title: D3-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample651
mRNA expression in microglia


title: D3-p2-K1_243_human_TREM2_R47H_het

status: Public on Dec 06 2021

type: SRA

city: San Francisco

first: Lay

last: Kodama

state: CA

address: 1650 Owens St.

department: Gladstone Institute of Neurological Disease

country: USA

institute: University of California San Francisco

description:
Sample645
mRNA expression in microglia

library_source: transcriptomic

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file (tsv) containing 1480 samples and mapped raw gene counts.

molecule: total RNA

organism: Mus musculus

source_name: FACS isolated adult microglia

extract_protocol:
In online methods
Smart-Seq2 protocol (in online methods)

tag: trem2 species

value: human

tag: p301s status

value: no

tag: brain region

value: hippocampus

tag: Sex

value: female

tag: gate

tag: cell type

value: microglia


title: D3-p2-K1_241_human_TREM2_R47H_het

description:
Sample644
mRNA expression in microglia


title: D9-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample745
mRNA expression in microglia

value: yes


title: D3-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample643
mRNA expression in microglia

value: mouse


title: D4-p1-NTG_232_mouse_Trem2_WT

description:
Sample654
mRNA expression in microglia


title: D3-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample648
mRNA expression in microglia


title: D3-p1-NTG_233_mouse_Trem2_WT

description:
Sample639
mRNA expression in microglia


title: D3-p1-K1_243_human_TREM2_R47H_het

description:
Sample637
mRNA expression in microglia


title: D4-p1-K1_241_human_TREM2_R47H_het

description:
Sample652
mRNA expression in microglia


title: D3-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample640
mRNA expression in microglia


title: D3-p1-K1_241_human_TREM2_R47H_het

description:
Sample636
mRNA expression in microglia


title: D3-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample641
mRNA expression in microglia


title: D4-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample656
mRNA expression in microglia


title: D2-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample635
mRNA expression in microglia


title: D2-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample634
mRNA expression in microglia


title: D4-p1-K1_243_human_TREM2_R47H_het

description:
Sample653
mRNA expression in microglia


title: D3-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample642
mRNA expression in microglia


title: D3-p2-NTG_233_mouse_Trem2_WT

description:
Sample647
mRNA expression in microglia


title: D2-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample632
mRNA expression in microglia


title: D8-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample731
mRNA expression in microglia


title: D2-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample633
mRNA expression in microglia


title: D3-p1-NTG_232_mouse_Trem2_WT

description:
Sample638
mRNA expression in microglia


title: D2-p1-NTG_232_mouse_Trem2_WT

description:
Sample622
mRNA expression in microglia


title: D2-p2-NTG_233_mouse_Trem2_WT

description:
Sample631
mRNA expression in microglia


title: D2-p1-K1_243_human_TREM2_R47H_het

description:
Sample621
mRNA expression in microglia


title: D2-p2-K1_243_human_TREM2_R47H_het

description:
Sample629
mRNA expression in microglia


title: D12-p2-K1_243_human_TREM2_R47H_het

description:
Sample614
mRNA expression in microglia


title: D12-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample619
mRNA expression in microglia


title: D12-p1-NTG_233_mouse_Trem2_WT

description:
Sample608
mRNA expression in microglia


title: D12-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample617
mRNA expression in microglia


title: D12-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample611
mRNA expression in microglia


title: D12-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample612
mRNA expression in microglia


title: D12-p1-K1_243_human_TREM2_R47H_het

description:
Sample606
mRNA expression in microglia


title: D2-p2-NTG_232_mouse_Trem2_WT

description:
Sample630
mRNA expression in microglia


title: D2-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample627
mRNA expression in microglia


title: D2-p2-K1_241_human_TREM2_R47H_het

description:
Sample628
mRNA expression in microglia


title: D2-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample625
mRNA expression in microglia


title: D2-p1-K1_241_human_TREM2_R47H_het

description:
Sample620
mRNA expression in microglia


title: D12-p2-NTG_232_mouse_Trem2_WT

description:
Sample615
mRNA expression in microglia


title: D12-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample616
mRNA expression in microglia


title: D12-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample618
mRNA expression in microglia


title: D12-p2-K1_241_human_TREM2_R47H_het

description:
Sample613
mRNA expression in microglia


title: D2-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample626
mRNA expression in microglia


title: D12-p1-NTG_232_mouse_Trem2_WT

description:
Sample607
mRNA expression in microglia


title: D11-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample595
mRNA expression in microglia


title: D11-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample604
mRNA expression in microglia


title: D11-p2-K1_243_human_TREM2_R47H_het

description:
Sample599
mRNA expression in microglia


title: D2-p1-NTG_233_mouse_Trem2_WT

description:
Sample623
mRNA expression in microglia


title: D11-p2-K1_241_human_TREM2_R47H_het

description:
Sample598
mRNA expression in microglia


title: D11-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample603
mRNA expression in microglia


title: D12-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample609
mRNA expression in microglia


title: D12-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample610
mRNA expression in microglia


title: D12-p1-K1_241_human_TREM2_R47H_het

description:
Sample605
mRNA expression in microglia


title: D4-p2-NTG_233_mouse_Trem2_WT

description:
Sample663
mRNA expression in microglia


title: D11-p2-NTG_233_mouse_Trem2_WT

description:
Sample600
mRNA expression in microglia


title: D11-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample601
mRNA expression in microglia


title: D10-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample589
mRNA expression in microglia


title: D11-p1-NTG_233_mouse_Trem2_WT

description:
Sample593
mRNA expression in microglia


title: D10-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample588
mRNA expression in microglia


title: D11-p1-NTG_232_mouse_Trem2_WT

description:
Sample592
mRNA expression in microglia


title: D11-p1-K1_243_human_TREM2_R47H_het

description:
Sample591
mRNA expression in microglia


title: D11-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample597
mRNA expression in microglia


title: D11-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample596
mRNA expression in microglia


title: D10-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample587
mRNA expression in microglia


title: D11-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample594
mRNA expression in microglia


title: D10-p2-NTG_233_mouse_Trem2_WT

description:
Sample585
mRNA expression in microglia


title: D11-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample602
mRNA expression in microglia


title: D10-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample586
mRNA expression in microglia


title: D10-p2-NTG_232_mouse_Trem2_WT

description:
Sample584
mRNA expression in microglia


title: D11-p1-K1_241_human_TREM2_R47H_het

description:
Sample590
mRNA expression in microglia


title: D10-p2-K1_241_human_TREM2_R47H_het

description:
Sample582
mRNA expression in microglia


title: D2-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample624
mRNA expression in microglia


title: D10-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample581
mRNA expression in microglia


title: D10-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample580
mRNA expression in microglia


title: D10-p2-K1_243_human_TREM2_R47H_het

description:
Sample583
mRNA expression in microglia


title: D1-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample570
mRNA expression in microglia


title: D10-p1-K1_241_human_TREM2_R47H_het

description:
Sample574
mRNA expression in microglia


title: D1-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample571
mRNA expression in microglia


title: D1-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample573
mRNA expression in microglia


title: D10-p1-NTG_232_mouse_Trem2_WT

description:
Sample576
mRNA expression in microglia


title: D10-p1-NTG_233_mouse_Trem2_WT

description:
Sample577
mRNA expression in microglia


title: D10-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample579
mRNA expression in microglia


title: D1-p2-K1_243_human_TREM2_R47H_het

description:
Sample567
mRNA expression in microglia


title: D10-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample578
mRNA expression in microglia


title: D1-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample566
mRNA expression in microglia


title: D1-p1-K1_243_human_TREM2_R47H_het

description:
Sample561
mRNA expression in microglia


title: D1-p1-NTG_233_mouse_Trem2_WT

description:
Sample563
mRNA expression in microglia


title: D1-p1-K1_241_human_TREM2_R47H_het

description:
Sample560
mRNA expression in microglia


title: C9-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample558
mRNA expression in microglia


