|
| Status |
Public on Aug 06, 2024 |
| Title |
SMN_e11.5_R1 |
| Sample type |
SRA |
| |
|
| Source name |
SMN e11.5 GFP-positive
|
| Organism |
Mus musculus |
| Characteristics |
cell type: SMN e11.5 GFP-positive
genotype: WILDTYPE
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GFP positive and negative cells FACS purified from e10.5 or e11.5 cells
Standard Illumina chemistry
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalling Illumina NextSeq 500
bcl outputs were converted to fastq using bcl2fastq conversion software (Illumina)
Bulk ATAC sequencing data was processed by running the .fastq files through the Encode ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) using default parameters.
To analyze peaks for each bulk sample, Irreproducible Discovery Rate (IDR) optimal peaks were used , generated between pseudoreplicates or biological replicates when appropriate.
After generating peaksets for each bulk sample, a bulk master peakset was created by concatenating all the individual peaksets and merging with bedtools merge. We further generated bulk peaksets specific to each sample using bedtools subtract, allowing for ≤ 50% overlap between peaks.
Assembly: mm10
Supplementary files format and content: .bam binary file containing aligned fragments
Supplementary files format and content: .bw bigwig track format to visualise accessibility profiles along the genome
|
| |
|
| Submission date |
Jan 24, 2024 |
| Last update date |
Aug 06, 2024 |
| Contact name |
Elizabeth C Engle |
| E-mail(s) |
elizabeth.engle@childrens.harvard.edu
|
| Phone |
6179194030
|
| Organization name |
Boston Childrens Hospital
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE254083 |
Noncoding Mendelian epigenomics - bulk ATAC mouse cMN data |
| GSE254090 |
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders |
|
| Relations |
| BioSample |
SAMN39597384 |
| SRA |
SRX23381833 |
