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Sample GSM8490459 Query DataSets for GSM8490459
Status Public on Sep 05, 2024
Title single cell ATAC seq library of human samples (day0 to 10)
Sample type SRA
 
Source name H9 human embryonic stem cells
Organism Homo sapiens
Characteristics cell line: H9 human embryonic stem cells
treatment: UPPS (pluripotency, day0) and NPC differentiation and maintenance media
library type: scATAC
time: day 0 - 10
Treatment protocol Neural induction for up to 10 days
Growth protocol PSCs were singularized using Accutase (Sigma Aldrich) and counted on the Countess II FL Automated Cell Counter (Invitrogen). For human ESCs and cynomolgus iPSCs 1.25 x 105 cells/cm2 were seeded onto Matrigel coated plates in UPPS media supplemented with 10 µM Y-27632 (R&D Systems) and incubated overnight, resulting in confluent cultures the following day for each species. For neural induction, media was exchanged to NPC differentiation and maintenance media consisting of 1:1 DMEM/F12 and Neuropan (PAN Biotech) supplemented with 0.5x N2 and B27 supplements, 1x MEM-NEAA, 1x GlutaMAX, 0.1 mM 2-Mercaptoethanol, 5 µg/mL Insulin, human recombinant (all Thermo Fisher Scientific), 10 µM SB431542 and 100 nM LDN193189 (both Peprotech). Cells were washed with Dulbecco’s phosphate buffered saline (DPBS; Thermo Fisher Scientific) before daily media exchange.
Extracted molecule genomic DNA
Extraction protocol Time course scATAC and scRNA libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturer’s protocol. Samples were collected at 0h, 8h, 1d, 2d, 3d, 4d, 7d and 10d post neural induction and cells of all three species were combined in equal amounts prior to the library preparation. The aimed target recovery was 10,000 single nuclei for sequencing.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturers instructions
scRNAseq and scATACseq
 
Library strategy ATAC-seq
Library source genomic single cell
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing For time course single-cell multiome sequencing experiments, CellRanger ARC (v2.0.0) provided by 10x Genomics was used to demultiplex binary Illumina base call (BCL) files into FASTQ files, align the data against the GRCh38 (human), GRCm39 (mouse), and Macaca_fascicularis_6.0 (cynomolgus) reference, filter reads, as well as count barcodes and scRNA and scATAC molecules to generate feature-barcode matrices.
To mitigate technical cross-species batch effects, we pooled an equal number of cells from the three species for each of the samples.
Assembly: human genome GRCh38 (GENCODE v32/Ensembl98) and mouse genome GRCm39 obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0)
Supplementary files format and content: For every species (containing RNA counts and ATAC counts for all timepoints): matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx; the numbers 1 to 8 in the cell barcodes do correspond to the timepoints 0 to 10 days (0d, 8h, 1d, 2d, 3d, 4d, 7d and 10d).
 
Submission date Aug 30, 2024
Last update date Sep 05, 2024
Contact name Max Fernkorn
E-mail(s) m.fernkorn@lacdr.leidenuniv.nl
Organization name University Leiden
Department Leiden Academic Centre for Drug Research (LACDR)
Lab Drukker
Street address Einsteinweg 55
City Leiden
ZIP/Postal code 2333 CC
Country Germany
 
Platform ID GPL24676
Series (2)
GSE275572 Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development
GSE276058 Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development [scRNAseq and scATACseq]
Relations
BioSample SAMN43427750
SRA SRX25919139

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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