title: D1-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample564
mRNA expression in microglia


title: C9-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample559
mRNA expression in microglia


title: C9-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample556
mRNA expression in microglia


title: D1-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample572
mRNA expression in microglia


title: D1-p2-NTG_232_mouse_Trem2_WT

description:
Sample568
mRNA expression in microglia


title: D1-p2-NTG_233_mouse_Trem2_WT

description:
Sample569
mRNA expression in microglia


title: D1-p1-NTG_232_mouse_Trem2_WT

description:
Sample562
mRNA expression in microglia


title: C9-p2-NTG_232_mouse_Trem2_WT

description:
Sample554
mRNA expression in microglia


title: C9-p2-NTG_233_mouse_Trem2_WT

description:
Sample555
mRNA expression in microglia


title: D10-p1-K1_243_human_TREM2_R47H_het

description:
Sample575
mRNA expression in microglia


title: C9-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample552
mRNA expression in microglia


title: C9-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample557
mRNA expression in microglia


title: C8-p2-K1_243_human_TREM2_R47H_het

description:
Sample538
mRNA expression in microglia


title: C9-p1-NTG_232_mouse_Trem2_WT

description:
Sample547
mRNA expression in microglia


title: C8-p2-K1_241_human_TREM2_R47H_het

description:
Sample537
mRNA expression in microglia


title: C8-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample544
mRNA expression in microglia


title: C9-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample551
mRNA expression in microglia


title: C9-p1-K1_243_human_TREM2_R47H_het

description:
Sample546
mRNA expression in microglia


title: C9-p1-K1_241_human_TREM2_R47H_het

description:
Sample545
mRNA expression in microglia


title: C8-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample541
mRNA expression in microglia


title: C9-p1-NTG_233_mouse_Trem2_WT

description:
Sample548
mRNA expression in microglia


title: C9-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample549
mRNA expression in microglia


title: C8-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample542
mRNA expression in microglia


title: C9-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample550
mRNA expression in microglia


title: C8-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample533
mRNA expression in microglia


title: C8-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample543
mRNA expression in microglia


title: C8-p2-NTG_233_mouse_Trem2_WT

description:
Sample540
mRNA expression in microglia


title: D1-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample565
mRNA expression in microglia


title: C8-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample534
mRNA expression in microglia


title: C8-p1-NTG_233_mouse_Trem2_WT

description:
Sample532
mRNA expression in microglia


title: C8-p2-NTG_232_mouse_Trem2_WT

description:
Sample539
mRNA expression in microglia


title: C8-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample536
mRNA expression in microglia


title: C8-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample535
mRNA expression in microglia


title: C8-p1-K1_243_human_TREM2_R47H_het

description:
Sample530
mRNA expression in microglia


title: C9-p2-K1_241_human_TREM2_R47H_het

description:
Sample553
mRNA expression in microglia


title: C8-p1-NTG_232_mouse_Trem2_WT

description:
Sample531
mRNA expression in microglia


title: C8-p1-K1_241_human_TREM2_R47H_het

description:
Sample529
mRNA expression in microglia


title: C7-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample528
mRNA expression in microglia


title: C7-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample526
mRNA expression in microglia


title: C7-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample527
mRNA expression in microglia


title: C7-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample525
mRNA expression in microglia


title: C7-p2-NTG_232_mouse_Trem2_WT

description:
Sample523
mRNA expression in microglia


title: C7-p1-NTG_233_mouse_Trem2_WT

description:
Sample516
mRNA expression in microglia


title: C7-p2-K1_243_human_TREM2_R47H_het

description:
Sample522
mRNA expression in microglia


title: C7-p2-NTG_233_mouse_Trem2_WT

description:
Sample524
mRNA expression in microglia


title: C7-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample518
mRNA expression in microglia


title: C7-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample519
mRNA expression in microglia


title: C7-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample520
mRNA expression in microglia


title: C6-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample511
mRNA expression in microglia


title: C7-p1-NTG_232_mouse_Trem2_WT

description:
Sample515
mRNA expression in microglia


title: C6-p2-NTG_233_mouse_Trem2_WT

description:
Sample509
mRNA expression in microglia


title: C6-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample510
mRNA expression in microglia


title: C6-p2-K1_243_human_TREM2_R47H_het

description:
Sample507
mRNA expression in microglia


title: C7-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample517
mRNA expression in microglia


title: C7-p2-K1_241_human_TREM2_R47H_het

description:
Sample521
mRNA expression in microglia


title: C6-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample506
mRNA expression in microglia


title: C6-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample505
mRNA expression in microglia


title: C6-p2-NTG_232_mouse_Trem2_WT

description:
Sample508
mRNA expression in microglia


title: C6-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample503
mRNA expression in microglia


title: C6-p1-NTG_233_mouse_Trem2_WT

description:
Sample502
mRNA expression in microglia


title: C6-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample504
mRNA expression in microglia


title: C6-p1-NTG_232_mouse_Trem2_WT

description:
Sample501
mRNA expression in microglia


title: C5-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample499
mRNA expression in microglia


title: C5-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample498
mRNA expression in microglia


title: C6-p1-K1_241_human_TREM2_R47H_het

description:
Sample500
mRNA expression in microglia


title: C5-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample497
mRNA expression in microglia


title: C5-p2-NTG_233_mouse_Trem2_WT

description:
Sample496
mRNA expression in microglia


title: C6-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample512
mRNA expression in microglia


title: C6-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample513
mRNA expression in microglia


title: C7-p1-K1_243_human_TREM2_R47H_het

description:
Sample514
mRNA expression in microglia


title: C5-p2-NTG_232_mouse_Trem2_WT

description:
Sample495
mRNA expression in microglia


title: C5-p2-K1_243_human_TREM2_R47H_het

description:
Sample494
mRNA expression in microglia


title: C5-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample490
mRNA expression in microglia


title: C4-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample484
mRNA expression in microglia


title: C4-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample483
mRNA expression in microglia


title: C5-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample489
mRNA expression in microglia


title: C5-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample491
mRNA expression in microglia


title: C5-p1-NTG_232_mouse_Trem2_WT

description:
Sample487
mRNA expression in microglia


title: C5-p1-NTG_233_mouse_Trem2_WT

description:
Sample488
mRNA expression in microglia


title: C4-p2-K1_243_human_TREM2_R47H_het

description:
Sample478
mRNA expression in microglia


title: C5-p1-K1_241_human_TREM2_R47H_het

description:
Sample485
mRNA expression in microglia


title: C4-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample481
mRNA expression in microglia


title: C4-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample482
mRNA expression in microglia


title: C4-p2-NTG_233_mouse_Trem2_WT

description:
Sample480
mRNA expression in microglia


title: C4-p2-K1_241_human_TREM2_R47H_het

description:
Sample477
mRNA expression in microglia


title: C4-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample476
mRNA expression in microglia


title: C4-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample475
mRNA expression in microglia


title: C4-p1-NTG_233_mouse_Trem2_WT

description:
Sample472
mRNA expression in microglia


title: C4-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample474
mRNA expression in microglia


title: C4-p1-NTG_232_mouse_Trem2_WT

description:
Sample471
mRNA expression in microglia


title: C4-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample473
mRNA expression in microglia


title: C5-p1-K1_243_human_TREM2_R47H_het

description:
Sample486
mRNA expression in microglia


title: C5-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample492
mRNA expression in microglia


title: C5-p2-K1_241_human_TREM2_R47H_het

description:
Sample493
mRNA expression in microglia


title: C4-p1-K1_243_human_TREM2_R47H_het

description:
Sample470
mRNA expression in microglia


title: C3-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample467
mRNA expression in microglia


title: C3-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample465
mRNA expression in microglia


title: C3-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample466
mRNA expression in microglia


title: C3-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample468
mRNA expression in microglia


