|
| Status |
Public on Feb 10, 2021 |
| Title |
scC&T H3K4me3 brain P15 GFP neg |
| Sample type |
SRA |
| |
|
| Source name |
Mouse brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6j
genotype: Sox10-Cre/RCE
tissue: brain
age: P15
c&t antibody: Diagenode C15410030
2nd antibody: Novus Biologicals NBP1-72763
tn5: In House pA-Tn5; 1:100
|
| Growth protocol |
Brain was dissociated using Miltenyi neural tissue dissociation kit P (130-092-628), cleared with Debris removal solution (130-109-398), filtered through 50 um strainer and FACS sorted for GFP+/GFP- on FACS Aria III or FACS Aria Fusion
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted using NP-40 / Digitonin buffer
Single Cell Cut&Tag was performed with 1:50 diluted primary and secondary antibody and 1:100 diluted in house produced proteinA-Tn5
Tagmented nuclei were processed using the 10x scATAC-seq kit according to manufactureres instructions skipping Step 1 "Transposition" and continuing from Step 2.0 "Generation and barcoding".
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
H3K4me3_fragments.tsv.gz
H3K4me3_Astrocytes.bw
H3K4me3_Microglia.bw
H3K4me3_mOL.bw
H3K4me3_Neurons_1.bw
H3K4me3_Neurons_2.bw
H3K4me3_Neurons_3.bw
H3K4me3_OEC.bw
H3K4me3_OPC.bw
H3K4me3_VLMC.bw
H3K4me3_seurat_object.Rds
H3K4me3_matrix.h5
|
| Data processing |
Library strategy: CUT&TAG
Fastq files were processed using cellranger-ATAC v1.2.0
Cellranger-ATAC was loaded into seurat object and cell by bin matrix was generated
Cells were filtered based on number of reads and fraction of reads coming from peak reagions called on bulk data
Reduction of dimensionality was done using package Signac's LSI and UMAP
Genome_build: mm10
Supplementary_files_format_and_content: Rds files containing Seurat object that can be loaded into R using `object <- readRDS(path)` function. Seurat object contain multiple assays and UMAP/LSI embeddings used in the paper. BigWig files merged per cluster.
|
| |
|
| Submission date |
Sep 08, 2020 |
| Last update date |
Feb 10, 2021 |
| Contact name |
Marek Bartosovic |
| E-mail(s) |
bartosovic.marek@gmail.com
|
| Organization name |
Karolinska Institute
|
| Lab |
Goncalo Castelo-Branco
|
| Street address |
Solnavagen 9
|
| City |
Stockholm |
| ZIP/Postal code |
12432 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE157637 |
Single cell Cut&Tag in the mouse brain |
| GSE163532 |
Single cell profiling of histone modifications and transcription factors in the mouse brain |
|
| Relations |
| BioSample |
SAMN16079026 |
| SRA |
SRX9090626 |
