Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc5610content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc5610 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: hc5610
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549632
  • sample_id: hc5610
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell ATCATCAAGCACTAGT-1, GGCTTAAGTGGATGTC-1, AGCTACGTCTCACATT-1, TCAGCCTTCGCACAAT-1, TGTTATGAGCAAGGGT-1 (top 5 of 671419 values)
count int

count
HISTOGRAM FOR count [1, 21]
n
178,989,378
mean
1.61
sd
0.944

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 178989378
chr1 16589351
chr2 13854466
chr3 11435201
chr4 8811218
chr5 9655658
chr6 9742440
chr7 9250108
chr8 7759519
chr9 7924910
chr10 8444120
chr11 9621025
chr12 8417588
chr13 4717832
chr14 5937795
chr15 5545467
chr16 6502660
chr17 8227608
chr18 3998956
chr19 7170530
chr20 4702788
chr21 2181932
chr22 3831568
chrX 4549340
chrY 31492
GL000009.2 3864
GL000194.1 8446
GL000195.1 12413
GL000205.2 14810
GL000213.1 44
GL000218.1 6265
GL000219.1 21908
KI270711.1 3207
KI270713.1 8549
KI270721.1 235
KI270726.1 411
KI270727.1 1082
KI270728.1 3034
KI270731.1 665
KI270734.1 873

Fragment lengths

fragments min max mean median
fragments 178989378 1 5092 218.12 174
global fragment-length histogram

Files

Filename Size md5
GSM8549632_hc5610_atac_fragments.tsv.gz 1.87 GB ca8f1e0e3aed1824be15deb0a76e0e4c
GSM8549632_hc5610_atac_fragments.tsv.gz.tbi 1.0 MB 3543c6a69c9947f98c2f1016d3bd8de9
GSM8549632_hc5610_atac_fragments.tsv.gz.tbi.gz 1.0 MB 575873aa25c74c81c072db82737353a8
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.44 KB 23842119d46df30560c4c0d136b8151a
statistics/