|
| Status |
Public on May 22, 2024 |
| Title |
scATACseq_CD34+_AOAtreatment_24h_multipledonors |
| Sample type |
SRA |
| |
|
| Source name |
umbilical cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: umbilical cord blood
cell type: CD34+ cells
disease state: Healthy
treatment: 1.9mM AOA
|
| Treatment protocol |
Cells were stimulated with cytokines after thawing and were grown in the same medium with or without metabolic inhibitor (2-DG, DON or AOA) until lysis was performed. Cells were collected and lysed after 24h of cytokine stimulation.
|
| Growth protocol |
CD34+ cells were purified from human healthy cord blood with a two-step immunomagnetic beads protocol and were then frozen in a cryopreservation medium. After thawing, CD34+ cells were cultured in a 96-well plate in a humidified 5% CO2 incubator at 37°C. Cells were grown in prestimulation medium made of X-Vivo (Lonza) supplemented with penicillin/streptomycin (respectively 100U/mL and 100µg/mL - Gibco, Thermo Scientific), 50 ng/ml h-FLT3, 25 ng/ml h-SCF, 25 ng/ml h-TPO, 10 ng/ml h-IL3 (Miltenyi) final concentration.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High viability percentage was obtained using a Dead Cell Removal kit (Miltenyi). scATACseq was then performed as described in the 10X Genomics protocol with Chromium Next GEM Single Cell ATAC-seq Kit v1.1. 15 000 nuclei were isolated and loaded on the chip to obtain around 4000-6000 nuclei encapsidated in GEM.
Library was prepared following the 10X Genomics protocol, controled with Qubit quantification and sequenced on a Novaseq6000.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X scATACseq
|
| Data processing |
Demultiplexing + Matrix generation with Cellranger (v6pipeline version cellranger-atac-2.0.0)
R (version 4.2,1) & Seurat (version 4.1.3) & Signac (version 1.9.0) & ggplot2 (version 3.4.2) & org.Hs.eg.db (version 3.16.0) & clusterProfiler (version 4.6.2)
Filters : 200 peaks detected per cell, nucleosome signal <2, blacklist ratio <0.05, TSS enrichment >2, 3000>number of fragments overlapping peaks> 50 000
Assembly: hg38 (GRCh38)
Supplementary files format and content: filtered_peak_bc_matrix.h5 files contain filtered peak barcode matrix with detected cellular barcodes
Supplementary files format and content: fragments.tsv.gz files contain chromosome, barcode, start and end position of each peak
Supplementary files format and content: singlecell.csv files contain QC per cellular barcode
|
| |
|
| Submission date |
Sep 12, 2023 |
| Last update date |
May 22, 2024 |
| Contact name |
Laëtitia RACINE |
| E-mail(s) |
laetitia.racine@hotmail.fr
|
| Organization name |
EPHE
|
| Lab |
CRSA
|
| Street address |
27 rue de Chaligny
|
| City |
Paris |
| ZIP/Postal code |
75012 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE243004 |
Metabolic adaptation pilots the differentiation of human hematopoietic cells (scATAC-Seq) |
| GSE243006 |
Metabolic adaptation pilots the differentiation of human hematopoietic cells |
|
| Relations |
| BioSample |
SAMN37367106 |
| SRA |
SRX21762775 |
