title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-J19


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-I8

status: Public on Jul 05 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: hg38-donor-snp-substituted
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: BNST

tag: Sex

value: M


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-D7


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-C8


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-C20


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-H8


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-C19


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-B20


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-B7


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-G20


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-F19


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-A7


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-E8


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-E7


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-A19


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-P6


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-O6


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-P18


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-P5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-P17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-O18


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-C7


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-N6


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-B8


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-N5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-M6


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-O5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-M5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-M18


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-N17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-O17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-M17


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title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-L18


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-L6


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-B19


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-L17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-L5


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-A20


title: HBA_210412_H1930002_CX47_BNST_1_P1-4-A1-A8


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-K6


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-K5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-J6


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-K18


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-K17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-J18


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-I6


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-I5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-H6


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-I18


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-I17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-H17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-G17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-G5


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title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-F5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-H5


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-D6


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title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-E17


title: HBA_210412_H1930002_CX47_BNST_1_P1-3-A1-E18


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title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-O4


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title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-O16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-N3


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title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-N16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-M3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-M15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-N4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-L16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-L4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-L15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-L3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-K4


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title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-J3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-J16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-J15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-N15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-I16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-I4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-I3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-I15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-H4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-H3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-H16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-H15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-G4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-F4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-G15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-G16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-G3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-F3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-F16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-F15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-D16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-E4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-C4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-D15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-D4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-E16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-E15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-E3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-D3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-C3


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title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-C15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-B4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-B15


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-A4


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-A3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-B3


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-B16


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-A15


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-P1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-P13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-O14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-O2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-P14


title: HBA_210412_H1930002_CX47_BNST_1_P1-2-A1-A16


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-P2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-O1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-O13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-N14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-L1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-N1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-L13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-M13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-L2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-M1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-M14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-N2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-N13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-K2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-L14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-K14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-K1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-K13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-J14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-J2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-J13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-I2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-I14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-I13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-H2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-H14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-H1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-H13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-G2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-M2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-G13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-G14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-F14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-F1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-F13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-E14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-F2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-G1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-E2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-E13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-D2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-D13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-E1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-D1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-D14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-C14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-J1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-C2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-C13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-I1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-A14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-C1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-A13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-B2


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-B13


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-A1


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-B14


title: HBA_210412_H1930002_CX47_BNST_1_P1-1-A1-B1


title: Primary AML bone marrow, HTO-derived cDNA, Pt-89_Dx

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
cell_metadata.tsv.gz
cell_barcodes.tsv.gz
totalvi_denoised_adt.mtx
totalvi_denoised_adt_features.tsv.gz
rna_normalized_counts.mtx
rna_normalized_counts_features.tsv.gz

library_source: other

data_processing:
Raw sequencing data for gene expression, antibody derived tag (ADT), and hashing (HTO) libraries were processed using STARsolo 2.7.8a with the 10X Genomics GRCh38/GENCODE v32 genome and transcriptome reference (version GRCh38_2020A) or a TotalSeq-A/B barcode reference, as appropriate.
Hashed samples were demultiplexed using GMM-Demux.
Cell-containing droplets were identified using dropkick 1.2.6 (using manual thresholds when automatic thresholding failed), ambient RNA was removed using DecontX 1.12 and cells estimated to contain >50% ambient RNA were removed, and multiplets were identified using DoubletFinder 2.0.3 and removed.
Remaining cells were filtered to retain only those with >200 genes, 500-80,000 UMIs, <10-20% of UMIs from genes encoded by the mitochondrial genome (sample dependent based on UMI distributions), <5% of UMIs derived from HBB, <20,000 UMIs from antibody-derived tags (ADTs), and >100-2,750 UMIs from antibody derived tags (sample dependent based on UMI distribution).
Filtered cells were modeled in latent space using TotalVI 0.18.0 to create a joint embedding derived from both RNA and ADT expression data corrected for batch effects, mitochondrial proportion, and cell cycle.
RNA counts were normalized using scanpy, denoised ADT counts were log-transformed, and each sample was downsamped to 1197 cells for plotting.
Assembly: GRCh38
Supplementary files format and content: cell_metadata.tsv.gz: sample assignments, UMAP and TotalVI embeddings for all cell barcodes.
Supplementary files format and content: cell_barcodes.tsv.gz, totalvi_denoised_adt.mtx, totalvi_denoised_adt_features.tsv.gz: log-transformed TotalVI denoised ADT count matrix and column/row labels
Supplementary files format and content: cell_barcodes.tsv.gz, rna_normalized_counts.mtx, rna_normalized_counts_features.tsv.gz: Normalized RNA count matrix and column/row labels
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: bone marrow

