title: WG17020_A02.W19


title: WG17020_A02.W18

status: Public on Jan 27 2021

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Reads flagged as invalid by the Illumina HiSeq control software were discarded. In the remaining reads, any 3′ bases with a quality score of B were removed. If any of the six UMI bases in the 5' end had a Phred score <17 the read was discarded, else the UMI was cut away and saved. The following three bases had to be G for the read to be kept. These, as well as any additional up to totally nine (presumably template-switch derived) G:s were cut away. Reads were discarded if the remaining transcript-derived sequence ended in a poly(A) sequence leaving <25 bases, or if the remaining sequence consisted of fewer than six non-A bases or a dinucleotide repeat with fewer than six other bases at either end. The reads were sorted by the well, as defined by the combined two index read barcodes.
Alignment was performed using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings. Reads with no alignments were realigned against an artificial chromosome, containing all possible splice junctions arising from the exons defined by the UCSC transcript models. The coordinates of aligned splice junctions were translated back to the corresponding genomic positions.
For expression level calculation, the exons of each locus with several transcript variants were merged to a combined model representing total expression of the locus. To account for incomplete cap site knowledge, the 5′ ends of all models were extended by 100 bases, but not beyond the 3′ end of any upstream nearby exon of another gene of the same orientation.
The annotation step was performed separately for each well. For each genomic position and strand combination the number of reads in each UMI was counted. Any multiread that mapped  to some repeat outside exons was assigned randomly as one of these repeats and did not contribute to the transcript corresponding to the exon. Else, if the multiread mapped to some exon, and not to any repeat outside exons, it was assigned to the exon where it was closest to the transcript model 5′ end. If it had no exon mapping, it was assigned randomly at one of the mappings. The total number of molecules at each mapping position was determined by the number of distinct UMIs observed. Any UMI represented by only a single read was excluded, in order to reduce false molecules due to PCR and sequencing errors. The raw UMI count was corrected for the UMI collision probability. For the human samples all reads mapping anywhere within the whole locus, defined as the region (including actual introns) from the start of the 100 base 5'end extension of the first exon up to the end of the last exon, were counted as exon-derived. The annotation gene set was extended by using liftOver between Homo sapiens hg38 to Mmul10 and transferring human genes and names to macaque.
Genome_build: Mmul10
Supplementary_files_format_and_content: Processed data includes raw UMI counts matrix with the assigned celltype clusters, where rows are geneIDs and columns cellIDs. Corresponding annotation text files, where rows are CellIDs and columns different annotation ( sample name, Celltype)

molecule: total RNA

organism: Macaca mulatta

source_name: Dorsal root ganglia

extract_protocol:
Extracted DRGs were cut once longitudinally (along the nerve) followed by chopping into ~0.5 mm slices. Samples were enzymatically treated for 1 h at 37°C with triturating every 15 min. The resulting cell suspension was then run through 100 µm cell-strainers. 1 ml of 10% Optiprep was loaded under the cell suspension solution using a gel loading tip and centrifugated at 200g for 6 min with a low break. Supernatant was discarded, the cell pellet resuspended and run through a 10 µm strainer. The strainer was rinsed twice and cells were then collected by flushing the filter twice. The cells were kept on ice for 15-20 min, centrifuged for 3 min  at 100 g and resuspended in 900 µl of filtered NMDG-SC/B27/12% optiprep and dispensed immediately into a WaferGen9600 Chip.
50nl lysis mix (500nM STRT-P1-T31, 4.5nM dNTP, 2% Triton-X-100, 20mM DTT, 1.5U/μl TaKaRa RNase Inhibitor) was dispensed, followed by 3min lysis at 72°C. Then, 85nl reverse transcription (RT) mix (2.1X SuperScript II First-Strand Buffer, 12.6mM MgCl2, 1.79M betaine, 14.7U/μl SuperScript II, 1.58U/μl TaKaRa RNase Inhibitor, 10.5μM P1B-UMI-RNA-TSO) were dispensed and RT carried out 42°C for 90 minutes. 96 Transposome stocks were assembled (6.25μM barcoded adapter (STRT-Tn5-Idx[1-96]), 6.25μM Tn5 transposase, 40% glycerol), 37°C 1h.  Tn5 reactions were assembled with 3μl transposome and 2μl amplified cDNA, in a total 20μl 1x CutSmart buffer (NEB), and incubated at 55°C 20min.

