|
| Status |
Public on Oct 10, 2018 |
| Title |
Lane 2 RPI23 |
| Sample type |
SRA |
| |
|
| Source name |
Isolated maize male germinal cell
|
| Organism |
Zea mays |
| Characteristics |
tissue: anther
|
| Growth protocol |
Maize (Zea mays) inbred line W23 bz2 was grown in a greenhouse at Stanford, CA with a 14-h day / 10-h night light cycle
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Maize anthers were dissected and placed in protoplasting enzymes. Released archesporial (AR) cell and pollen mother cell (PMC) protoplasts were then recognized by their large size, picked up manually using blunted syringe needles, and placed on the cap of an 8-tube PCR strip.
Library protocol based on CelSeq2, modified to allow for split-cell technical replicates. Read 1 contains a 10 bp unique molecular identifier (UMI) followed by a 6-7 bp sample barcode. Read 2 contains transcript sequence.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
AR scRNAseq transcript counts.csv
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Unique molecular identifiers (UMIs) and sample barcodes were extracted from the first read of each read pair using a custom R script. The second read of each read pair were 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
Genome_build: AgpV4
Supplementary_files_format_and_content: csv file containing transcript counts for each each gene and split-cell sample
|
| |
|
| Submission date |
Oct 09, 2018 |
| Last update date |
Nov 22, 2022 |
| Contact name |
Brad Nelms |
| Organization name |
University of Georgia
|
| Street address |
120 E Green St
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE121039 |
Defining the developmental program leading to meiosis in maize |
|
| Relations |
| BioSample |
SAMN10224727 |
| SRA |
SRX4820974 |
