Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc5579content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc5579 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: hc5579
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549617
  • sample_id: hc5579
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell AAGTAGCCATTGTCCT-1, GCTAAGCGTCAAAGGG-1, CCAAGTTAGGGTGAAC-1, GGGTGAAGTCATGAGC-1, GTTTGTAAGGAAGTAT-1 (top 5 of 582034 values)
count int

count
HISTOGRAM FOR count [1, 28]
n
295,631,461
mean
1.51
sd
0.842

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 295631461
chr1 26415113
chr2 23058802
chr3 19392337
chr4 15654367
chr5 16632106
chr6 16199802
chr7 15688521
chr8 13780590
chr9 12786112
chr10 13564577
chr11 15526283
chr12 14300462
chr13 8250191
chr14 9708995
chr15 8803500
chr16 10144772
chr17 12516182
chr18 6966023
chr19 10834709
chr20 7554074
chr21 3530452
chr22 5885544
chrX 8282899
chrY 52584
GL000009.2 10299
GL000194.1 8531
GL000195.1 17324
GL000205.2 19493
GL000213.1 809
GL000218.1 4750
GL000219.1 14283
KI270711.1 2329
KI270713.1 7625
KI270721.1 1227
KI270726.1 1184
KI270727.1 1797
KI270728.1 10447
KI270731.1 777
KI270734.1 1589

Fragment lengths

fragments min max mean median
fragments 295631461 1 5091 211.11 175
global fragment-length histogram

Files

Filename Size md5
GSM8549617_hc5579_atac_fragments.tsv.gz 3.08 GB 00a9e92d3427f7d8fa6e19257bde3d12
GSM8549617_hc5579_atac_fragments.tsv.gz.tbi 1.32 MB a9a39da785cf199464cd0a7806788b49
GSM8549617_hc5579_atac_fragments.tsv.gz.tbi.gz 1.32 MB 09b4d98393cfa334295b36e36b00cb81
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.44 KB 7d710ea0d027aca2c84cb42759ad217d
statistics/