tag: animal id

tag: gender

value: Female

tag: age(years)

tag: region

value: Lumbar

tag: cell identity


title: WG17020_A02.W17


title: WG17020_A02.W13


title: WG17020_A02.W12

value: lowq/nonneuron


title: WG17020_A02.W14


title: WG17020_A02.W10

value: C-LTMR


title: WG17020_A02.W11


title: WG17020_A03.W14


title: WG17020_A02.W07


title: WG17020_A02.W09


title: WG17020_A03.W07


title: WG17020_A03.W06


title: WG17020_A02.W05


title: WG17020_A02.W08


title: WG17020_A02.W02


title: WG17020_A01.W14


title: WG17020_A02.W01


title: WG17020_A01.W13


title: WG17020_A02.W03


title: WG17020_A01.W12


title: WG17020_A01.W10


title: WG17020_A01.W11


title: WG17020_A01.W09


title: WG17020_A01.W07


title: WG17020_A01.W06


title: WG17020_A01.W03


title: WG17020_A01.W05


title: WG17020_A01.W04


title: WG17020_A01.W02


title: WG17020_A01.W01


title: WG17019_H12.W30


title: WG17019_H12.W26


title: WG17019_H12.W28


title: WG17020_A02.W04


title: WG17019_H12.W20


title: WG17019_H12.W14


title: WG17019_H12.W08


title: WG17019_H12.W12


title: WG17019_H12.W18


title: WG17019_H12.W22


title: WG17019_H12.W10


title: WG17019_H12.W06


title: WG17019_H12.W04


title: WG17019_H12.W16


title: WG17019_H12.W01


title: WG17019_H11.W17


title: WG17019_H12.W02


title: WG17019_H11.W25


title: WG17019_H11.W18


title: WG17019_H11.W16


title: WG17019_H11.W15


title: WG17019_H11.W09


title: WG17019_H11.W14


title: WG17019_H11.W13


title: WG17019_H11.W08


title: WG17019_H11.W12


title: WG17019_H11.W10


title: WG17019_H11.W11


title: WG17019_H11.W06


title: WG17019_H11.W04


title: WG17019_H11.W07


title: WG17019_H11.W05


title: WG17019_H11.W02


title: WG17019_H11.W03


title: WG17019_H10.W11


title: WG17019_H10.W13


title: WG17019_H10.W03


title: WG17019_H10.W09


title: WG17019_H10.W12


title: WG17019_H10.W10


title: WG17019_H10.W08


title: WG17019_H11.W01


title: WG17019_H10.W14


title: WG17019_H10.W07


title: WG17019_H09.W15


title: WG17019_H10.W01


title: WG17019_H09.W17


title: WG17019_H10.W15


title: WG17019_H09.W14


title: WG17019_H09.W08


title: WG17019_H09.W09


title: WG17019_H10.W02


title: WG17019_H09.W03


title: WG17019_H09.W04


title: WG17019_H08.W18


title: WG17019_H08.W21


title: WG17019_H08.W28


title: WG17019_H08.W17


title: WG17019_H08.W16


title: WG17019_H08.W14


title: WG17019_H08.W13


title: WG17019_H08.W11


title: WG17019_H08.W10


title: WG17019_H10.W06


title: WG17019_H10.W05


title: WG17019_H08.W07


title: WG17019_H08.W08


title: WG17019_H10.W04


title: WG17019_H09.W13


title: WG17019_H09.W12


title: WG17019_H09.W11


title: WG17019_H09.W10


title: WG17019_H09.W07


title: WG17019_H10.W16


title: WG17019_H09.W06


title: WG17019_H09.W16


title: WG17019_H08.W02


title: WG17019_H09.W05


title: WG17020_A02.W06


title: WG17019_H09.W02


title: WG17019_H08.W26


title: WG17019_H08.W27


title: WG17019_H07.W15


title: WG17019_H07.W25


title: WG17019_H07.W16


title: WG17019_H09.W01


title: WG17019_H08.W25


title: WG17019_H08.W20


title: WG17019_H08.W19


title: WG17019_H07.W13


title: WG17019_H08.W15


title: WG17019_H08.W29


title: WG17019_H08.W09


title: WG17019_H08.W06


title: WG17019_H08.W05


title: WG17019_H07.W17