title: C4-p1-K1_241_human_TREM2_R47H_het

description:
Sample469
mRNA expression in microglia


title: C3-p2-NTG_232_mouse_Trem2_WT

description:
Sample463
mRNA expression in microglia


title: C3-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample460
mRNA expression in microglia


title: C4-p2-NTG_232_mouse_Trem2_WT

description:
Sample479
mRNA expression in microglia


title: C3-p2-K1_243_human_TREM2_R47H_het

description:
Sample462
mRNA expression in microglia


title: C3-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample459
mRNA expression in microglia


title: C3-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample457
mRNA expression in microglia


title: C3-p1-NTG_232_mouse_Trem2_WT

description:
Sample455
mRNA expression in microglia


title: C3-p1-K1_243_human_TREM2_R47H_het

description:
Sample454
mRNA expression in microglia


title: C2-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample452
mRNA expression in microglia


title: C2-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample450
mRNA expression in microglia


title: C2-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample451
mRNA expression in microglia


title: C2-p2-NTG_233_mouse_Trem2_WT

description:
Sample448
mRNA expression in microglia


title: C2-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample449
mRNA expression in microglia


title: C2-p2-K1_243_human_TREM2_R47H_het

description:
Sample446
mRNA expression in microglia


title: C2-p2-NTG_232_mouse_Trem2_WT

description:
Sample447
mRNA expression in microglia


title: C2-p2-K1_241_human_TREM2_R47H_het

description:
Sample445
mRNA expression in microglia


title: C3-p2-NTG_233_mouse_Trem2_WT

description:
Sample464
mRNA expression in microglia


title: C2-p1-K1_243_human_TREM2_R47H_het

description:
Sample438
mRNA expression in microglia


title: C2-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample443
mRNA expression in microglia


title: C2-p1-NTG_232_mouse_Trem2_WT

description:
Sample439
mRNA expression in microglia


title: C2-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample442
mRNA expression in microglia


title: C3-p2-K1_241_human_TREM2_R47H_het

description:
Sample461
mRNA expression in microglia


title: C12-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample436
mRNA expression in microglia


title: C2-p1-NTG_233_mouse_Trem2_WT

description:
Sample440
mRNA expression in microglia


title: C2-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample441
mRNA expression in microglia


title: C12-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample437
mRNA expression in microglia


title: C3-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample458
mRNA expression in microglia


title: C3-p1-NTG_233_mouse_Trem2_WT

description:
Sample456
mRNA expression in microglia


title: C12-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample435
mRNA expression in microglia


title: C12-p2-NTG_232_mouse_Trem2_WT

description:
Sample433
mRNA expression in microglia


title: C12-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample430
mRNA expression in microglia


title: C12-p2-K1_241_human_TREM2_R47H_het

description:
Sample431
mRNA expression in microglia


title: C12-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample429
mRNA expression in microglia


title: C12-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample427
mRNA expression in microglia


title: C3-p1-K1_241_human_TREM2_R47H_het

description:
Sample453
mRNA expression in microglia


title: C12-p1-NTG_233_mouse_Trem2_WT

description:
Sample426
mRNA expression in microglia


title: C12-p1-K1_243_human_TREM2_R47H_het

description:
Sample424
mRNA expression in microglia


title: C12-p1-K1_241_human_TREM2_R47H_het

description:
Sample423
mRNA expression in microglia


title: C11-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample422
mRNA expression in microglia


title: C2-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample444
mRNA expression in microglia


title: C11-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample421
mRNA expression in microglia


title: C11-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample420
mRNA expression in microglia


title: C11-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample419
mRNA expression in microglia


title: C12-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample434
mRNA expression in microglia


title: C11-p2-NTG_233_mouse_Trem2_WT

description:
Sample418
mRNA expression in microglia


title: C11-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample413
mRNA expression in microglia


title: C11-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample414
mRNA expression in microglia


title: C11-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample412
mRNA expression in microglia


title: C11-p1-NTG_232_mouse_Trem2_WT

description:
Sample409
mRNA expression in microglia


title: C11-p2-NTG_232_mouse_Trem2_WT

description:
Sample417
mRNA expression in microglia


title: C11-p2-K1_241_human_TREM2_R47H_het

description:
Sample415
mRNA expression in microglia


title: C11-p1-NTG_233_mouse_Trem2_WT

description:
Sample410
mRNA expression in microglia


title: C11-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample411
mRNA expression in microglia


title: C12-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample428
mRNA expression in microglia


title: C11-p1-K1_241_human_TREM2_R47H_het

description:
Sample407
mRNA expression in microglia


title: C10-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample406
mRNA expression in microglia


title: C10-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample404
mRNA expression in microglia


title: C12-p1-NTG_232_mouse_Trem2_WT

description:
Sample425
mRNA expression in microglia


title: C12-p2-K1_243_human_TREM2_R47H_het

description:
Sample432
mRNA expression in microglia


title: C10-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample405
mRNA expression in microglia


title: C11-p1-K1_243_human_TREM2_R47H_het

description:
Sample408
mRNA expression in microglia


title: C10-p2-K1_243_human_TREM2_R47H_het

description:
Sample400
mRNA expression in microglia


title: C10-p2-K1_241_human_TREM2_R47H_het

description:
Sample399
mRNA expression in microglia


title: C10-p2-NTG_233_mouse_Trem2_WT

description:
Sample402
mRNA expression in microglia


title: C10-p2-NTG_232_mouse_Trem2_WT

description:
Sample401
mRNA expression in microglia


title: C10-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample398
mRNA expression in microglia


title: C10-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample397
mRNA expression in microglia


title: C10-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample396
mRNA expression in microglia


title: C10-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample395
mRNA expression in microglia


title: C10-p1-NTG_233_mouse_Trem2_WT

description:
Sample394
mRNA expression in microglia


title: C10-p1-NTG_232_mouse_Trem2_WT

description:
Sample393
mRNA expression in microglia


title: C11-p2-K1_243_human_TREM2_R47H_het

description:
Sample416
mRNA expression in microglia


title: C10-p1-K1_241_human_TREM2_R47H_het

description:
Sample392
mRNA expression in microglia


title: C1-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample391
mRNA expression in microglia


title: C10-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample403
mRNA expression in microglia


title: C1-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample390
mRNA expression in microglia


title: C1-p2-NTG_232_mouse_Trem2_WT

description:
Sample386
mRNA expression in microglia


title: C1-p2-K1_241_human_TREM2_R47H_het

description:
Sample384
mRNA expression in microglia


title: C1-p2-NTG_233_mouse_Trem2_WT

description:
Sample387
mRNA expression in microglia


title: C1-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample389
mRNA expression in microglia


title: C1-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample382
mRNA expression in microglia


title: C1-p1-K1_243_human_TREM2_R47H_het

description:
Sample377
mRNA expression in microglia


title: C1-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample380
mRNA expression in microglia


title: C1-p1-NTG_232_mouse_Trem2_WT

description:
Sample378
mRNA expression in microglia


title: C1-p1-K1_241_human_TREM2_R47H_het

description:
Sample376
mRNA expression in microglia


title: B9-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample373
mRNA expression in microglia


title: C1-p1-NTG_233_mouse_Trem2_WT

description:
Sample379
mRNA expression in microglia


title: B9-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample367
mRNA expression in microglia


title: B9-p2-K1_241_human_TREM2_R47H_het

description:
Sample368
mRNA expression in microglia


title: B9-p2-NTG_232_mouse_Trem2_WT

description:
Sample370
mRNA expression in microglia


title: C1-p2-K1_243_human_TREM2_R47H_het

description:
Sample385
mRNA expression in microglia


title: B9-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample374
mRNA expression in microglia


title: B9-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample366
mRNA expression in microglia


title: B9-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample375
mRNA expression in microglia


title: B9-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample372
mRNA expression in microglia


title: B9-p2-K1_243_human_TREM2_R47H_het

description:
Sample369
mRNA expression in microglia


title: B9-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample365
mRNA expression in microglia


