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Sample GSM4679297 Query DataSets for GSM4679297
Status Public on Feb 04, 2021
Title P20190410 ESCA
Sample type SRA
 
Source name ESCA
Organism Homo sapiens
Characteristics tissue: Non-cancer, Tumor
patient id: P20190410
Extracted molecule total RNA
Extraction protocol Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.
10x Chromium Single cell 5’ Library
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description ESCA_normalized_expression.csv.gz
ESCA_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz
Data processing Cell Ranger 3.0.0 was used to quantify gene expression level.
Scanpy 1.4.3 was used to conduct the scRNA-seq analysis.
Genome_build: GRCh38
 
Submission date Jul 20, 2020
Last update date Feb 04, 2021
Contact name Sijin Cheng
E-mail(s) chengsj@mail.cbi.pku.edu.cn
Organization name Peking University
Department School of Life Science
Lab Zhang Lab
Street address Haidian District, Beijing Summer Palace Road No. 5
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL28896
Series (1)
GSE154763 A pan-cancer single-cell landscape of tumor-infiltrating myeloid cells
Relations
BioSample SAMN15585188

Supplementary data files not provided
Processed data are available on Series record
Raw data not provided for this record

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