extract_protocol:
Cells were processed using the 10X Genomics Chromium platform to generate single-cell mRNA, ADT, and HTO libraries.
10X Genomics 3' end library kit (v3/v3.1)

tag: tissue

value: bone marrow

tag: cell type

value: mononuclear cells

tag: lsc subtype

value: Uni-MMP

tag: library type

value: HTO

tag: antibodies/tags

value: anti-human Hashtag 1/TotalSeq-B 0251; anti-human Hashtag 2/TotalSeq-B 0252


title: Primary AML bone marrow, ADT-derived cDNA, Pt-69_Dx

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
cell_metadata.tsv.gz
cell_barcodes.tsv.gz
totalvi_denoised_adt.mtx
totalvi_denoised_adt_features.tsv.gz
rna_normalized_counts.mtx
rna_normalized_counts_features.tsv.gz

value: Multi-MMP

value: ADT

value: anti-human CD4/TotalSeq-A 0045; anti-human CD7/TotalSeq-A 0066; anti-human CD56 (NCAM)/TotalSeq-A 0047; anti-human CD3/TotalSeq-A 0049; anti-human CD19/TotalSeq-A 0050; anti-human CD33/TotalSeq-A 0052; anti-human CD34/TotalSeq-A 0054; anti-human CD90 (Thy1)/TotalSeq-A 0060; anti-human CD117 (c-kit)/TotalSeq-A 0061; anti-human CD45RA/TotalSeq-A 0063; anti-human CD123/TotalSeq-A 0064; anti-human CD14/TotalSeq-A 0081; anti-human HLA-DR/TotalSeq-A 0159; anti-human CD11b/TotalSeq-A 0161; anti-human CD64/TotalSeq-A 0162; anti-human CD38/TotalSeq-A 0389; anti-human CD45/TotalSeq-A 0391; anti-human CD36/TotalSeq-A 0407; anti-human CD93/TotalSeq-A 0446; anti-human CD9/TotalSeq-A 0579


title: Primary AML peripheral blood, ADT-derived cDNA, AML-24

source_name: peripheral blood

value: peripheral blood

value: mono


title: Primary AML bone marrow, ADT-derived cDNA, Pt-89_Dx


title: Primary AML bone marrow, ADT-derived cDNA, Pt-16_Dx


title: Primary AML peripheral blood, ADT-derived cDNA, AML-22

value: anti-human CD4/TotalSeq-A 0045; anti-human CD7/TotalSeq-A 0066; anti-human CD56 (NCAM)/TotalSeq-A 0047; anti-human CD3/TotalSeq-A 0049; anti-human CD19/TotalSeq-A 0050; anti-human CD33/TotalSeq-A 0052; anti-human CD34/TotalSeq-A 0054; anti-human CD90 (Thy1)/TotalSeq-A 0060; anti-human CD45RA/TotalSeq-A 0063; anti-human CD123/TotalSeq-A 0064; anti-human HLA-DR/TotalSeq-A 0159; anti-human CD11b/TotalSeq-A 0161; anti-human CD64/TotalSeq-A 0162; anti-human CD38/TotalSeq-A 0389; anti-human CD45/TotalSeq-A 0391; anti-human CD36/TotalSeq-A 0407; anti-human CD93/TotalSeq-A 0446; anti-human CD9/TotalSeq-A 0579; anti-human CD70/TotalSeq-A0027; anti-human CD27/TotalSeq-A0154


