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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2020 |
| Title |
KO-GT cortex1 |
| Sample type |
SRA |
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| Source name |
KO-GT cortex
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: MECP2 KO
treatment: Gene therapy-treated
tissue: Cerebral cortex
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| Treatment protocol |
3 WT and 3 KO mice were treated with the PHP.eB-iMeCP2 AAV9 vector; 3 WT and 3 KO mice were treated with the PHP.eB-GFP AAV9 vector
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
FASTQ reads were quality checked and adaptor trimmed with FastQC (Andrews, S.. FastQC A Quality Control tool for High Throughput Sequence Data).
High quality trimmed reads were mapped to the mm10/GRCm38.p6 reference genome with Bowtie2 v2.3.4.3 (Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359).
Gene counts were calculated with featureCount using latest GENCODE main annotation file (Liao, Y., Smyth, G. K., & Shi, W. (2014). FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930).
Differential gene expression was calculated with DESeq2 (Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550).
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: featureCount read counts
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| Submission date |
Jan 16, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Luca Massimino |
| E-mail(s) |
admin@lucamassimino.com
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| Phone |
+393389039500
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| Organization name |
Ospedale San Raffaele
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| Department |
Gastroenterology
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| Street address |
Via Olgettina, 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE125155 |
Whole brain delivery of an instability-prone Mecp2 transgene improves behavioral and molecular pathological defects in mouse models of Rett syndrome |
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| Relations |
| BioSample |
SAMN10754821 |
| SRA |
SRX5254281 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3564334_D1_trimmed_counts.tabular.txt.gz |
282.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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