|
| Status |
Public on Jun 27, 2023 |
| Title |
Kir21_VIP_Non_Trans_BioRep_2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Visual Cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Visual Cortex
Sex: f
genotype: INTACT wt/ki x VIP Cre wt/ki
treatment: 10 days dark housed
aav injection: AAV-Syn1-Kir2.1-2a-mScarlet-KASH
transduced: Non Transduced (i.e. non infected)
cell type: VIP
|
| Treatment protocol |
At P55-60 animals were injected with one of the above AAVs in the visual cortex and were put in dark housing 3 days later for 10-12 days. Visual cortices were harvested in the dark or after 1hr of re-exposure to light and the tissue was stored in -80C
|
| Growth protocol |
Animals were standard housed until p55-60
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A nuclear suspension was prepared from frozen visual cortices and subsequently nuclei were FACS sorted directly into a lysis buffer.
Libraries were prepared based on Meso-Seq protocol. Briefly, 50-100 nuclei were collected by FACS directly into 2.03 µl lysis buffer (0.2% Triton X-100 in ddW) supplemented with dNTPs (2mM each), SMART-dT30VN primers (1mM), ERCC (1:1.25x107), and RNAse inhibitor. RT was performed directly on isolated nuclei, followed by PCR-amplification (17 cycles). RNA is cleaned using Agencourt Ampure XP beads (Beckman Coulter) and cDNA libraries were generated using Nextera XT (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Kir21_VIP_Non_Trans_BioRep_2
|
| Data processing |
Basecall and quality scoring was performed by the RTA software, version 2.11.3.0
Sequenced reads were trimmed for adaptor sequence using Cutadapt v1.18 and mapped to the mm10 genome using STAR version 2.5.3a.
Reads in genes (intronic and exonic together) were counted using Homer v4.9.1.
Assembly: mm10
Supplementary files format and content: .csv files include raw read counts for every gene in the sample
|
| |
|
| Submission date |
Mar 14, 2023 |
| Last update date |
Jul 28, 2023 |
| Contact name |
Ivo Spiegel |
| E-mail(s) |
ivo.spiegel@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
234 Herzl St
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE210658 |
Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex |
| GSE227342 |
Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex (RNA-Seq II) |
|
| Relations |
| BioSample |
SAMN33760176 |
| SRA |
SRX19676760 |