title: Primary AML peripheral blood, ADT-derived cDNA, AML-21

value: prim


title: Primary AML peripheral blood, ADT-derived cDNA, AML-20


title: Primary AML peripheral blood, ADT-derived cDNA, AML-23


title: Primary AML peripheral blood, ADT-derived cDNA, AML-17


title: Primary AML peripheral blood, ADT-derived cDNA, AML-18


title: Primary AML peripheral blood, ADT-derived cDNA, AML-14


title: Primary AML peripheral blood, ADT-derived cDNA, AML-16


title: Primary AML peripheral blood, ADT-derived cDNA, AML-12

value: anti-human CD4/TotalSeq-B 0072; anti-human CD7/TotalSeq-B 0066; anti-human CD56 (NCAM)/TotalSeq-B 0047; anti-human CD3/TotalSeq-B 0049; anti-human CD33/TotalSeq-B 0052; anti-human CD34/TotalSeq-B 0054; anti-human CD90 (Thy1)/TotalSeq-B 0060; anti-human CD117 (c-kit)/TotalSeq-B 0061; anti-human CD45RA/TotalSeq-B 0063; anti-human CD123/TotalSeq-B 0064; anti-human CD14/TotalSeq-B 0081; anti-human HLA-DR/TotalSeq-B 0159; anti-human CD11b/TotalSeq-B 0161; anti-human CD64/TotalSeq-B 0162; anti-human CD38/TotalSeq-B 0389; anti-human CD45/TotalSeq-B 0391; anti-human CD36/TotalSeq-B 0407; anti-human CD93/TotalSeq-B 0446; anti-human CD9/TotalSeq-B 0579; anti-human CD19/TotalSeq-B 0050; anti-human CD70/TotalSeq-B 0027; anti-human CD27/TotalSeq-B 0154


title: Primary AML peripheral blood, ADT-derived cDNA, AML-13


title: Primary AML peripheral blood, ADT-derived cDNA, AML-10


title: Primary AML peripheral blood, ADT-derived cDNA, AML-08


title: Primary AML peripheral blood, ADT-derived cDNA, AML-07


title: Primary AML peripheral blood, ADT-derived cDNA, AML-03


title: Primary AML peripheral blood, ADT-derived cDNA, AML-04


title: Primary AML peripheral blood, ADT-derived cDNA, AML-02


title: Primary AML bone marrow, mRNA-derived cDNA, Pt-69_Rl

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
cell_metadata.tsv.gz
cell_barcodes.tsv.gz
totalvi_denoised_adt.mtx
totalvi_denoised_adt_features.tsv.gz
rna_normalized_counts.mtx
rna_normalized_counts_features.tsv.gz

library_source: transcriptomic

molecule: polyA RNA

value: mRNA


title: Primary AML bone marrow, ADT-derived cDNA, Pt-69_Rl


title: Primary AML bone marrow, mRNA-derived cDNA, Pt-20_Dx


title: Primary AML peripheral blood, ADT-derived cDNA, AML-01


title: Primary AML bone marrow, mRNA-derived cDNA, Pt-69_Dx


title: Primary AML bone marrow, mRNA-derived cDNA, Pt-89_Dx


title: Primary AML bone marrow, ADT-derived cDNA, Pt-20_Dx


title: Primary AML bone marrow, mRNA-derived cDNA, Pt-16_Dx


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-22


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-21


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-23


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-20


title: Primary AML peripheral blood, ADT-derived cDNA, AML-19


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-18


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-24


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-14


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-19


title: Primary AML peripheral blood, ADT-derived cDNA, AML-09


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-12


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-13


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-17


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-16


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-10


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-09


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-08


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-04


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-02


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-03


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-01


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-07


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-O12

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files
Assembly: hg38-donor-snp-substituted
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Supplementary files format and content: tab-delimited files (HIC files) describing the chromatin contacts. Columns are: 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, Conor Fitzpatrick, Carolyn O’Connor,Jesse R. Dixon, Joseph R. Ecker. 2019. “Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.” Nat Methods. 16(10): 999–1006.

