Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc35content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc35 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: hc35
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549653
  • sample_id: hc35
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell GTTCATTTCTTAATGG-1, TGATCAATCGAAGTGA-1, TCCCGGACACCTATAG-1, CAGGGTGAGGAAGTAT-1, AGGATGCAGCAGGTTT-1 (top 5 of 531711 values)
count int

count
HISTOGRAM FOR count [1, 54]
n
177,696,176
mean
2.22
sd
1.49

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 177696176
chr1 16005727
chr2 13545656
chr3 11214585
chr4 9439573
chr5 9815899
chr6 9791574
chr7 9473606
chr8 7995601
chr9 8146536
chr10 8438881
chr11 9555557
chr12 8457556
chr13 4934980
chr14 5868887
chr15 5193776
chr16 6170215
chr17 7860679
chr18 4194393
chr19 7033590
chr20 4508180
chr21 2316118
chr22 3561870
chrX 3801150
chrY 308076
GL000009.2 3652
GL000194.1 8806
GL000195.1 9558
GL000205.2 10814
GL000213.1 274
GL000218.1 2121
GL000219.1 9063
KI270711.1 1862
KI270713.1 6339
KI270721.1 425
KI270726.1 378
KI270727.1 386
KI270728.1 8133
KI270731.1 454
KI270734.1 1246

Fragment lengths

fragments min max mean median
fragments 177696176 1 5092 241.02 189
global fragment-length histogram

Files

Filename Size md5
GSM8549653_hc35_atac_fragments.tsv.gz 1.89 GB fa5da32b1ad73bf75903c89638888c61
GSM8549653_hc35_atac_fragments.tsv.gz.tbi 1023.23 KB fcd06004d306fa1e5a025d8c1ceb960e
GSM8549653_hc35_atac_fragments.tsv.gz.tbi.gz 1020.41 KB ee38dadef2aa2fcddd339e6869d0133d
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.43 KB ad2a0b23dac5d00294e437ef953cc68b
statistics/