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| Status |
Public on Sep 12, 2022 |
| Title |
Neurons D868D ATAC #2 |
| Sample type |
SRA |
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| Source name |
NPC-derived Neurons
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| Organism |
Homo sapiens |
| Characteristics |
cell type: NPC-derived Neurons
genotype: SETBP1 D868D
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed using a previously described protocol 3. Briefly, 50000 of cells for each experimental replicated were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630, Sigma aldrich) to perform crude nuclei isolation. Trasposition reaction was then performed using Tn5 transposase (Illumina). After transposition, DNA was purified using Zymo DNA Clean & Concentrator kit (cat. D4013) and amplified by PCR (NebNext ultra II polymerase, cat. M0544S). After 5 cycles the reaction was stopped, the necessary amount of cycles needed for the final amplification were calculated with qPCR. After amplification libraires were purified using Ampure XPbeads selection fragments between 100-1000 bp. Subsequently samples were sequenced paired-end on NovaSeq6000 by GeneWiz.
NexTera
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
NeuD868D2
single index library
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| Data processing |
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome hg38 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used. Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ATAC-seq peak calling was performed on the Tn5- corrected single-base insertions using the following parameters --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all –qvalue 0.01.
Genome_build: hg38
Supplementary files format and content: macs narrowpeaks
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| Submission date |
Aug 29, 2022 |
| Last update date |
Sep 12, 2022 |
| Contact name |
Luca Massimino |
| E-mail(s) |
admin@lucamassimino.com
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| Phone |
+393389039500
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| Organization name |
Ospedale San Raffaele
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| Department |
Gastroenterology
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| Street address |
Via Olgettina, 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE212252 |
Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition |
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| Relations |
| BioSample |
SAMN30566542 |
| SRA |
SRX17313976 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6519823_NeuD868D2_peaks.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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