Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc40content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc40 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: hc40
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549651
  • sample_id: hc40
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell GCCTGTGCAGTAAGTA-1, CGAACCGGTTAGCGTA-1, GCGCCTTGTTGAAGCC-1, ATGATGACATTGTCCT-1, GTGTTCCTCGAGCAAA-1 (top 5 of 611852 values)
count int

count
HISTOGRAM FOR count [1, 17]
n
221,375,029
mean
1.69
sd
1.01

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 221375029
chr1 18624079
chr2 17617500
chr3 15132066
chr4 13549479
chr5 13455216
chr6 13068119
chr7 12295646
chr8 11338229
chr9 9377365
chr10 10275901
chr11 11306152
chr12 10841345
chr13 6802632
chr14 7199439
chr15 5967250
chr16 6282270
chr17 7469725
chr18 5795206
chr19 6150487
chr20 5159387
chr21 2762468
chr22 3391286
chrX 7383218
chrY 46815
GL000009.2 9409
GL000194.1 8189
GL000195.1 9620
GL000205.2 13969
GL000213.1 384
GL000218.1 6047
GL000219.1 20591
KI270711.1 2661
KI270713.1 4478
KI270721.1 298
KI270726.1 5
KI270727.1 1335
KI270728.1 4857
KI270731.1 434
KI270734.1 1472

Fragment lengths

fragments min max mean median
fragments 221375029 1 5092 209.07 178
global fragment-length histogram

Files

Filename Size md5
GSM8549651_hc40_atac_fragments.tsv.gz 2.31 GB be602eabf563250201f3efa66f766003
GSM8549651_hc40_atac_fragments.tsv.gz.tbi 1.2 MB c3395fb4ecca49e5232f81eef2bf3812
GSM8549651_hc40_atac_fragments.tsv.gz.tbi.gz 1.2 MB b910a3716f213bf3a42ac5b92c1153a3
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.43 KB 23b9ebf9436310d0bdc41b2275fb558a
statistics/