title: C1-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample388
mRNA expression in microglia


title: B9-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample364
mRNA expression in microglia


title: B9-p1-NTG_233_mouse_Trem2_WT

description:
Sample363
mRNA expression in microglia


title: B9-p2-NTG_233_mouse_Trem2_WT

description:
Sample371
mRNA expression in microglia


title: B9-p1-NTG_232_mouse_Trem2_WT

description:
Sample362
mRNA expression in microglia


title: C1-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample383
mRNA expression in microglia


title: B9-p1-K1_241_human_TREM2_R47H_het

description:
Sample360
mRNA expression in microglia


title: B8-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample358
mRNA expression in microglia


title: B9-p1-K1_243_human_TREM2_R47H_het

description:
Sample361
mRNA expression in microglia


title: B8-p2-NTG_233_mouse_Trem2_WT

description:
Sample355
mRNA expression in microglia


title: B8-p2-K1_241_human_TREM2_R47H_het

description:
Sample352
mRNA expression in microglia


title: B8-p2-K1_243_human_TREM2_R47H_het

description:
Sample353
mRNA expression in microglia


title: B8-p2-NTG_232_mouse_Trem2_WT

description:
Sample354
mRNA expression in microglia


title: B8-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample359
mRNA expression in microglia


title: B8-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample357
mRNA expression in microglia


title: B8-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample349
mRNA expression in microglia


title: C1-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample381
mRNA expression in microglia


title: B8-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample350
mRNA expression in microglia


title: B8-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample348
mRNA expression in microglia


title: B8-p1-NTG_233_mouse_Trem2_WT

description:
Sample347
mRNA expression in microglia


title: B8-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample351
mRNA expression in microglia


title: B8-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample356
mRNA expression in microglia


title: B8-p1-K1_243_human_TREM2_R47H_het

description:
Sample345
mRNA expression in microglia


title: B8-p1-K1_241_human_TREM2_R47H_het

description:
Sample344
mRNA expression in microglia


title: B7-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample343
mRNA expression in microglia


title: B7-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample342
mRNA expression in microglia


title: B7-p2-K1_241_human_TREM2_R47H_het

description:
Sample336
mRNA expression in microglia


title: B7-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample341
mRNA expression in microglia


title: B7-p2-NTG_232_mouse_Trem2_WT

description:
Sample338
mRNA expression in microglia


title: B7-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample340
mRNA expression in microglia


title: B7-p2-K1_243_human_TREM2_R47H_het

description:
Sample337
mRNA expression in microglia


title: B8-p1-NTG_232_mouse_Trem2_WT

description:
Sample346
mRNA expression in microglia


title: B7-p2-NTG_233_mouse_Trem2_WT

description:
Sample339
mRNA expression in microglia


title: B7-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample335
mRNA expression in microglia


title: B7-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample332
mRNA expression in microglia


title: B7-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample334
mRNA expression in microglia


title: B7-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample333
mRNA expression in microglia


title: B7-p1-NTG_232_mouse_Trem2_WT

description:
Sample330
mRNA expression in microglia


title: B7-p1-K1_241_human_TREM2_R47H_het

description:
Sample328
mRNA expression in microglia


title: B7-p1-NTG_233_mouse_Trem2_WT

description:
Sample331
mRNA expression in microglia


title: B6-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample327
mRNA expression in microglia


title: B7-p1-K1_243_human_TREM2_R47H_het

description:
Sample329
mRNA expression in microglia


title: B6-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample325
mRNA expression in microglia


title: B6-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample324
mRNA expression in microglia


title: B6-p2-NTG_233_mouse_Trem2_WT

description:
Sample323
mRNA expression in microglia


title: B6-p2-K1_241_human_TREM2_R47H_het

description:
Sample320
mRNA expression in microglia


title: B6-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample319
mRNA expression in microglia


title: B6-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample317
mRNA expression in microglia


title: B6-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample318
mRNA expression in microglia


title: B6-p1-NTG_233_mouse_Trem2_WT

description:
Sample315
mRNA expression in microglia


title: B6-p2-NTG_232_mouse_Trem2_WT

description:
Sample322
mRNA expression in microglia


title: B6-p1-NTG_232_mouse_Trem2_WT

description:
Sample314
mRNA expression in microglia


title: B6-p1-K1_243_human_TREM2_R47H_het

description:
Sample313
mRNA expression in microglia


title: B6-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample316
mRNA expression in microglia


title: B5-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample310
mRNA expression in microglia


title: B6-p1-K1_241_human_TREM2_R47H_het

description:
Sample312
mRNA expression in microglia


title: B5-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample309
mRNA expression in microglia


title: B5-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample311
mRNA expression in microglia


title: B5-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample308
mRNA expression in microglia


title: B5-p2-NTG_232_mouse_Trem2_WT

description:
Sample306
mRNA expression in microglia


title: B5-p2-NTG_233_mouse_Trem2_WT

description:
Sample307
mRNA expression in microglia


title: B5-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample303
mRNA expression in microglia


title: B5-p2-K1_243_human_TREM2_R47H_het

description:
Sample305
mRNA expression in microglia


title: B5-p2-K1_241_human_TREM2_R47H_het

description:
Sample304
mRNA expression in microglia


title: B6-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample326
mRNA expression in microglia


title: B5-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample302
mRNA expression in microglia


title: B5-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample301
mRNA expression in microglia


title: B5-p1-K1_243_human_TREM2_R47H_het

description:
Sample297
mRNA expression in microglia


title: B5-p1-NTG_233_mouse_Trem2_WT

description:
Sample299
mRNA expression in microglia


title: B6-p2-K1_243_human_TREM2_R47H_het

description:
Sample321
mRNA expression in microglia


title: B5-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample300
mRNA expression in microglia


title: B4-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample294
mRNA expression in microglia


title: B5-p1-K1_241_human_TREM2_R47H_het

description:
Sample296
mRNA expression in microglia


title: B4-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample295
mRNA expression in microglia


title: B5-p1-NTG_232_mouse_Trem2_WT

description:
Sample298
mRNA expression in microglia


title: B4-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample292
mRNA expression in microglia


title: B4-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample293
mRNA expression in microglia


title: B4-p2-K1_241_human_TREM2_R47H_het

description:
Sample289
mRNA expression in microglia


title: B4-p2-NTG_233_mouse_Trem2_WT

description:
Sample291
mRNA expression in microglia


title: B4-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample285
mRNA expression in microglia


title: B4-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample287
mRNA expression in microglia


title: B4-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample288
mRNA expression in microglia


title: B4-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample286
mRNA expression in microglia


title: B4-p1-NTG_232_mouse_Trem2_WT

description:
Sample283
mRNA expression in microglia


title: B4-p1-NTG_233_mouse_Trem2_WT

description:
Sample284
mRNA expression in microglia


title: B4-p1-K1_243_human_TREM2_R47H_het

description:
Sample282
mRNA expression in microglia


title: B4-p2-K1_243_human_TREM2_R47H_het

description:
Sample290
mRNA expression in microglia


title: Vagus nerve ribotag (vagus_67_ribotag_CCGATTA)

city: St Louis

first: Jeffrey

last: Milbrandt

state: Missouri

address: 660 S Euclid Ave #5101

department: Genetics

institute: Washington University School of Medicine

data_processing:
Demultiplexed by bcl2fastq
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts was estimated with Salmon version 0.8.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Supplementary_files_format_and_content: raw_expression_matrix.txt

source_name: Peripheral nerves

extract_protocol:
The protocol was modified based on Sanz et al. Specifically, we generated Mpz-Cre:Ribo-Tag mice that, upon the expression of Mpz, cells would express HA-tagged ribosomal protein RPL22. The mRNA of Mpz-expressing cells from the nerve was then isolated by immunoprecipitation of polyribosomes with anti-HA and subjected to RNA-seq. Both direct and indirect pull down approaches were tested and indirect pull down was selected because of higher yields. Both sciatic and vagus nerves were dissected from Mpz-Cre:RiboTag mice and immediately placed into PBS with RNaseIn and SuperaseIn on ice. The epineurium of sciatic nerve was also carefully removed by forceps before placing the remaining nerves into PBS. Upon dissection, the nerves were transferred to dissociation media with TL liberase, RNaseIn and SuperaseIn for enzymatic dissociation for 15min at 37°C. The cells were pelleted by spinning at 1500rpm for 5 min, homogenized using Dounce homogenizer in Polysome buffer and then spin at 10,000g for 10min. Supernatant was then collected, with HA antibody-coupled magnetic beads added to the cleared supernatant. After an overnight incubation at 4°C, the magnetic beads that contained immunoadsorbed polysomes were washed with a high salt buffer. mRNA was then extracted using the Qiagen RNA extraction kit according to manufacturer’s protocol.
Samples were prepared according to Illumina library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.

