|
| Status |
Public on Sep 07, 2018 |
| Title |
miR-CKO1 |
| Sample type |
SRA |
| |
|
| Source name |
miR-CKO_DRG
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed C57/Bl6 x 129/SvEv
genotype/variation: miR conditional knockout
developmental stage: E12.5
tissue: lumbar dorsal root ganglia (DRG)
|
| Growth protocol |
miR-183-96-182-flox/+ mice (Peng et al. (2017) Science 356, 1168-1171) were crossed with Wnt1-Cre-129/SvEv mice (Danielian et al. (1998) Current biology 8, 1323-1326) to obtain Wnt1-Cre; miR-183-96-182-flox/+ mice. These were in turn mated to obtain Wnt1-Cre; miR-183-96-182-flox/flox mice and Wnt1-Cre control mice.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mouse lumber DRG tissue was dissected from E12.5 embryos.
Total RNA was isolated using Trizol Reagent (Invitrogen) and processed with TruSeq Stranded mRNA Sample Prep Kit (Illumina/USA) .
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
miR CKO1
Run00182_L6_BC1V41ACXX_TS5_ACAGTG
|
| Data processing |
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that the molecule counting by unique molecule identifiers was omitted.
Sequence reads were aligned to the mouse genome using Bowtie1 allowing for up to 3 mismatches.
The data was further analyzed using Qlucore omics explorer.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Comma separated table of read counts normalized by kilobase transcript length and to a million per sample (RPKM)
|
| |
|
| Submission date |
Feb 16, 2018 |
| Last update date |
Sep 07, 2018 |
| Contact name |
Sten Linnarsson |
| Organization name |
Karolinska Institutet
|
| Department |
Medical Biochemistry and Biophysics
|
| Lab |
Molecular Neurobiology
|
| Street address |
Scheeles väg 1
|
| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE110714 |
RNA-seq of miR-183 knockout mouse dorsal root ganglia |
|
| Relations |
| BioSample |
SAMN08556549 |
| SRA |
SRX3714431 |