title: WG17019_H08.W04


title: WG17019_H08.W12


title: WG17019_H07.W09


title: WG17019_H08.W03


title: WG17019_H08.W01


title: WG17019_H07.W05


title: WG17019_H07.W06


title: WG17019_H07.W02


title: WG17019_H07.W03


title: WG17019_H07.W11


title: WG17019_H07.W10


title: WG17019_H07.W12


title: WG17019_H07.W08


title: WG17019_H07.W07


title: WG17019_H06.W11


title: WG17019_H07.W01


title: WG17019_H06.W10


title: WG17019_H07.W14


title: WG17019_H07.W04


title: WG17019_H05.W14


title: WG17019_H05.W12


title: WG17019_H06.W03


title: WG17019_H06.W01


title: WG17019_H05.W13


title: WG17019_H06.W09


title: WG17019_H05.W11


title: WG17019_H05.W10


title: WG17019_H05.W07


title: WG17019_H05.W05


title: WG17019_H05.W06


title: WG17019_H05.W04


title: WG17019_H05.W03


title: WG17019_H05.W01


title: WG17019_H04.W31


title: WG17019_H04.W29


title: WG17019_H06.W02


title: WG17019_H04.W30


title: WG17019_H04.W22


title: WG17019_H04.W28


title: WG17019_H04.W19


title: WG17019_H04.W25


title: WG17019_H04.W18


title: WG17019_H04.W20


title: WG17019_H04.W27


title: WG17019_H04.W23


title: WG17019_H04.W21


title: WG17019_H04.W26


title: WG17019_H05.W09


title: WG17019_H04.W17


title: WG17019_H04.W14


title: WG17019_H04.W16


title: WG17019_H04.W10


title: WG17019_H04.W12


title: WG17019_H05.W02


title: WG17019_H04.W09


title: WG17019_H04.W08


title: WG17019_H04.W06


title: WG17019_H04.W07


title: WG17019_H04.W03


title: WG17019_H03.W16


title: WG17019_H04.W01


title: WG17019_H04.W02


title: WG17019_H04.W13


title: WG17019_H04.W15


title: WG17019_H04.W11


title: WG17019_H03.W14


title: WG17019_H03.W13


title: WG17019_H03.W11


title: WG17019_H03.W05


title: WG17019_H03.W04


title: WG17019_H04.W05


title: WG17019_H03.W07


title: WG17019_H03.W06


title: WG17019_H03.W12


title: WG17019_H03.W10


title: WG17019_H02.W30


title: WG17019_H02.W31


title: WG17019_H03.W09


title: WG17019_H03.W01


title: WG17019_H03.W02


title: WG17019_H04.W04


title: WG17019_H03.W15


title: WG17019_H03.W08


title: WG17019_H02.W28


title: WG17019_H02.W26


title: WG17019_H02.W27


title: WG17019_H02.W25


title: WG17019_H02.W29


title: WG17019_H03.W03


title: WG17019_H02.W21


title: WG17019_H02.W22


title: WG17019_H02.W23


title: WG17019_H02.W24


title: WG17019_H02.W20


title: WG17019_H02.W19


title: WG17019_H02.W18


title: WG17019_H02.W17


title: WG17019_H02.W13


title: WG17019_H02.W16


title: WG17019_H02.W10


title: WG17019_H02.W11


title: WG17019_H02.W12


title: WG17019_H02.W08


title: WG17019_H02.W15


title: WG17019_H02.W14


title: WG17019_H02.W05


title: WG17019_H02.W06


title: WG17019_H02.W04


title: WG17019_H02.W03


title: WG17019_H02.W07


title: WG17019_H01.W27


title: WG17019_H02.W01


title: WG17019_H01.W26


title: WG17019_H01.W25


title: WG17019_H01.W19


title: WG17019_H01.W18


title: WG17019_H02.W02


title: WG17019_H01.W16


title: WG17019_H01.W15


title: WG17019_H01.W17


title: WG17019_H01.W13


title: WG17019_H01.W11


title: WG17019_H01.W12


title: WG17019_H02.W09


title: WG17019_H01.W10


title: WG17019_H01.W09


title: WG17019_H01.W08


title: WG17019_H01.W07


title: WG17019_H01.W06


title: WG17019_H01.W04


