|
| Status |
Public on Mar 20, 2023 |
| Title |
Wild-type; sample 1 (adult mesenteric lymph nodes) |
| Sample type |
SRA |
| |
|
| Source name |
mesenteric lymph node
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mesenteric lymph node
genotype: wild-type C57/BL6
Sex: Male
age in_weeks: 18.0
treatment: N/A
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from tissue samples was extracted using TRIzol reagent (Invitrogen) following the manufacture’s protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Wild-type; sample 1
|
| Data processing |
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts, normalized fragments-per-kilobase-per-million-mapped (FPKM), or normalized transcripts-per-million-mapped (TPM).
|
| |
|
| Submission date |
Nov 28, 2022 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Matthew D Galbraith |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pharmacology & Linda Crnic Institute for Down Syndrome
|
| Street address |
RC1-N, Mail Stop 8303, Rm. P18-6114 12800 E. 19th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE218890 |
Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult mouse mesenteric lymph nodes |
| GSE219039 |
Transcriptome analysis of interferon receptor locus dosage correction in a mouse model of Down syndrome |
|
| Relations |
| BioSample |
SAMN31891895 |
| SRA |
SRX18397908 |
