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Sample GSM5359603 Query DataSets for GSM5359603
Status Public on Sep 16, 2024
Title B_TCR
Sample type SRA
 
Source name liver
Organism Homo sapiens
Characteristics diagnosis: Biliary Atresia
tissue: liver
Extracted molecule total RNA
Extraction protocol 0.5 cm3 liver tissue was cut into very small fragments. The tissue was digested in dissociation buffer (0.8 mg/ml of Collagenase II, 1.5 mg/ml of Collagenase IV, Dispase,12 U/ml of DNase I, 3 mmol/L of CaCl2 in DMEM media with 10% FBS) for 30 minutes at 37℃. The cell suspensions were filtered through 40 µm cell strainers. Then, red cells were removed by ACK lysing buffer with incubation at ice for 10 minutes. Cell pellets were washed twice with 1xDPBS buffer and resuspended in 200 µl 1xDPBS buffer.
Single cell suspensions were subjected to single cell 5’ RNA sequencing library construction according to the instructions of the Chromium Next GEM Single Cell 5' Kit v2. (10X Genomics). Briefly, single cell suspensions mixed with RT-PCR master mix was loaded with partitioning oil and nanoliter-scale gel beads into the single-cell 5’ chip. Then, RNA transcripts were barcoded within single cells and reverse transcribed into cDNA, which were purified, amplified, end-repaired, and ligated with adapters to generate a single multiplexed library. The TCR- and BCR V(D)J libraries were generated with aliquots of cDNA using the Chromium Single Cell V(D)J Enrichment Kit v1.1.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing The raw data of 5’ single cell RNA sequencing were aligned to human transcriptome (GRCh38) using CellRanger (v3.1.0) count function.
The raw data of TCR and BCR V(D)J sequencing were aligned to human transcriptome (GRCh38) using CellRanger (v3.1.0) vdj function.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.tar: Tar archives include matrix.mtx, barcodes.tsv, and features.tsv files. Matrix table with raw gene counts for every gene and every single cells.
Supplementary_files_format_and_content: *_annotations.csv: High-level annotations of each high-confidence, cellular contig information of B cell receptor and T cell receptor for each patient.
 
Submission date Jun 04, 2021
Last update date Sep 16, 2024
Contact name Zhenhua Luo
E-mail(s) luozhh35@mail.sysu.edu.cn
Organization name The First Affiliated Hospital, Sun Yat-sen University
Street address Number 58, zhongshan er road, Yuexiu,
City Guangzhou
State/province Guangzhou
ZIP/Postal code 510080
Country China
 
Platform ID GPL24676
Series (1)
GSE176189 Integrative single-cell and spatial transcriptomic analyses identify a pathogenic cholangiocyte niche and TNFRSF12A as therapeutic target for biliary atresia
Relations
BioSample SAMN19573121

Supplementary file Size Download File type/resource
GSM5359603_B_TCR_filtered_contig_annotations.csv.gz 284.2 Kb (ftp)(http) CSV
Processed data provided as supplementary file
Raw data not provided for this record

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