NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6645128 Query DataSets for GSM6645128
Status Public on Jan 17, 2023
Title lung,PCW8, rep1 [10X158w3]
Sample type SRA
 
Source name lung
Organism Homo sapiens
Characteristics tissue: lung
age: PCW8
technology: Chromium
library technology: 10Xv2
gender: female
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol  The tissues were triturated with glass Pasteur pipettes every 15-20 min to enhance dissociation. After digestion, the cell suspension was filtered in a 15ml Falcon tube using a 30μm cell strainer (CellTrics, Sysmex), to remove clumps and debris. The cell suspension was kept ice cold and was diluted (roughly 1:2) with ice cold HBSS. The filtered cells were pelleted at 200g for 5 min at 4 °C and the pellet resuspended in a small volume of calcium- and magnesium-free HBSS (Gibco, cat no. 14170) and transferred to 1.5ml Eppendorf tubes precoated with 30% BSA (A9576, Sigma-Aldrich). A Bürker chamber was used for cell counting.
Single-cell RNAseq was carried out with the Chromium Single Cell 3´ Reagent Kit v2 and v3. Cell suspensions were counted and diluted to concentrations of 800 – 1200 cells/μl for a target recovery of 5000 cells on the Chromium platform. Downstream procedures including cDNA synthesis, library preparation and sequencing were performed according to the manufacturer’s instructions (10X Genomics Inc.). Libraries were sequenced on an Illumina NovaSeq 6000 (Illumina). We aimed to obtain 75.000 and 200.000 sequencing reads/cell for the v2 and v3 libraries respectively to match the different performances of the Chromium Single Cell 3´ Reagent v2 and v3 Kits and to achieve sufficient sequencing saturation. Across all 39 libraries we obtained an average of 187242 reads/cell.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing Reads were aligned to the human reference genome and libraries were demultiplexed and aligned with the 10X Genomics pipeline CellRanger (version 3.0.2).
Loom files were generated for each sample by running Velocyto (0.17.17) 76 in order to map molecules to unspliced and spliced transcripts.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample
 
Submission date Oct 17, 2022
Last update date Jan 17, 2023
Contact name Paulo Czarnewski
E-mail(s) czarnewski@gmail.com
Organization name KTH
Street address Tomtebodavägen 23b
City Solna
ZIP/Postal code 171 65
Country Sweden
 
Platform ID GPL30173
Series (2)
GSE215895 A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung [SC]
GSE215898 A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung

Supplementary file Size Download File type/resource
GSM6645128_Sountoulidis2022_10X158w3_counts.h5 23.2 Mb (ftp)(http) H5
Processed data provided as supplementary file
Raw data not provided for this record

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