title: WG17019_H01.W01


title: WG17019_G12.W13


title: WG17019_G12.W12


title: WG17019_G12.W15


title: WG17019_H01.W14


title: WG17019_G12.W09


title: WG17019_G12.W11


title: WG17019_H01.W03


title: WG17019_G12.W04


title: WG17019_G12.W02


title: WG17019_G12.W01


title: WG17019_G12.W05


title: WG17019_G12.W03


title: WG17019_G11.W12


title: WG17019_G11.W10


title: WG17019_G11.W13


title: WG17019_G11.W11


title: WG17019_G11.W04


title: WG17019_G11.W05


title: WG17019_H01.W05


title: WG17019_H01.W20


title: WG17019_H01.W02


title: WG17019_G12.W07


title: WG17019_G11.W03


title: WG17019_G11.W09


title: WG17019_G11.W01


title: WG17019_G12.W10


title: WG17019_G10.W18


title: WG17019_G10.W15


title: WG17019_G10.W13


title: WG17019_G10.W14


title: WG17019_G10.W25


title: WG17019_G10.W16


title: WG17019_G10.W08


title: WG17019_G10.W17


title: WG17019_G11.W02


title: WG17019_G10.W26


title: WG17019_G10.W02


title: WG17019_G10.W11


title: WG17019_G09.W16


title: WG17019_G10.W12


title: WG17019_G09.W14


title: WG17019_G10.W01


title: WG17019_G10.W09


title: WG17019_G10.W10


title: WG17019_G09.W10


title: WG17019_G09.W09


title: WG17019_G10.W07


title: WG17019_G10.W06


title: WG17019_G10.W05


title: WG17019_G10.W03


title: WG17019_G09.W15


title: WG17019_G09.W13


title: WG17019_G09.W06


title: WG17019_G09.W11


title: WG17019_G09.W07


title: WG17019_G09.W04


title: WG17019_G10.W04


title: WG17019_G09.W05


title: WG17019_G09.W03


title: WG17019_G09.W02


title: WG17019_G08.W16


title: WG17019_G08.W25


title: WG17019_G09.W12


title: WG17019_G08.W14


title: WG17019_G08.W17


title: WG17019_G08.W13


title: WG17019_G08.W10


title: WG17019_G08.W11


title: WG17019_G08.W12


title: WG17019_G08.W08


title: WG17019_G08.W06


title: WG17019_G08.W15


title: WG17019_G08.W03


title: WG17019_G09.W08


title: WG17019_G08.W07


title: WG17019_G08.W02


title: WG17019_G08.W04


title: WG17019_G08.W05


title: WG17019_G08.W09


title: WG17019_G09.W01


title: WG17019_G07.W26


title: WG17019_G07.W27


title: WG17019_G08.W01


title: WG17019_G07.W19


title: WG17019_G07.W25


title: WG17019_G07.W17


title: WG17019_G07.W20


title: WG17019_G07.W18


title: WG17019_G07.W16


title: WG17019_G07.W15


title: WG17019_G07.W14


title: WG17019_G07.W11


title: WG17019_G07.W12


title: WG17019_G07.W09


title: WG17019_G07.W08


title: WG17019_G07.W10


title: WG17019_G07.W13


title: WG17019_G07.W07


title: WG17019_G07.W04


title: WG17019_G07.W03


title: WG17019_G07.W05


title: WG17019_G07.W01


title: WG17019_G07.W02


title: WG17019_G06.W12


title: WG17019_G06.W10


title: WG17019_G06.W11


title: WG17019_G06.W04


title: WG17019_G06.W03


title: WG17019_G06.W01


title: WG17019_G06.W02


title: WG17019_G05.W09


title: WG17019_G05.W02


title: WG17019_G04.W16


title: WG17019_G05.W01


title: WG17019_G04.W14


title: WG17019_G04.W13


title: WG17019_G04.W12


title: WG17019_G04.W11


title: WG17019_G04.W09


title: WG17019_G07.W06


title: WG17019_G04.W10


title: WG17019_G04.W03


title: WG17019_G04.W05


title: WG17019_G04.W08


title: WG17019_G04.W07


title: WG17019_G04.W02


title: WG17019_G04.W06


title: WG17019_G04.W04


title: WG17019_G03.W15


title: WG17019_G03.W17


