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Sample GSM7051533

Query DataSets for GSM7051533

Status

Public on Jun 07, 2023

Title

10_1110.Liver_Arcy_M

Sample type

SRA

Source name

liver

Organism

Mus musculus

Characteristics

tissue: liver
Sex: M
genotype: Ar c/y
age: 11.2857142857143
treatment: N/A
time: N/A
fragment length: 150bp
library kit: mRNA Direct kit, Life Technologies

Extracted molecule

total RNA

Extraction protocol

Whole kidney total RNA were extracted using Qiagen’s RNeasy Mini Kit.
Sample 1- 67 and sample 98 - 188 were submitted to the Genome Access Technology Center at the McDonnell Genome Institute at University of Washington in St. Louis. Samples 1- 67, sample 98 - 145 were prepared according to Clontech SMARTer library kit manufacturer’s protocol, sample 146 - 188 were prepared according to polyA selection library kit manufacturer’s protocol. Sample 1- 67 were indexed, pooled, and sequenced on Illumina HiSeq2500 platform for 50-bp single-end. Sample 98 - 188 were indexed, pooled, and sequenced on llumina NovaSeq S4 2X150 (4 lanes). Sample 68 to Sample 97 were indexed, pooled and sequenced at BGI genomics with DNBseq platform according to the manufacturer's protocol. For sample 146 - 188, Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

146_155_all.gene_counts.txt

Data processing

For sample 1- 145, RNA-seq reads from fastq with length lower than 20, average quality lower than 20 were filtered through Fastp version 0.20.1. Filtered reads were then aligned to the Ensembl release 103 primary assembly by STAR version 2.7.9a. Gene counts were derived from featureCount version 2.0.1.
For sample 146 - 188, RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa; For sample 1 - 145: Mus_musculus.GRCm39.103.gtf; For sample 146 - 188: Mus_musculus.GRCm39.101.gtf
Supplementary files format and content: 1_WashU_50SE_counts.txt; 2_BGI_PE150_counts.txt; 3_WashU_PE150_counts.txt
Supplementary files format and content: 146_155_all.gene_counts.txt, 156_188_all.gene_counts.txt

Submission date

Feb 20, 2023

Last update date

Jun 07, 2023

Contact name

Jing Liu

E-mail(s)

jing.liu@med.usc.edu

Phone

3034428077

Organization name

University of Southern California