SAMN39421023
External Id
The Chinese University of Hongkong
INSDC center name
2024-01-12T00:00:00Z
INSDC first public
2024-01-12T21:34:43.303Z
INSDC last update
SRS20126910
INSDC secondary accession
live
INSDC status
Plant
NCBI submission model
Plant.1.0
NCBI submission package
SRS20126910
SRA accession
harvested when the ligule of the third leaf is visible
age
2020
collection_date
LBJWC-52
cultivar
Each plate contains nuclei from replicate 1 and replicate 2. The two replicates were tagged using Tn5 with different ME-A and ME-B barcode adapters in four 96-well plates, and can be separated during the demultiplexing step.ME-A sequence: GGCGGTAGGCGTG NNNNN AGATGTGTATAAGAGACAGME-B sequence: CCAACACCCGTGCG NNNNN AGATGTGTATAAGAGACAGThe 12 column ME-A barcodes used by rep 1 were: ATACG, AGCGA, CTAAG, TGTCG, GTAGT, GTATA, ATTCC, GACTT, TTACT, CAATT, CATCT, TCGCG.The 12 column ME-A barcodes used by rep 2 were: TGTTT, TCCCT, GGCAG, CAAAA, GTGAG, TGGAT, CCGAG, ACTCG, GTCCT, TAAGA, ACCCC, AAACA.The 8 row ME-B barcodes used by rep 1 were: TCGGA, GTTTC, AGCTT, TCATT, GCTCC, ACTAA, CGAGG, ACCGG.The 8 row ME-B barcodes used by rep 2 were: CGGTT, GGAAC, GATGA, AACAT, CGCAC, TGACC, CGCGT, TTCCC.After Tn5 tagmentation, nuclei from rep1 and rep2 were mixed and approximately 10 nuclei were distributed to each well of a 96-well plate. PCR was performed using 8 well-indexed forward primers (ScPCR_F) and 12 well-indexed reverse primers (scPCR_R), each containing 6 nt barcodes.ScPCR_F: ACACTCTTTCCCTACACGACGCTCTTCCGATCT NNNNNN GGCGGTAGGCGTGScPCR_R: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT NNNNNN CCAACACCCGTGCGThe 8 forward primer barcodes used were: GATCAG, TAGCTT, GGCTAC, CTTGTA, AGTCAA, AGTTCC, ATGTCA, CCGTCC.The 12 reverse primer barcodes used were: GTAGAG, GTCCGC, GTGAAA, GTGGCC, GTTTCG, CGTACG, GAGTGG, GGTAGC, ACTGAT, ATGAGC, ATTCCT, CAAAAG.After sequencing, the data from each plate was demultiplexed using the 24x16 cell and 8x12 well barcodes. Additionally, a 6 nt plate barcode was added to the cell+well barcode before combining the data from each plate.
description
three leaves stage
dev_stage
Hong Kong
geo_loc_name
Urochloa fusca
http://purl.obolibrary.org/obo/NCBITaxon_744485
organism
P5
pcr_plate
CAGATC
plate_barcode
leaf
tissue
Uf scATAC plate P5
title