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| Status |
Public on Aug 01, 2024 |
| Title |
MP-9_DMSO_4hrBIC |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
cell type: DIV17 Cortical Cultures
drug: DMSO
treatment: 4hr bicuculline
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| Growth protocol |
Day in vitro (DIV) primary neuron cultures from mouse cortex
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed in Tri-reagent BD (Sigma, T3809) and frozen for future procedures. RNA was purified by phenol-chloroform extraction and isopropaonol precipitation, treated with DNase-I (NEB, M0303) then fragmented by high-magnesium, high-temperature incubation.
One 1μg of Bru-containing RNA was used for library preparation. The library was prepared in collaboration with the BrU-seq lab of the University of Michigan (Paulsen et al., 2013, 2014)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
DMSO_4h_Bic_rep2
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| Data processing |
For RNA-Seq, reads were mapped to mm10 using Bowtie2
Counts matrix for DESeq2 was generated using FeatureCounts
For RNA-Seq, BAM files were deduplicated (UMI_tools) and converted to BigWig files (bamCoverage) in a strand specific manner.
For RNA-Seq,DESeq2 was used to call differential gene expression between genotypes, and calculate FPKM.
Assembly: mm10
Supplementary files format and content: Bigwig files (.bw) represent genome coverage by the reads in a strand specific manner. Counts file represent the FeatureCounts output that was used for DESeq2
Library strategy: BrU-Seq
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| Submission date |
Jul 27, 2023 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Shigeki Iwase |
| E-mail(s) |
siwase@umich.edu
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| Organization name |
University of Michigan
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| Street address |
1241 E. Catherine St.
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| City |
Ann Arbor |
| ZIP/Postal code |
48108 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE239471 |
Division of labor among H3K4 Methyltransferases Define Distinct Facets of Homeostatic Plasticity |
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| Relations |
| BioSample |
SAMN36733256 |
| SRA |
SRX21176313 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7665725_DMSO_Bic_4h_rep2.fwd.bw |
52.9 Mb |
(ftp)(http) |
BW |
| GSM7665725_DMSO_Bic_4h_rep2.rev.bw |
51.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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