|
| Status |
Public on Feb 18, 2022 |
| Title |
male cerebellum replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
male cerebellum replicate2
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cerebellum
development stage: Adult
gender: male
strain: C57BL/6J
library type: fr-firststrand (dUTP)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from mouse (C57BL/6J) adult brain, cerebellum, heart, colon, and gonad in both sexes were extracted. The RNAs were classified into two parts, one part was subsequently treated with Ribo-off rRNA Depletion Kit to remove ribosome RNA (rRNA). Then the VAHTS TM Stranded mRNA-seq Library Prep Kit for Illumina was used for strand-specific library preparation. After finished, the library was suquenced on the Illumina Nova platform. The another part was used to constructe for cDNA using P Clontech SMARTer PCR cDNA Synthesis Kit and PrimeSTAR GXL DNA Polymerase, followed by library preparation by using SMRTbellTM Template prep and sequencing on the Pacific Biosciences Sequel I platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
62_clean
|
| Data processing |
RNA-Seq: High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis.
RNA-Seq: We used FastqC (0.11.8) to evaluate the raw reads quality. Sequencing report tool was MultiQC (0.9).
Iso-seq: The Raw data was subjected to SmrtLink Pipeline ccs to self-correct and obtain full-length circular consensus sequencing (CCS) reads based on PacBio recommended pipeline. We used the SmrtLink Pipeline classify subprogram to distinguish full-length non-chimeric sequences with the limitation of the transcript length longer than 300bp and applied the SmrtLink Pipeline cluster subprogram to cluster the full-length non-chimeric sequences into full-length transcripts, and retained the full-length transcript supported by at least one full-length non-chimeric sequences. The LoRDEC program was used to correct the full-length transcripts based on the results of Illumina RNA-seq to improve the accuracy of the third-generation transcripts.
RNA-Seq: Reads were mapped to the corresponding reference genomes (mm10, ENSEMBL98) by Hisat2 (2.0.5) with parameters “-x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation that conbined reference annotation and Iso-seq full-length transcript.
RNA-Seq: The output of Hisat2 were converted to BAM format, sorted and only uniqe mapped reads were retained.
RNAseq: featurecounts (1.6.3) was used for counting reads with parameters "-s 2 -t exon -g gene_id".
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts of all the genes for each RN-Aseq sample, as well as Iso-seq full transcript gtf files.
Supplementary_files_format_and_content: mouse_reference_iso.txt: conversion from PacBioID to geneID
Supplementary_files_format_and_content: mouse_final.gtf: full length transcripts
Supplementary_files_format_and_content: Count.matrix.txt: count matrix table
|
| |
|
| Submission date |
Jun 02, 2021 |
| Last update date |
Mar 10, 2022 |
| Contact name |
Zhen-Xia Chen |
| E-mail(s) |
zhen-xia.chen@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Department |
College of Life Science and Technology
|
| Street address |
No.1 Shizishan Street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE176018 |
Hybrid sequencing characterizes expression and function of mouse pseudogenes |
|
| Relations |
| BioSample |
SAMN19514299 |
| SRA |
SRX11050001 |
