Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc19content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc19 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: hc19
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549649
  • sample_id: hc19
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell AAGCCTCCAGAGGCTA-1, GGCGGTTTCGTTAGTA-1, AGAGATTAGTAGCGGG-1, CGGACCTAGGCGTAAA-1, CGCAATGTCAACCAAC-1 (top 5 of 565419 values)
count int

count
HISTOGRAM FOR count [1, 27]
n
173,614,814
mean
1.81
sd
1.15

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 173614814
chr1 14483164
chr2 13918179
chr3 11950505
chr4 10569218
chr5 10749512
chr6 10211790
chr7 9906142
chr8 9110546
chr9 7363493
chr10 8086517
chr11 8753242
chr12 8649256
chr13 5506914
chr14 5791219
chr15 4902357
chr16 4953612
chr17 5064597
chr18 4895405
chr19 3815218
chr20 4184438
chr21 2292501
chr22 2600010
chrX 5750358
chrY 48572
GL000009.2 7755
GL000194.1 10882
GL000195.1 10149
GL000205.2 11659
GL000213.1 594
GL000218.1 2546
GL000219.1 6864
KI270711.1 796
KI270713.1 2319
KI270721.1 414
KI270726.1 295
KI270727.1 1094
KI270728.1 1184
KI270731.1 322
KI270734.1 1176

Fragment lengths

fragments min max mean median
fragments 173614814 1 5092 256.48 185
global fragment-length histogram

Files

Filename Size md5
GSM8549649_hc19_atac_fragments.tsv.gz 1.86 GB 1c64bf38208f29f27eddf7cc60d7d760
GSM8549649_hc19_atac_fragments.tsv.gz.tbi 1.08 MB a2da3492e9bb86acc909ae3f5d578e56
GSM8549649_hc19_atac_fragments.tsv.gz.tbi.gz 1.08 MB f25ffbfd902a5e2521a4bb179eb0cefe
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.43 KB 3c1a55c18558df232c606cb646ac103f
statistics/