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| Status |
Public on Mar 17, 2019 |
| Title |
Mouse_IVD_Col2Cre_Control_RNAseq_replicaC1 |
| Sample type |
SRA |
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| Source name |
Intervertebral disc
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| Organism |
Mus musculus |
| Characteristics |
strain: C57B6/J
age: postnatal day 20
genotype: wild type
tissue: intervertebral disc
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| Extracted molecule |
total RNA |
| Extraction protocol |
Intervertebral discs from the thoracic and lumbar spine (T8-L5) of the 20-day-old Col2Cre; Adgrg6f/f and wild type control mice were isolated in cold PBS, snap frozen in liquid N2 and pulverized in liquid nitrogen. Each biological replicate contains itervertebral discs isolated from 2-3 mice.Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analyzed on Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). RNA fragments were reverse-transcribed to create the final cDNA libraries following the NEBNext® Ultra™ RNA Library Prep Kit (Illumina, San Diego, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
NM10
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| Data processing |
star (STAR_2.5.3a) --genomeDir mm10 --outSAMtype BAM SortedByCoordinate
htseq-count -s yes -r pos -t gene -f bam -i gene_name Mus_musculus.GRCm38.78.gtf
DESeq2 R library
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads count and normalized values for each Sample ...
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| Submission date |
Mar 16, 2019 |
| Last update date |
Mar 18, 2019 |
| Contact name |
Nadav Ahituv |
| E-mail(s) |
nadav.ahituv@ucsf.edu
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| Organization name |
UCSF
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| Street address |
1550 4th Street
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE128402 |
Transcriptomic analysis of intervertebral discs isolated from wild type and Adgrg6-deficient mice |
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| Relations |
| BioSample |
SAMN11153496 |
| SRA |
SRX5528175 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3673725_NM10.counts.txt.gz |
153.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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