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Status |
Public on Jan 15, 2020 |
Title |
01wCHSCB |
Sample type |
SRA |
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Source name |
subcondral bone
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Organism |
Equus caballus |
Characteristics |
age: 1 week Sex: male tissue: subcondral bone location: tarsocrural joint individual: foal_3
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Extracted molecule |
total RNA |
Extraction protocol |
Samples were collected immediately following euthanasia and were flash frozen in liquid nitrogen or placed in RNAlater (Qiagen, Valencia, CA) at 4°C for 24-48 hours prior to storage at -80°C. Frozen samples were pulverized and placed in TRIzol reagent (Invitrogen, Carlsbad, CA) prior to mechanical homogenization. RNA extraction was performed on spin columns using the RNeasy Micro Kit (Qiagen, Valencia, CA) per manufacturer instructions. Standard library preparation and sequencing (100 base-pair, paired-end) on an Illumina Hi-Seq sequencer (90 samples on a Hi-Seq 2500, 22 samples on a Hi-Seq 4000)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
Quality control on all 56 samples (112 paired-end files) was performed using fastp (version 0.19.5) and summarized using MultiQC (version 1.6) All fastq files were trimmed using Trimmomatic(version 0.38) in paired end mode to trim any remaining adaptors, then trim leading or trailing bases with quality scores below 28, then discarding a read pair if either read was shorter than 30 bases Salmon (version 0.11.3) was used to quasi-map reads in paired-end mode to quantify transcript abundance (with additional arguments –seqBias --gcBias –numBootstraps=30) to the EquCab3.0 genome assembly utilizing NCBI Annotation Release 103 R package tximport was used to estimate gene-level counts from transcript-level quantification. For the articular cartilage tissue (AC0), two individual horses had two samples taken at slightly different locations (ACD vs. ACS) in the stifle joint. Gene-level counts for the ACD and ACS samples from the same horse were added together at the gene-level as they looked extremely similar to each other. Reads were filtered and normalized (TMM) using edgeR, surrogate variables were calculated and counts were corrected using sva, and DE analysis performed using limma-trend Genome_build: EquCab3.0 Supplementary_files_format_and_content: tab-delimited files with normalized log2(cpm) values for 54 of 56 samples
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Submission date |
Aug 02, 2019 |
Last update date |
Jan 15, 2020 |
Contact name |
Ann Marie Kemper |
E-mail(s) |
amkemper@illinois.edu
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Organization name |
University of Illinois
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Street address |
1008 W Hazelwood Dr
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City |
Urbana |
State/province |
IL |
ZIP/Postal code |
61802 |
Country |
USA |
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Platform ID |
GPL24409 |
Series (1) |
GSE135322 |
Differential gene expression in articular cartilage and subchondral bone of neonatal and adult horses |
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Relations |
BioSample |
SAMN12476147 |
SRA |
SRX6647502 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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