tag: strain

tag: treatment

value: untreated

tag: tissue

value: vagus nerve

tag: rip antibody

value: HA antibody


title: B3-p1-K1_243_human_TREM2_R47H_het

description:
Sample266
mRNA expression in microglia


title: B3-p2-K1_241_human_TREM2_R47H_het

description:
Sample273
mRNA expression in microglia


title: B3-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample279
mRNA expression in microglia


title: B3-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample272
mRNA expression in microglia


title: B3-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample271
mRNA expression in microglia


title: B2-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample263
mRNA expression in microglia


title: B3-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample280
mRNA expression in microglia


title: B2-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample262
mRNA expression in microglia


title: B2-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample264
mRNA expression in microglia


title: B3-p2-NTG_233_mouse_Trem2_WT

description:
Sample276
mRNA expression in microglia


title: B2-p2-NTG_233_mouse_Trem2_WT

description:
Sample260
mRNA expression in microglia


title: B3-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample270
mRNA expression in microglia


title: B3-p1-NTG_232_mouse_Trem2_WT

description:
Sample267
mRNA expression in microglia


title: B3-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample269
mRNA expression in microglia


title: B3-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample277
mRNA expression in microglia


title: B3-p1-K1_241_human_TREM2_R47H_het

description:
Sample265
mRNA expression in microglia


title: B4-p1-K1_241_human_TREM2_R47H_het

description:
Sample281
mRNA expression in microglia


title: B3-p2-NTG_232_mouse_Trem2_WT

description:
Sample275
mRNA expression in microglia


title: B2-p2-NTG_232_mouse_Trem2_WT

description:
Sample259
mRNA expression in microglia


title: B3-p2-K1_243_human_TREM2_R47H_het

description:
Sample274
mRNA expression in microglia


title: B2-p2-K1_241_human_TREM2_R47H_het

description:
Sample257
mRNA expression in microglia


title: B3-p1-NTG_233_mouse_Trem2_WT

description:
Sample268
mRNA expression in microglia


title: Vagus nerve ribotag (vagus_67_ribotag_CCATCAT)


title: B3-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample278
mRNA expression in microglia


title: B2-p2-K1_243_human_TREM2_R47H_het

description:
Sample258
mRNA expression in microglia


title: B2-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample261
mRNA expression in microglia


title: Vagus nerve whole (vagus_whole_GGCAGCG)


title: Vagus nerve ribotag (vagus_67_ribotag_GGCAGCG)


title: B2-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample255
mRNA expression in microglia


title: Vagus nerve whole (vagus_whole_CCGATTA)


title: Vagus nerve whole (vagus_whole_CCATCAT)


title: B2-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample256
mRNA expression in microglia


title: Sciatic nerve whole (SN_TTTTGTC)

value: sciatic nerve


title: Sciatic nerve ribotag (SN_ribotag_1_ATGACAG)


title: Sciatic nerve ribotag (SN_ribotag_3_TGAGGTT)


title: B14: B cell population at day 14 scRNA-seq

city: Stockholm

first: Eduardo

middle: J

last: Villablanca

address: visiongatan 18

department: CMM

country: Sweden

institute: Karolinska Institute

data_processing:
Base calling and preprocessing using cell ranger
alignment and count using cell ranger pipline
seurat 3.0 pipeline for downstream analysis
Genome_build: mm10

source_name: B cell population at day 14

growth_protocol: B cells were isolated from the colon of mice on day 0 (no treatment) or day 14 (recovery) after 7 days of DSS treatment by flow cytometric sorting and analyzed by 10X sequencing

extract_protocol: cells were processed according to 10x Genomics protocol for Chromium Single cell 3’ kit (version 2)

tag: gender

value: Female

value: day 14  colon derived B cells

value: DSS treatment


title: Sciatic nerve ribotag (SN_ribotag_2_GCTTAGA)


title: Sciatic nerve whole (SN_CGTCGCT)


title: IEC-stroma-control scRNA-seq

source_name: IEC-stroma cell population at Day 14 in B cell presence

growth_protocol: Female C57BL/6J mice were irradiated and received BM transplants with either CD19cre (ctrl) or CD19cre x iDTR cells. 8 weeks after BM transfer mice were treated with 2%DSS via the drinking water followed by 7 days of recovery. On days 9, 10, 12 and 13 mice received i.p. injections of diphteria toxin (25ng/g BW) in PBS. On day 14 colonic epithelial cells and stromal cells were sorted by flow cytometry and processed according to 10x Genomics protocol for Chromium Single cell 3’ kit (version 2) and submitted for sequencing

value: IEC-stroma cells


title: Overexpressor line BRL3ox hypocotyls grown at 28ºC Rep2

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

description:
Overexpression line (transgenic) 35S:BRL3-GFP (Described in Fàbregas et al., 2018)
BRL3ox_28_R2

data_processing:
Quality filter and read trimming: 75bp paired-reads were quality checked with FastQC software (v0.11.2) and trimmed with Trimmomatic (v0.38) 9bp at 3’ end and trimmed until minimum average quality of 25. Minimum read length to keep of 45bp.
Alignment to TAIR10 genome using HISAT2 (v2.1) aligner
Features quantification: Gene expression calculated as raw fragment counts, at gene level, using FeatureCounts (v1.6.2) on Araport11.gff3 annotation file.
Downstream processing included low-counts genes filtering out, chloroplast genes discard (artifact detected in one sample)m, TMM normalization and differential expression analysis using edgeR (v3.34.1) package in R
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-separated text file containing raw fragment counts of each Arabidopsis thaliana gene and for each sample

organism: Arabidopsis thaliana

source_name: 6DAG hypocotyls

growth_protocol: Arabidopsis thaliana seeds were surfaced sterilized with 35% sodium hypochlorite and grown vertically in plates containg half-strength Murashige and Skoog (MS) medium supplemented with vitamins. Plates were grown either at 22ºC or 28ºC in long-day conditions (16h light + 8h dark), at 60% relative humidity and under white light at 80umol/m2/s.

