NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7774385 Query DataSets for GSM7774385
Status Public on Apr 16, 2024
Title C30S70_Rep1-3
Sample type SRA
 
Source name Uterus
Organism Homo sapiens
Characteristics tissue: Uterus
cell type: Carcinosarcoma
disease state: Carcinoma70%,Sarcoma30%
Extracted molecule total RNA
Extraction protocol 30um of tissue sections were lysed in TRIzol reagent (Thermo Fisher Science) and extract RNA by using Direct-zol Kit (Zymo Research).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description sample_barcodes.txt.gz
RawCountTable.tsv.gz
Data processing Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCh38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)
 
Submission date Sep 11, 2023
Last update date Apr 16, 2024
Contact name Yasuyuki Ohkawa
E-mail(s) yohkawa@bioreg.kyushu-u.ac.jp
Organization name Medical Institute of Bioregulation
Lab Division of Transcriptomics
Street address 3-1-1 Maidashi
City Fukuoka
ZIP/Postal code 8128582
Country Japan
 
Platform ID GPL24676
Series (2)
GSE242886 Precise immuno-fluorescence canceling enables highly multiplexed imaging [RNA-seq]
GSE242887 Precise immuno-fluorescence canceling enables highly multiplexed imaging
Relations
BioSample SAMN37354395
SRA SRX21751074

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap