|
| Status |
Public on Nov 03, 2023 |
| Title |
Negative control.2 |
| Sample type |
SRA |
| |
|
| Source name |
-
|
| Organism |
Mus musculus |
| Characteristics |
tissue: -
cell type: -
genotype: -
|
| Treatment protocol |
MADM clone induction in the SC was adapted from previously described protocols (doi: 10.3791/61147; doi: 10.1016/j.neuron.2010.09.027).
|
| Growth protocol |
All animal procedures were approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and European Union animal law (license number: BMWF-66.018/0007-II/3b/2012 and BMWFW-66.018/0006-WF/V/3b/2017). Experimental mice were bred and maintained according to regulations approved by institutional animal care and use committee, institutional ethics committee and the guidelines of the preclinical facility (PCF) at IST Austria. Mice were housed at 21±1°C ambient temperature and 40–55% humidity in 12 hrs dark/light cycles. All mouse lines were kept in mixed C57/Bl6, FVB and CD1 genetic background. In some experiments, wild-type CD1 mice were also used. Both male and female littermates of the desired genotypes were used randomly. Mice were used at an age range from 2 – 8 months for breeding and from E9.5 to P30 for experiments. All efforts were made to minimize the number of animals used following the 3R principles.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (doi: 10.7554/eLife.52951; doi: 10.1038/nprot.2017.120) and optimized for speed and coverage of sparsely labelled cells of MADM clones. For details see publication.
cDNA libraries from E10 clones were prepared followed by Smart-seq2 protocol (doi: 10.1038/nprot.2014.006) using custom reagents (VBCF GmbH, Vienna)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
123625
|
| Data processing |
Read alignment with STAR (v.2.7.9a)
all downstream analyses were performed in R(v4.0.3)
Sum of exonic and intronic TPM values were calculated using the scater package (v1.18.6).
Assembly: GRCm39 and Gencode vM27
Supplementary files format and content: comma delimited text, matrix of combined exonic/introinc TPMs
|
| |
|
| Submission date |
Oct 11, 2023 |
| Last update date |
Nov 03, 2023 |
| Contact name |
Florian M Pauler |
| E-mail(s) |
florian.pauler@ista.ac.at
|
| Organization name |
Institute of Science and Technology Austria (IST Austria)
|
| Lab |
Hippenmeyer
|
| Street address |
Am Campus 1
|
| City |
Klosterneuburg |
| ZIP/Postal code |
3400 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE245102 |
Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus – MADM-CloneSeq E10 |
| GSE245106 |
Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus |
|
| Relations |
| BioSample |
SAMN37778734 |
| SRA |
SRX22066918 |