title: WG17019_G04.W01


title: WG17019_G06.W09


title: WG17019_G03.W16


title: WG17019_G03.W14


title: WG17019_G03.W12


title: WG17019_G03.W10


title: WG17019_G03.W08


title: WG17019_G03.W09


title: WG17019_G03.W11


title: WG17019_G03.W04


title: WG17019_G04.W15


title: WG17019_G03.W05


title: WG17019_G03.W01


title: WG17019_G03.W07


title: WG17019_G03.W06


title: WG17019_G03.W03


title: WG17019_G03.W02


title: WG17019_G02.W31


title: WG17019_G02.W30


title: WG17019_G02.W28

value: A-LTMR


title: WG17019_G02.W27


title: WG17019_G02.W25


title: WG17019_G02.W26


title: WG17019_G02.W23


title: WG17019_G02.W24


title: WG17019_G02.W32


title: WG17019_G02.W22


title: WG17019_G02.W20


title: WG17019_G02.W18


title: WG17019_G02.W16


title: WG17019_G02.W14


title: WG17019_G02.W17


title: WG17019_G02.W19


title: WG17019_G02.W21


title: WG17019_G02.W12


title: WG17019_G02.W15


title: WG17019_G02.W10


title: WG17019_G02.W09


title: WG17019_G02.W08


title: WG17019_G02.W11


title: WG17019_G02.W29


title: WG17019_G02.W07


title: WG17019_G02.W06


title: WG17019_G02.W04


title: WG17019_G02.W05


title: WG17019_G02.W02


title: WG17019_G02.W03


title: WG17019_G01.W32


title: WG17019_G01.W31


title: WG17019_G01.W29


title: WG17019_G01.W28


title: WG17019_G01.W27


title: WG17019_G01.W26


title: WG17019_G02.W13


title: WG17019_G01.W23


title: WG17019_G01.W24


title: WG17019_G01.W22


title: WG17019_G01.W18


title: WG17019_G01.W21


title: WG17019_G01.W19


title: WG17019_G01.W17


title: WG17019_G01.W20


title: WG17019_G01.W15


title: WG17019_G01.W14


title: WG17019_G01.W12


title: WG17019_G01.W16


title: WG17019_G02.W01


title: WG17019_G01.W09


title: WG17019_G01.W11


title: WG17019_G01.W10


title: WG17019_G01.W13


title: WG17019_G01.W30


title: WG17019_G01.W07


title: WG17019_G01.W08


title: WG17019_G01.W05


title: WG17019_G01.W03


title: WG17019_G01.W02


title: WG17019_G01.W06


title: WG17019_G01.W04


title: WG17019_G01.W01


title: WG17019_F12.W15


title: WG17019_F12.W14


title: WG17019_F12.W13


title: WG17019_F12.W12


title: WG17019_F12.W11


title: WG17019_G01.W25


title: WG17019_F12.W10


title: WG17019_F12.W07


title: WG17019_F12.W06


title: WG17019_F12.W09


title: WG17019_F12.W05


title: WG17019_F12.W03


title: WG17019_F12.W04


title: WG17019_F12.W02


title: WG17019_F12.W01


title: WG17019_F11.W13


title: WG17019_F11.W10


title: WG17019_F11.W11


title: WG17019_F11.W12


title: WG17019_F11.W14


title: WG17019_F11.W09


title: WG17019_F11.W04


title: WG17019_F11.W03


title: WG17019_F11.W02


title: WG17019_F10.W29


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title: WG17019_A02.W14


title: WG17019_A02.W12


title: WG17019_A03.W08


title: WG17019_A02.W11


title: WG17019_A02.W24


title: WG17019_A02.W10


title: WG17019_A02.W09


title: WG17019_A02.W08


title: WG17019_A02.W03


title: WG17019_A02.W07


title: WG17019_A02.W04


title: WG17019_A02.W01


title: WG17019_A01.W15


title: WG17019_A02.W02


title: WG17019_A01.W14


title: WG17019_A02.W06


title: WG17019_A02.W05


title: WG17019_A01.W09


title: WG17019_A01.W07


title: WG17019_A01.W11


title: WG17019_A01.W12


title: WG17019_A01.W10


title: WG17019_A01.W13


