|
| Status |
Public on Jan 21, 2022 |
| Title |
HcordbloodN1_1 |
| Sample type |
SRA |
| |
|
| Source name |
CD34- CD38+ CD5- CD7+ GFP+
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: cord blood CD34 cells
group: N1
replicate: 1
batch: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20'000 induced immature cells were isolated from cultured human cord blood and processed as in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Library was amplify using NEBNext High-Fidelity 2X PCR Master Mix and size selection was performed using Agencourt AMPure XP beads. The primer list can be found in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
sequencing protocol: Sequencing was performed by Novogene using the Illumina NovaSeq and the 150-bp paired-end configuration to obtain at least 100 million reads per sample.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HcordbloodN1_1_FKDL202595133-1a_HHGCHDSXY_L4
|
| Data processing |
Illumina bcl2fastq 2.19.1 software was used for base calling.
Reads were trimmed using atropos (1.1.21) to remove the Illumina TruSeq adapter sequences.
Trimmed reads were aligned to the human genome (hg38) using BWA-MEM (0.7.17).
The aligned reads were filtered to include reads from chromosomes 1 - 22, X, and Y using samtools (1.9) and duplicates were marked using “MarkDuplicates” from Picard (2.18.27).
ATAC-seq peaks were called with MACS2 (2.1.1.20160309).
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph file for each ChIP sample - generated by MACS2
|
| |
|
| Submission date |
Mar 17, 2021 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Nadine Fournier |
| E-mail(s) |
nadine.fournier@sib.swiss
|
| Organization name |
Agora Cancer Research Center & Swiss Institute of Bioinformatics
|
| Lab |
Translational Data Science Facility
|
| Street address |
Agora Cancer Research Center, Bugon 25A
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1000 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE169119 |
Chromatin accessibility analysis of human cord blood cells with hyperactivated Notch1 [ATAC-seq_human] |
| GSE169121 |
Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology. |
|
| Relations |
| BioSample |
SAMN18341006 |
| SRA |
SRX10372551 |
