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| Status |
Public on Oct 23, 2020 |
| Title |
GM12878 rep3 (ATAC-Seq) |
| Sample type |
SRA |
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| Source name |
GM12878
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| Organism |
Homo sapiens |
| Characteristics |
strain: none
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| Growth protocol |
GM12878 cells were cultured in RPMI 1640 medium (11875-093, ThermoFisher) supplemented with 15% FBS (16000044, ThermoFisher) and 1% Penicillin-Streptomycin (15140122, ThermoFisher). NIH/3T3 and RAW 264.7 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, 11965092, ThermoFisher) with the addition of 10% FBS and 1% of Penicillin-Streptomycin. The cells were incubated at 37 °C in 5% CO2 and maintained at exponential phase.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Female mouse dorsal skin was collected at first telogen (P21), anagen III (P28), late anagen (P32) and 2nd telogen (P55). The hair cycle stages were confirmed using cryosectioning. To dissociate skin cells, the skin samples were incubated in 0.25% collagenase in HBSS at 37°C for 35-45 minutes on an orbital shaker, followed by incubation in 0.25% trypsin-EDTA at 37°C for 35-45 minutes on the shaker. The skin samples were gently scraped from the dermal side. The single cell suspension was centrifuged for 5 minutes at 4°C, resuspended in 0.25% FBS in PBS and stained with fluorescent dye-conjugated antibodies and DAPI. Mouse brain were dissected, snap frozen on dry ice, and stored at -80 °C. The brain single nuclei suspension was prepared following OMNI-ATAC protocol. Mouse lungs were dissociated with fine scissors and then proteolytic digestion was performed using the Lung Dissociation kit (Miltenyi Biotech). Dissociated cells were then incubated at 37 °C for 20 minutes with rotation. Red blood cells were lysed using ACK buffer.
Libraries are contructed using SHARE-seq procotol.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
GM12878 rep3
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| Data processing |
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts
Paired-end reads were aligned to mm10 using bowtie or STAR.
Duplicate reads were removed using picard or UMItools.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Counts Data is indexed by genes (row), cell (column)
Supplementary_files_format_and_content: Fragments data contains fragment position (1-3 column), and assigned cell barcode (4th column)
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| Submission date |
Nov 11, 2019 |
| Last update date |
Oct 04, 2022 |
| Contact name |
Sai Ma |
| E-mail(s) |
masai.zju@gmail.com
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Street address |
1425 Madison Ave
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| City |
New York |
| ZIP/Postal code |
10026 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE140203 |
Integrative single-cell chromatin and transcriptome profiling uncovers cell-type specific regulatory interactions |
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| Relations |
| BioSample |
SAMN13256638 |
| SRA |
SRX7124442 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4156592_GM12878.rep3.atac.fragments.bed.gz |
710.7 Mb |
(ftp)(http) |
BED |
| GSM4156592_GM12878.rep3.barcodes.txt.gz |
303.8 Kb |
(ftp)(http) |
TXT |
| GSM4156592_GM12878.rep3.counts.txt.gz |
108.8 Mb |
(ftp)(http) |
TXT |
| GSM4156592_GM12878.rep3.peaks.bed.gz |
3.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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