title: WG17019_A01.W06


title: WG17019_A01.W02


title: WG17019_A01.W03


title: WG17019_A01.W04


title: WG17019_A01.W01


title: SS2.416_P22

description: SS2-16-416_expression_for_R_from_comb_plate.tab

data_processing:
Read processing was essentially performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that no UMIs were analysed. and that the reads were not analysed without strand specificity and not trimmed before alignment.
Genome_build: Mmul10
Supplementary_files_format_and_content: Processed data includes raw UMI counts matrix with the assigned celltype clusters, where rows are geneIDs and columns cellIDs. Corresponding annotation text files, where rows are CellIDs and columns different annotation ( sample name, Celltype)

molecule: polyA RNA

source_name: dorsal root ganglion

extract_protocol:
Extracted DRGs were cut once longitudinally (along the nerve) followed by chopping into ~0.5 mm slices. Samples were enzymatically treated for 1 h at 37°C with triturating every 15 min. The resulting cell suspension was then run through 100 µm cell-strainers. 1 ml of 10% Optiprep was loaded under the cell suspension solution using a gel loading tip and centrifugated at 200g for 6 min with a low break. Supernatant was discarded, the cell pellet resuspended and run through a 10 µm strainer. The strainer was rinsed twice and cells were then collected by flushing the filter twice. The cells were kept on ice for 15-20 min, centrifuged for 3 min  at 100 g and resuspended in 900 µl of filtered NMDG-SC/B27/12% optiprep and dispensed immediately into a WaferGen9600 Chip.
RNA libraries were prepared for sequencing using the Smart-Seq2 protocol (Picelli et al, Nat Protoc. 2014)

value: Thoracic


title: SS2.416_P20


title: SS2.416_O24


title: SS2.416_P21


title: SS2.416_P24


title: SS2.416_O23


title: SS2.416_O22


title: WG17019_A01.W05


title: SS2.416_O21


title: SS2.416_N24


title: SS2.416_O20


title: SS2.416_M23


title: SS2.416_M24


title: SS2.416_N23


title: SS2.416_P23


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title: SS2.416_L22


title: SS2.416_N20


title: SS2.416_M21


title: SS2.416_L24


title: SS2.416_L20


title: SS2.416_K23


title: SS2.416_N22


title: SS2.416_K24


title: SS2.416_M22


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title: SS2.416_L21


title: SS2.416_M20


title: SS2.416_K22


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title: SS2.416_J20


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title: SS2.416_E21


title: SS2.416_A23


title: SS2.416_A24


title: SS2.415_P16

description: SS2-16-415_expression_for_R_from_comb_plate.tab


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title: SS2.415_P13


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title: SS2.416_A20


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title: SS2.415_M06


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title: SS2.415_M02


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title: SS2.414_P24

description: SS2-16-414_expression_for_R_from_comb_plate.tab


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description: SS2-16-305_expression_for_R_from_comb_plate.tab


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