Resource

Id summary/zemke2024Epigenetic/atac_fragments/hc29content_copy
Type fragment_score
Version 0
Summary ATAC fragments for hc29 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: hc29
  • modalities: ATAC
  • processing_level: aligned
  • reference_genome: reference/Human/genome/ucsc-hg38
  • resolution: single_nucleus
  • run_id: GSM8549619
  • sample_id: hc29
  • sequencing_platform: Illumina
  • species: human
  • vendor: 10x_Genomics

Scores (2)

ID Type Default annotation Description Histogram Range Summary
cell str

cell
HISTOGRAM FOR cell TGTAATGTCACGTTAA-1, CGTTATTTCGCTAGTG-1, CATAGTCAGTAAGGGC-1, ATTTGCAAGGTTACGT-1, TATGGTCAGTTCCCGT-1 (top 5 of 487844 values)
count int

count
HISTOGRAM FOR count [1, 22]
n
104,765,807
mean
2.28
sd
1.48

n counts fragments; sd is the population standard deviation.

Fragments

Chromosome Fragments
all chromosomes 104765807
chr1 9564611
chr2 8140319
chr3 6871700
chr4 5527474
chr5 5833537
chr6 5773399
chr7 5619043
chr8 4906159
chr9 4562450
chr10 4893765
chr11 5667329
chr12 5077559
chr13 2915701
chr14 3544767
chr15 3103184
chr16 3555608
chr17 4379586
chr18 2513644
chr19 3668467
chr20 2708331
chr21 1280163
chr22 2108325
chrX 2321819
chrY 191610
GL000009.2 1918
GL000194.1 5402
GL000195.1 5799
GL000205.2 7384
GL000213.1 13
GL000218.1 2805
GL000219.1 7269
KI270711.1 315
KI270713.1 3272
KI270721.1 377
KI270726.1 150
KI270727.1 783
KI270728.1 354
KI270731.1 312
KI270734.1 1104

Fragment lengths

fragments min max mean median
fragments 104765807 1 5071 216.77 184
global fragment-length histogram

Files

Filename Size md5
GSM8549619_hc29_atac_fragments.tsv.gz 1.12 GB 468c8bdf6d397218ccc0cd6b0a3f2bee
GSM8549619_hc29_atac_fragments.tsv.gz.tbi 819.05 KB e037df6c40eb6f81f98e0f903b20e51e
GSM8549619_hc29_atac_fragments.tsv.gz.tbi.gz 818.26 KB b72e07074201d1826c5b944214142e73
fragment_count_dist_plot.py 853.0 B 9d735ee8c687286d50484e7f1e398e60
genomic_resource.yaml 1.43 KB c8f1c82ad8bde197f33eabba18221bf9
statistics/