value: SEP

tag: gender


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-O11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-M23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-N12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-K24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-N24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-L12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-P12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-M24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-L24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-O23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-O24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-N11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-M12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-I24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-P11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-L11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-K12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-M11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-J11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-P23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-J24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-J23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-I23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-I12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-K23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-P24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-H23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-L23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-H12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-F11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-E24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-G23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-G11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-G12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-D11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-H11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-B23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-B11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-D23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-B12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-B24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-E23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-F23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-A11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-P9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-C24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-E12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-P22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-F12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-C12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-A23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-D12


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-P21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-D24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-E11


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-F24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-A24


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-6-D8-C23


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-O22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-P10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-O10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-N9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-M9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-N22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-M21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-N10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-L21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-K9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-L9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-K22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-K10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-J10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-J21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-I22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-H21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-H22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-I21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-H9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-I9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-H10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-O21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-M10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-M22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-G9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-L22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-N21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-K21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-F9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-G22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-F22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-F10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-G10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-J9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-F21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-G21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-E22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-D9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-E21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-E9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-E10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-D10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-C9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-B9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-C22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-C10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-C21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-A22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-B22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-B21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-A9


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-P7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-A21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-D22


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-A10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-B10


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-P8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-O7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-O20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-N8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-N7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-N20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-N19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-P20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-M7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-M8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-5-D8-D21


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-M20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-L8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-L7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-M19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-K8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-L19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-P19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-L20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-K7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-O19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-K19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-J7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-I20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-I19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-J20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-J8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-H7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-K20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-I7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-J19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-H20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-G19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-G8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-F20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-G20


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-F19


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-G7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-E8


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-E7


title: HBA_220615_H1930004_CX46_SEP_3C_2_P8-4-D8-E20


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title: HBA_220615_H1930004_CX46_SEP_3C_2_P7-2-H6-I3


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title: HBA_220615_H1930004_CX46_SEP_3C_2_P7-2-H6-G16


title: HBA_220615_H1930004_CX46_SEP_3C_2_P7-2-H6-H3


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title: HBA_220615_H1930004_CX46_SEP_3C_2_P7-2-H6-D4


title: HBA_200818_H1930002_CX47_Pir_1_P5-4-M21-B20

value: Pir


title: HBA_200818_H1930002_CX47_Pir_1_P5-4-M21-B19

value: M


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title: HBA_200818_H1930002_CX47_Pir_1_P4-6-C19-D23


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title: HBA_200818_H1930002_CX47_Pir_1_P4-1-A2-L2


title: HBA_200818_H1930002_CX47_Pir_1_P4-1-A2-L13


title: HBA_200818_H1930002_CX47_Pir_1_P4-1-A2-L1


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title: HBA_200818_H1930002_CX47_Pir_1_P4-1-A2-K13


title: HBA_200818_H1930002_CX47_Pir_1_P4-1-A2-J14


title: HBA_200818_H1930002_CX47_Pir_1_P4-1-A2-O13


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title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-H5


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title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-E5


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-F18


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-F17


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-F6


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-I17


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-D18


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-E6


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-G18


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-G17


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-F5


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-D5


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-E17


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-C18


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-B18


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-C6


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-O16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-O4


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-A18


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-O3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-P3


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-D17


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-A5


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-P4


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-B6


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-C5


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-B17


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-N16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-P15


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-A6


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-N15


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-O15


title: HBA_200818_H1930002_CX47_Pir_1_P3-3-I6-A17


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-M3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-M16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-P16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-M15


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-L4


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-L3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-N3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-N4


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-M4


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-L16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-L15


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-K4


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-J4


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-H16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-H3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-I3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-J16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-G4


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-K3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-K16


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-J15


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-H15


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-J3


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-I15


title: HBA_200818_H1930002_CX47_Pir_1_P3-2-L21-I4