|
Status |
Public on Aug 06, 2024 |
Title |
CN7neg_e11.5_R1 |
Sample type |
SRA |
|
|
Source name |
CN7 e11.5 GFP-negative
|
Organism |
Mus musculus |
Characteristics |
cell type: CN7 e11.5 GFP-negative 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
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|
|
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 |
SAMN39597388 |
SRA |
SRX23381829 |