|
| Status |
Public on Feb 19, 2020 |
| Title |
C1_R1_Non-adherent precursors_mouse1 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow derived
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: male
age: 8 to 10 weeks
|
| Growth protocol |
After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS, non-adherent cells were incubated for a second day in a fresh dish containing 0.6ng/ml CSF1 in alpha+ MEM /15% FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was harvested using RNeasy kit( QIAGEN) with DNase treatment on column. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
C1_R1
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt
|
| Data processing |
Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence- returning a fastq file (raw data)
Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner.
The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60
The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions
Tab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)
Ampliseq
Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Returning a fastq file (raw data) of reads associated with each of the 16000 barcoded primer pairs.
Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner.
The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60
The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions
Tab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)
Genome_build: Genome Reference Consortium mouse genome (GRCm39.p6)
Supplementary_files_format_and_content: tab-delimited text files include reads or log2 RPM for each sample showing all genes or differential expression between conditions.
|
| |
|
| Submission date |
Feb 18, 2020 |
| Last update date |
Feb 19, 2020 |
| Contact name |
James Harvey Steer |
| E-mail(s) |
jaysteer@gmail.com
|
| Organization name |
University of Western Australia
|
| Street address |
Hospital Avenue, QEII Medical Centre, M Block
|
| City |
Perth |
| State/province |
Western Australia |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE145437 |
Adhesion, motility and matrix-degrading gene expression changes in CSF-1-induced mouse macrophage differentiation |
|
| Relations |
| BioSample |
SAMN14124416 |
| SRA |
SRX7738687 |
