Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc935content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc935 from zemke2024Epigenetic.
Description
Labels
  • assay: 10x_Multiome
  • brain_region: hippocampus
  • cell_meta_resource_id: summary/zemke2024Epigenetic/10x_multiomics_cell_meta_data
  • data_types: fragments
  • dataset: zemke2024Epigenetic
  • individual_id: hc935
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549623
  • sample_id: hc935
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell ACCTGGTCATGTTGCA-1, GCATCCTTCTGTAAGC-1, TCGATTAAGTGAGCAA-1, CTGTATTTCTTGCAGG-1, ACTTTGTTCCGCCTCA-1 (top 5 of 618302 values)
count int

count
HISTOGRAM FOR count [1, 42]
n
228,129,844
mean
1.75
sd
1.07

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 228129844
chr1 21228363
chr2 17320406
chr3 14209010
chr4 10892882
chr5 12116077
chr6 12182003
chr7 11727786
chr8 9727567
chr9 10146606
chr10 10637832
chr11 12469028
chr12 10817275
chr13 5870748
chr14 7558897
chr15 6981143
chr16 8478199
chr17 10993437
chr18 4925397
chr19 10300629
chr20 6030345
chr21 2771790
chr22 4952069
chrX 5671427
chrY 30189
GL000009.2 5090
GL000194.1 7103
GL000195.1 16190
GL000205.2 16788
GL000213.1 334
GL000218.1 2387
GL000219.1 17012
KI270711.1 3069
KI270713.1 15285
KI270721.1 395
KI270726.1 352
KI270727.1 1316
KI270728.1 4044
KI270731.1 603
KI270734.1 771

Fragment lengths

fragments min max mean median
fragments 228129844 1 5092 216.62 177
global fragment-length histogram

Files

Filename Size md5
GSM8549623_hc935_atac_fragments.tsv.gz 2.33 GB 2f6c48098c95c51bbbdd17ad74a82797
GSM8549623_hc935_atac_fragments.tsv.gz.tbi 1.13 MB 39c76c06cb70238b513149002729d999
GSM8549623_hc935_atac_fragments.tsv.gz.tbi.gz 1.12 MB f18c7e8b3ffa668e69a047a44169a774
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.43 KB 5b5c5444c24b96e48d68363bf0088d01
statistics/