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| Status |
Public on Jan 01, 2023 |
| Title |
MiSeq 2 2.0mm 56s |
| Sample type |
SRA |
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| Source name |
anther
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| Organism |
Zea mays |
| Characteristics |
tissue: anther
cell type: anther single cell
genotype: W23
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| Treatment protocol |
None
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
UMI Matrix
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| 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)
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| Submission date |
Nov 30, 2022 |
| Last update date |
Jan 01, 2023 |
| Contact name |
D. Blaine Marchant |
| E-mail(s) |
dbmarchant@gmail.com
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| Phone |
6507997768
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| Organization name |
Stanford University
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| Department |
Biology
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| Lab |
Walbot
|
| Street address |
Gilbert Biological Sciences Building, 371 Serra Mall
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL19255 |
| Series (1) |
| GSE219091 |
The establishment of the anther somatic niche with single cell sequencing |
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| Relations |
| BioSample |
SAMN31948143 |
| SRA |
SRX18433701 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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