extract_protocol:
Between 150 and 200 mg of fresh hypocotyl tissue (per sample) was extracted using the Rneasy plant mini kit (Qiagen 74904). To remove contaminating DNA, the TURBO DNAfreeTM Kit. (Ambion AM1907) was used according to the manufacturer’s recommendations.  Quality of RNA was checked with Bioanalyzer. All samples had a RNA Integrity Number (RIN) > 7.
TruSeq Stranded mRNA Sample Prep kit

treatment_protocol: Seedlings were grown (in plates) for 6 days at 22ºC or 28ºC

tag: genotype

value: BRL3ox (Fabregas et al., 2018)

tag: temperature

tag: replicate

tag: developmental stage

value: hypocotyls


title: B0: B cell population at day 0 scRNA-seq

source_name: B cell population at day 0

value: day 0 colon derived B cells


title: B12-p2-K1_243_human_TREM2_R47H_het

description:
Sample243
mRNA expression in microglia

value: human

value: no


title: B12-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample246
mRNA expression in microglia

value: hippocampus

value: female


title: B2-p1-NTG_232_mouse_Trem2_WT

description:
Sample252
mRNA expression in microglia

value: microglia


title: B2-p1-K1_241_human_TREM2_R47H_het

description:
Sample250
mRNA expression in microglia


title: B12-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample249
mRNA expression in microglia

value: mouse


title: B12-p2-NTG_233_mouse_Trem2_WT

description:
Sample245
mRNA expression in microglia


title: B12-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample247
mRNA expression in microglia

value: yes


title: B12-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample248
mRNA expression in microglia


title: B12-p2-NTG_232_mouse_Trem2_WT

description:
Sample244
mRNA expression in microglia


title: B2-p1-NTG_233_mouse_Trem2_WT

description:
Sample253
mRNA expression in microglia


title: B2-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample254
mRNA expression in microglia


title: B12-p2-K1_241_human_TREM2_R47H_het

description:
Sample242
mRNA expression in microglia


title: Overexpressor line BRL3ox hypocotyls grown at 28ºC Rep1

description:
Overexpression line (transgenic) 35S:BRL3-GFP (Described in Fàbregas et al., 2018)
BRL3ox_28_R1


title: B12-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample241
mRNA expression in microglia


title: Sciatic nerve whole (SN_GAGGCGT)

value: untreated


title: B2-p1-K1_243_human_TREM2_R47H_het

description:
Sample251
mRNA expression in microglia


title: IEC-stroma-depleted scRNA-seq

source_name: IEC-stroma cell population at Day 14 in B cell depletion


title: Overexpressor line BRL3ox hypocotyls grown at 22ºC Rep2

description:
Overexpression line (transgenic) 35S:BRL3-GFP (Described in Fàbregas et al., 2018)
BRL3ox_22_R2


title: B12-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample240
mRNA expression in microglia


title: Overexpressor line BRL3ox hypocotyls grown at 22ºC Rep1

description:
Overexpression line (transgenic) 35S:BRL3-GFP (Described in Fàbregas et al., 2018)
BRL3ox_22_R1


title: B12-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample239
mRNA expression in microglia


title: B12-p1-NTG_233_mouse_Trem2_WT

description:
Sample237
mRNA expression in microglia


title: B12-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample238
mRNA expression in microglia


title: B12-p1-NTG_232_mouse_Trem2_WT

description:
Sample236
mRNA expression in microglia


title: Complementation line pSUC2:BRL3;brl3-2 hypocotyls grown at 28ºC Rep1

description:
Complementation transgenic line: phloem specific promoter SUC2 fused to BRL3 receptor and transformed in brl3-2 mutant
pSUC2:BRL3;brl3-2_28_R1

value: pSUC2::BRL3-GFP; brl3-2


title: Complementation line pSUC2:BRL3;brl3-2 hypocotyls grown at 22ºC Rep1

description:
Complementation transgenic line: phloem specific promoter SUC2 fused to BRL3 receptor and transformed in brl3-2 mutant
pSUC2:BRL3;brl3-2_22_R1


title: B12-p1-K1_243_human_TREM2_R47H_het

description:
Sample235
mRNA expression in microglia


title: Complementation line pSUC2:BRL3;brl3-2 hypocotyls grown at 22ºC Rep2

description:
Complementation transgenic line: phloem specific promoter SUC2 fused to BRL3 receptor and transformed in brl3-2 mutant
pSUC2:BRL3;brl3-2_22_R2


title: B11-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample233
mRNA expression in microglia


title: brl3-2 hypocotyls grown at 28ºC Rep1

description:
T-DNA insertion mutant (SALK_006024C)
brl3-2_28_R1


title: Complementation line pSUC2:BRL3;brl3-2 hypocotyls grown at 28ºC Rep2

description:
Complementation transgenic line: phloem specific promoter SUC2 fused to BRL3 receptor and transformed in brl3-2 mutant
pSUC2:BRL3;brl3-2_28_R2


title: B11-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample232
mRNA expression in microglia


title: B11-p2-NTG_233_mouse_Trem2_WT

description:
Sample229
mRNA expression in microglia


title: B11-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample230
mRNA expression in microglia


title: B11-p2-NTG_232_mouse_Trem2_WT

description:
Sample228
mRNA expression in microglia


title: B12-p1-K1_241_human_TREM2_R47H_het

description:
Sample234
mRNA expression in microglia


title: brl3-2 hypocotyls grown at 28ºC Rep2

description:
T-DNA insertion mutant (SALK_006024C)
brl3-2_28_R2


title: Col-0 WT hypocotyls grown at 28ºC Rep2

description:
Wild-type plant (Columbia-0 ecotype)
Col-0_28_R2

value: Col-0 WT


title: B11-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample231
mRNA expression in microglia


title: Col-0 WT hypocotyls grown at 22ºC Rep2

description:
Wild-type plant (Columbia-0 ecotype)
Col-0_22_R2


title: brl3-2 hypocotyls grown at 22ºC Rep1

description:
T-DNA insertion mutant (SALK_006024C)
brl3-2_22_R1


title: brl3-2 hypocotyls grown at 22ºC Rep2

description:
T-DNA insertion mutant (SALK_006024C)
brl3-2_22_R2


title: Col-0 WT hypocotyls grown at 28ºC Rep1

description:
Wild-type plant (Columbia-0 ecotype)
Col-0_28_R1


title: Col-0 WT hypocotyls grown at 22ºC Rep1

description:
Wild-type plant (Columbia-0 ecotype)
Col-0_22_R1


title: B11-p2-K1_243_human_TREM2_R47H_het

description:
Sample227
mRNA expression in microglia


title: B11-p2-K1_241_human_TREM2_R47H_het

description:
Sample226
mRNA expression in microglia


title: B11-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample225
mRNA expression in microglia


title: B11-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample224
mRNA expression in microglia


title: P2counts

city: Birmingham

first: Paige

last: Porrett

state: AL

address: 701 19th Street South, Lyons Harrison Research Building Rm 728

department: Surgery

institute: University of Alabama at Birmingham

description:
Raw_Gene_Counts_Matrix_PorrettPregExh.txt
LogCPM_AllSamples_PorrettPregExh.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence.
Transcripts were aligned to the mouse reference genome (Mus musculus UCSC mm10) using the STAR aligner (STAR_2.5.0b).
Cufflinks was used to assemble transcripts and quantify transcript abundance.
Differential gene expression analysis of assembled transcriptomes for each of the nine samples (3 samples/group) was subsequently performed using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: LogCPM_AllSamples_PorrettPregExh.txt
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: OVA mated parous mice

extract_protocol:
OT-1 T cells were FACS sorted and RNA was extracted using RNeasy Plus Micro kit (Qiagen, USA). cDNA was synthesized using SMART-Seq V4 Ultra Low Input RNA kit for Sequencing (Takara Bio USA, Inc., USA).The products were sequenced on an Illumina NextSeq 500 platform (Illumina, Inc., San Diego, CA, USA)  using a NextSeq 500/550 v2 kit, following the manufacturer’s instructions.
cDNA library was constructed using Nextera® XT DNA Library Prep Kit (Illumina, USA) and quantified by qPCR using a KAPA Library Quantification Kit (Kapa Biosystems, USA).

treatment_protocol: All mice received adoptive transfer of 3x10^6 congenic OT-1 T cells. Naïve mice had no OVA exposure or any treatment. gOVA mice received an Act-mOVA skin graft. pOVA mice (parous mice) were mated with an Act-mOVA male. 50-60 days after OT-1 cell transfer and antigen exposure through grafting or pregnancy, all mice were sacrificed and OT-1 cells were FACS sorted from the spleen.

