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Sample GSM3737488 Query DataSets for GSM3737488
Status Public on Nov 01, 2019
Title Cell Mix DNA
Sample type SRA
Source name Cell line
Organisms Homo sapiens; Mus musculus
Characteristics tissue: cell line
Treatment protocol HepG2 and 3T3 cells were harvested by centrifugation, washed with PBS (Thermo Fisher Scientific) and counted using BioRad TC20 cell counter. The percentage of live cells should higher than 95%. The cells were then resuspended in cold Lysis Buffer (10 mM Tris-HCl pH 7.4 (Sigma), 10 mM NaCl (Sigma), 3 mM MgCl2 (Sigma), 0.1% IGEPAL CA-630 (Sigma)) and centrifuged for 15 min at 600 g, 4 °C. For the species mixing experiment, nuclei were then washed with PBS and resuspended, counted using BioRad TC20 cell counter. HepG2 and 3T3 nuclei were then mixed in equal proportions and applied to Paired-seq.
Growth protocol HEK293T (human), HepG2 (human) and NIH/3T3 (mouse) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) and 1% penicillin–streptomycin (Thermo Fisher Scientific) at 37 °C with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Male C57BL/6J mice were purchased from Jackson laboratories at 8 weeks of age and maintained in the Salk animal barrier facility on 12 hr dark-light cycles with food ad libitum for four weeks before dissection. Cerebral cortex was dissected and snap-frozen in dry ice. All protocols were approved by the Salk Institute’s Institutional Animal Care and Use Committee (IACUC).
Libraries were constructed by Paired-seq workflow.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description Cell_Line.xls
Data processing Library strategy: Paired-seq
Cellular barcodes and the linker sequences are read by Read2. The first base of BC#1, BC#2, BC#3 and BC#4 should locate within 121-124th, 84-87th, 47-50th and 10-13rd base of read2
Nextera adaptor sequences were trimmed from 3’ of DNA libraries, Poly-dT sequences were trimmed from 3’ of RNA libraries and low-quality reads (length < 30, quality < 20) were excluded for further analysis.
Reads were first mapped to a reference genome using STAR (version: 2.6.0a) with the combined reference genome (GRCh37 for human and GRCm38 for mouse). Duplicates were removed based on the mapped position and UMI.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files include cell embeddings for each cell.
Submission date Apr 26, 2019
Last update date Nov 01, 2019
Contact name Zhu Chenxu
Organization name New York Genome Center
Street address 101 Avenue of the Americas
City New York
State/province New York
ZIP/Postal code 10044
Country USA
Platform ID GPL22245
Series (1)
GSE130399 An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
BioSample SAMN11519099
SRA SRX5759486

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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