mzhangcool@yeah.net)
Organizationthe Fifth Medical Center of PLA General Hospital
Date submitted2022-03-07
Related experiments
Experiments(3)