value: OT-1 T cells from spleen

tag: age

value: 8-16 weeks

value: wild type

tag: cell line

value: OVA mated


title: M3counts

source_name: OVA skin grafted mice

value: OVA skin graft


title: P3counts


title: P1counts


title: B11-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample222
mRNA expression in microglia

tag: trem2 species


title: M1counts


title: B11-p1-NTG_232_mouse_Trem2_WT

description:
Sample220
mRNA expression in microglia

tag: p301s status


title: B11-p1-NTG_233_mouse_Trem2_WT

description:
Sample221
mRNA expression in microglia

tag: brain region


title: B11-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample223
mRNA expression in microglia

tag: Sex


title: B11-p1-K1_243_human_TREM2_R47H_het

description:
Sample219
mRNA expression in microglia

tag: gate


title: B11-p1-K1_241_human_TREM2_R47H_het

description:
Sample218
mRNA expression in microglia

tag: cell type


title: Dppa2-4_ctrl-x-WT_mating2_WT-n

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were trimmed using Trim Galore (v0.6.5, Cutadapt v2.3) and mapped to the mouse GRCm38 genome assembly using HISAT2 (v2.1.0, --no-softclip) and filtered to have MAPQ scores of 20 and above.
Genome_build: Grcm38
Supplementary_files_format_and_content: RNA-seq_report_all_genes.txt (A tab-delimted SeqMonk report with log2 RPM values for each gene (Ensembl IDs))

source_name: 2 cell stage embryo

extract_protocol:
[Sample collection protocol]  Embryos from the Dppa2/4m- were generated from natural matings between males and females of relevant genotypes. The zona pellucida was removed using Tyrode’s solution (Sigma, T1788)
Individual embryos were placed in in 2.5µl methyltransferase reaction mixture, according to the published protocol (Clark et al., 2018). mRNA was captured using Smart-seq2 oligo-dT pre-annealed to magnetic beads (MyOne C1, Invitrogen).
The lysate containing the gDNA was transferred to a separate PCR plate, and the beads were washed 3 times in 15 ml FSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.5 U/ml of RNAsin (Promega). The beads were then resuspended in 10 ml of reverse transcriptase mastermix (100 U SuperScript II (Invitrogen), 10 U RNAsin (Promega), 1 X Superscript II First-Strand Buffer, 2.5 mM DTT (Invitrogen), 1M Betaine (Sigma), 9mM MgCl2 (Invitrogen), 1 mM Template-Switching Oligo (Exiqon), 1 mM dNTP mix (Roche)) and incubated on a thermocycler for 60 min at 42oC, followed by 30 min at 50oC and 10 min at 60oC. PCR was then performed by adding 11 ml of 2 X KAPA HiFi HotStart ReadyMix and 1 ml of 2 mM ISPCR primer, and cycling as follows: 98oC for 3 min, 15 cycles of 98oC for 15 sec, 67oC for 20 sec, 72oC for 6 min, and finally 72oC for 5 min.  cDNA was purified using a 1:1 volumetric ratio of Ampure Beads (Beckman Coulter) and eluted in 20 ml of water. Libraries were prepared from 100 to 400 pg of cDNA using Nextera XT Kit (Illumina), per manufacturer’s instructions but with one-fifth volumes for each sample.

tag: mating

value: 2 cell stage embryo


title: C2counts

source_name: Naïve control mice

tag: strain

tag: treatment

value: No Ova Exposure


title: B10-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample217
mRNA expression in microglia


title: B10-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample216
mRNA expression in microglia


title: B10-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample215
mRNA expression in microglia

value: human


title: C3counts

tag: tissue


title: Dppa2-4_ctrl-x-WT_mating2_WT-m


title: B10-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample214
mRNA expression in microglia


title: B10-p2-K1_243_human_TREM2_R47H_het

description:
Sample212
mRNA expression in microglia

value: no


title: Dppa2-4_ctrl-x-WT_mating1_WT-i


title: Dppa2-4_ctrl-x-WT_mating1_WT-j


title: Dppa2-4_ctrl-x-WT_mating2_WT-k


title: Dppa2-4_ctrl-x-WT_mating2_WT-l


title: B10-p2-NTG_233_mouse_Trem2_WT

description:
Sample213
mRNA expression in microglia

value: hippocampus


title: B10-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample210
mRNA expression in microglia

value: female


title: M2counts


title: B10-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample209
mRNA expression in microglia

value: microglia


title: Dppa2-4_ctrl-x-WT_mating1_WT-h


title: Dppa2-4_ctrl-x-WT_mating1_WT-e


title: B10-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample208
mRNA expression in microglia


title: Dppa2-4_ctrl-x-WT_mating1_WT-g


title: Dppa2-4_ctrl-x-WT_mating1_WT-f


title: C1counts


title: B10-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample207
mRNA expression in microglia


title: B10-p1-NTG_232_mouse_Trem2_WT

description:
Sample205
mRNA expression in microglia

value: mouse


title: Dppa2-4_ctrl-x-WT_mating1_WT-a


title: B10-p1-K1_241_human_TREM2_R47H_het

description:
Sample203
mRNA expression in microglia


title: Dppa2-4_ctrl-x-WT_mating1_WT-c


title: B10-p1-K1_243_human_TREM2_R47H_het

description:
Sample204
mRNA expression in microglia


title: Dppa2-4_ctrl-x-WT_mating1_WT-b


title: B1-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample202
mRNA expression in microglia


title: Dppa2-4_cKO-x-WT_mating2_HET1n


title: Dppa2-4_cKO-x-WT_mating2_HET1o


title: Dppa2-4_cKO-x-WT_mating2_HET1m


title: B1-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample201
mRNA expression in microglia

value: yes


title: B10-p2-K1_241_human_TREM2_R47H_het

description:
Sample211
mRNA expression in microglia


title: Dppa2-4_cKO-x-WT_mating2_HET1j


title: Dppa2-4_cKO-x-WT_mating2_HET1k


title: B1-p2-NTG_233_mouse_Trem2_WT

description:
Sample198
mRNA expression in microglia


title: B1-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample200
mRNA expression in microglia


title: B1-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample199
mRNA expression in microglia


title: Dppa2-4_cKO-x-WT_mating2_HET1l


title: B1-p2-NTG_232_mouse_Trem2_WT

description:
Sample197
mRNA expression in microglia


title: B10-p1-NTG_233_mouse_Trem2_WT

description:
Sample206
mRNA expression in microglia


title: zebrafish_monosome_codontag_rep1

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

country: Japan

institute: Riken

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina Casava 1.8 software.
3' adapter trimming with Fastp-toolkit.
Library sorting based on sample barcode sequence and random barcode trimming with custom script.
rRNA and other non-coding RNA alignment with bowtie2 v2.4.1.
Alignment with TopHat v2.1.1.
Read quantitation using custom scripts.
Genome_build: GRCz11
Supplementary_files_format_and_content: *.txt: Tab-delimited text files contain five columns: 1. transcript name; 2. from 5end of the transcript (nt) used for read counting; 3. from start codon of the transcript (nt) used for read counting; 4. codon; 5. read count.

organism: Danio rerio

source_name: whole embryo

growth_protocol: Fertilized eggs were obtained by natural breedings.

extract_protocol:
Fifty to sixty zebrafish embryos injected with PACE reporter mRNAs were snap frozen at the sphere stage and lysed with lysis buffer containing cycloheximide.
RNA extraction, preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, PCR amplification for ribosome profiling.

treatment_protocol: PACE reporter mRNA library was injected at 1-cell stage.

