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Sample GSM6768184 Query DataSets for GSM6768184
Status Public on Jan 01, 2023
Title Pilot 1 2.0mm 7s
Sample type SRA
 
Source name anther
Organism Zea mays
Characteristics tissue: anther
cell type: anther single cell
genotype: W23
Treatment protocol None
Growth protocol individuals were grown under greenhouse conditions in Stanford, CA, USA with 14-h day/10-h night lighting, approximating half of peak summer solar radiation including UV-A. Daily irrigation and fertilization maintained robust growth
Extracted molecule polyA RNA
Extraction protocol Anthers dissected, fixed, digested, isolated using a Hana Cell Sorter (NamoCell) following FX-Cell protocol (Marchant et al. 2022)
CEL-Seq2 (Hashimshony et al., 2016) with modifications per Nelms and Walbot 2019.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description UMI Matrix
Data processing Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Assembly: AgpV4
Supplementary files format and content: CSV containing the UMI counts for each cell (column) and gene (row)
 
Submission date Nov 30, 2022
Last update date Jan 01, 2023
Contact name D. Blaine Marchant
E-mail(s) dbmarchant@gmail.com
Phone 6507997768
Organization name Stanford University
Department Biology
Lab Walbot
Street address Gilbert Biological Sciences Building, 371 Serra Mall
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
 
Platform ID GPL17628
Series (1)
GSE219091 The establishment of the anther somatic niche with single cell sequencing
Relations
BioSample SAMN31948097
SRA SRX18433974

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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