Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc5087content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc5087 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: hc5087
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549628
  • sample_id: hc5087
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell CGCTCCATCAAACTCA-1, AGGGTTGCAGAACCGA-1, GCGAGTGAGTAAGTGG-1, GGGCAATAGCAAGACA-1, TCTCGCCCATCCCTCA-1 (top 5 of 637842 values)
count int

count
HISTOGRAM FOR count [1, 26]
n
243,561,926
mean
1.52
sd
0.856

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 243561926
chr1 21667745
chr2 19370776
chr3 16164340
chr4 13482304
chr5 13837293
chr6 13576133
chr7 13099451
chr8 11384696
chr9 10586892
chr10 11628081
chr11 12750482
chr12 11633787
chr13 7053928
chr14 8078259
chr15 7265732
chr16 8186925
chr17 9794355
chr18 5878779
chr19 8043299
chr20 6238939
chr21 3126158
chr22 4623350
chrX 5474058
chrY 515946
GL000009.2 7669
GL000194.1 8527
GL000195.1 11736
GL000205.2 21154
GL000213.1 67
GL000218.1 9127
GL000219.1 15848
KI270711.1 3295
KI270713.1 5468
KI270721.1 390
KI270726.1 458
KI270727.1 1597
KI270728.1 11803
KI270731.1 985
KI270734.1 2094

Fragment lengths

fragments min max mean median
fragments 243561926 1 5092 208.02 170
global fragment-length histogram

Files

Filename Size md5
GSM8549628_hc5087_atac_fragments.tsv.gz 2.56 GB dc3e57dd2016cb8e64dbae7af58c0eb5
GSM8549628_hc5087_atac_fragments.tsv.gz.tbi 1.22 MB 40e84aa63a03de7fedb693a63f967ccc
GSM8549628_hc5087_atac_fragments.tsv.gz.tbi.gz 1.22 MB 42e2e723e958eec94c93741fb9a5d024
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.44 KB 3f8bab85a42bbe12d82bc08dea447a94
statistics/