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| Status |
Public on Aug 16, 2024 |
| Title |
Neocortex Chd8+/- 1 |
| Sample type |
SRA |
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| Source name |
P5 neocortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: P5 neocortex
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using DNeasy DNA extraction (Qiagen, 69504) kit. DNA concentrations were checked using Qubit Fluorometry and 100ng of DNA was used for RRBS library preparation using the Premium RRBS kit (Diagenode, C02030032).
DNA was digested using MspI overnight at 37˚C after which adapters were ligated. Prior to quantification by qPCR, fragments were selected based on fragment size using AMPure XP beads (Beckman Coulter, A63880). For qPCR quantification, 1µl of size-selected library, LUNA Universal qPCR Master Mix (New England Biolabs, M3003), 3.5µl of nuclease free H2O, and 0.5µl primer mix (from the RRBS kit) transferred to 96-well PCR plate. Libraries were pooled based on the formula (17 x 2-ΔCt , where ΔCt = Ctmax –Ctsample). Pooled libraries were topped up with nuclease free H2O before clean up with AMPure XP beads. Bisulfite conversion was performed using BS Conversion reagent (from the Premium RRBS kit), before enrichment PCR, quality control and clean-up.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RRBS single-end reads were trimmed using TrimGalore v0.4.4 with `--rrbs` option
Reads were aligned to reference mm39 genome using Bismark v0.20.0 aligner with option `--nucleotide_coverage`.
Aligned BAM files were sorted by coordinate using Samtools v1.9.
Reads mapped to Mitochondrial chromosomes or to unassembled contigs were removed.
Assembly: mm39
Supplementary files format and content: Methylation call files
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| Submission date |
Aug 15, 2024 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Albert Basson |
| E-mail(s) |
m.a.basson@exeter.ac.uk
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| Organization name |
University of Exeter
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| Street address |
Stocker Road
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| City |
Exeter |
| ZIP/Postal code |
EX44PY |
| Country |
United Kingdom |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE274977 |
Genotype-phenotype-epiphenotype analysis to decipher severity, penetrance, pleiotropy and mechanisms in CHD8-related neurodevelopmental disorder |
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| Relations |
| BioSample |
SAMN43210232 |
| SRA |
SRX25721711 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8463339_rrbshet1_CpG.txt.gz |
9.8 Mb |
(ftp)(http) |
TXT |
| GSM8463339_rrbshet1_CpG_conversionStats.txt.gz |
218 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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