value: AB

value: whole embryo

value: PACE library injected


title: rad24-3

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: h+ rad24∆::NatMX

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York). Stranded polyA+ RNA Seq

value: rad24 delta

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

value: vegetative growth


title: zebrafish_monosome_codontag_rep2


title: B1-p2-K1_243_human_TREM2_R47H_het

description:
Sample196
mRNA expression in microglia


title: Dppa2-4_ctrl-x-WT_mating1_WT-d


title: B1-p2-K1_241_human_TREM2_R47H_het

description:
Sample195
mRNA expression in microglia


title: Dppa2-4_cKO-x-WT_mating1_HET1g


title: B1-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample194
mRNA expression in microglia


title: WT-2

source_name: h+

tag: genotype

value: wt


title: Dppa2-4_cKO-x-WT_mating1_HET1f


title: Dppa2-4_cKO-x-WT_mating1_HET1e


title: WT-3


title: Dppa2-4_cKO-x-WT_mating2_HET1i


title: Dppa2-4_cKO-x-WT_mating1_HET1d


title: B1-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample193
mRNA expression in microglia


title: Posterior brain WT biol rep 1

city: Vienna

first: Marcus

last: Dekens

state: Vienna

address: Dr.-Bohr-Gasse 9

country: Austria

institute: Max Perutz Laboratory

description:
Each replicate consists of parts of 3 fish
whole mid-hindbrain and whole hypothalamus and pretectum, and part of the epithalamus (i.e. habenula), thalamus and posterior tuberculum, but not the pituitary

data_processing:
Mapped to the reference genome (GRCz10.86) with NextGenMap software
Read count per transcript executed with the featureCounts tool
Statistical analysis for differential expression was implemented with edgeR software (version3.9)
Genome_build: reference genome assembly GRCz10.86

source_name: posterior brain

extract_protocol:
Eyes were removed by cutting the optic nerves with surgical scissors and the brain was carefully removed after lifting the skullcap with surgical forceps and cutting the spinal cord. The brain was separated in an anterior and posterior part with a surgical blade. For each biological replicate the same tissue parts of three individuals were pooled and frozen in liquid nitrogen. A total of three biological replicates were processed. Total RNA was isolated by adding RNAzol (Sigma-Aldrich) and a steal bead to the frozen sample, followed by disruption in a bead mill for 3 min at 30 Hz (TissueLyser II, Qiagen) and extraction of total RNA (Direct-zol RNA kit, Zymo Research). mRNA was isolated from total RNA by selective binding to oligo-dT coupled beads (Dynabeads mRNA purification kit, Invitrogen) followed by washes and elution. To increase purity the eluate was bound, washed, and eluted for a second round, and thereafter quality checked (Bioanalyzer RNA 6000 Pico assay, Agilent). Next, mRNA was fragmented for 3 min at 75 °C (fragmentation reagents, Invitrogen) and the fragment size distribution was quality checked (Bioanalyzer RNA 6000 Pico assay, Agilent).
mRNA was transcribed with the SuperScript VILO cDNA synthesis Kit (Invitrogen) and libraries were constructed with the ultra II kit (NEB), followed by adding barcodes with PCR (multiplexed). The samples were single read 100bp RNA sequenced with the Illumina HiSeq 2500 v4 chemistry.

treatment_protocol: Described in: Dekens, M.P.S., N.S. Foulkes, and K. Tessmar-Raible, Instrument design and protocol for the study of light controlled processes in aquatic organisms, and its application to examine the effect of infrared light on zebrafish. PLoS ONE, 2017. 12(2): p. e0172038.

value: Tubingen

value: ~ 1.5 year

value: wild type


title: Posterior brain WT biol rep 3


title: Posterior brain WT biol rep 2


title: Posterior brain opn4 dko biol rep 1


title: B1-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample191
mRNA expression in microglia

value: human


title: Dppa2-4_cKO-x-WT_mating1_HET1c

value: 2 cell stage embryo


title: B1-p1-NTG_233_mouse_Trem2_WT

description:
Sample190
mRNA expression in microglia

value: no

value: hippocampus


title: Anterior brain opn4 dko biol rep 3

description:
Each replicate consists of parts of 3 fish
whole telencephalon and pineal and part of the epithalamus, thalamus and posterior tuberculum, but not the olfactory bulbs

source_name: anterior brain


title: B1-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample192
mRNA expression in microglia

value: female

value: microglia


title: Dppa2-4_cKO-x-WT_mating2_HET1h


title: Dppa2-4_cKO-x-WT_mating1_HET1a


title: rad24-1


title: B1-p1-NTG_232_mouse_Trem2_WT

description:
Sample189
mRNA expression in microglia

value: mouse


title: rad24-2


title: Anterior brain opn4 dko biol rep 1


title: Anterior brain WT biol rep 3


title: Dppa2-4_cKO-x-WT_mating1_HET1b


title: Dppa2-4_cKO-x-HET_mating2_HOM-j


title: Posterior brain opn4 dko biol rep 3


title: WT-1


title: B1-p1-K1_243_human_TREM2_R47H_het

description:
Sample188
mRNA expression in microglia


title: Anterior brain WT biol rep 2


title: Anterior brain WT biol rep 1


title: B1-p1-K1_241_human_TREM2_R47H_het

description:
Sample187
mRNA expression in microglia


title: Posterior brain opn4 dko biol rep 2


title: Eye opn4 dko biol rep 2

description:
Each replicate consists of parts of 3 fish
whole eye

source_name: eye


title: Dppa2-4_cKO-x-HET_mating2_HOM-i


title: Dppa2-4_cKO-x-HET_mating2_HOM-h


title: Anterior brain opn4 dko biol rep 2


title: Eye opn4 dko biol rep 1


title: A9-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample185
mRNA expression in microglia

source_name: FACS isolated adult microglia

value: yes


title: Eye WT biol rep 1


title: Eye WT biol rep 2


title: Dppa2-4_cKO-x-HET_mating2_HOM-g


title: A9-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample184
mRNA expression in microglia


title: Dppa2-4_cKO-x-HET_mating2_HOM-f


title: Eye WT biol rep 3


title: Dppa2-4_cKO-x-HET_mating2_HOM-e


title: Dppa2-4_cKO-x-HET_mating2_HOM-d


title: Eye opn4 dko biol rep 3


title: Center region of mouse skin

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

description: Sample collected from the center of wound after wound closure

data_processing:
Cell demultiplexing, alignment and filtering were performed within 10X Genomics CellRanger package version 3.0.1, mapping to mm10
CellRanger v3.0.1
Seurat
Genome_build: mm10
Supplementary_files_format_and_content: 10x multiplex barcode, feature and matrix .gz files

source_name: full thickness of mouse back skin

growth_protocol: C57BL/6J mice were mainteined in JHU animal facility (JHU IACUC, MO17M298) and telogen mice (21-day old) were used for the experiment

extract_protocol:
Small pieces of tissues were incubated with 1 mL of 0.4 mg/mL of Liberase TL (Roche, 05401020001) in DMEM with 100 units/ml of penicillin, 100 mg/ml of streptomycin and washed with PBS then incubated with 0.05% TrypLE™ Select. Cell suspension was washed with 10 % FBS in DMEM with 100 units/ml of penicillin, 100 mg/ml of streptomycin then incubated with 100 Unit/ml of DNAse I (New England BioLabs, M0303). Cell suspension was washed with 0.04 (w/v) % BSA in PBS and cell suspension was prepared by filtering through 40 mm strainer. To achieve live single cell suspension, Propidium Iodide (BioLegend, 421301) negative and Vybrant DyeCycle Violet (Invitrogen, V35003) positive single cells were sorted.
Library construction was 10x Chromium Single Cell v3. Sequencing was performed on the NovaSeq 6000, v1.5 reagents.  Basecalling and sample demultiplexing is performed within Illumina’s BaseSpace software.

treatment_protocol: Full-thickness section of skin (1 cm2) on the backs of mice was excised using sterile scissors. At post wounding day 11-12, tissue from the center of wound was collected (multiple pooled mice, n=10)

value: back skin

value: wound (1 cm^2)


title: Dppa2-4_cKO-x-HET_mating2_HET2e


title: A9-p2-NTG_233_mouse_Trem2_WT

description:
Sample182
mRNA expression in microglia


title: Male_VTA_THC FTL_378

city: La Jolla

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

data_processing:
Raw sequencing reads were cleaned to remove adapter sequences and low-quality sequences using cutadapt v2.9 (Martin 2011) with the paired-end trimming mode and the minimum 18-base setting
The cleaned reads were aligned to mouse genome (mm10) using STAR v2.7.3a (Dobin et al. 2013) following ENCODE parameters and options
The aligned reads were quantified at the gene level using RSEM v1.3.1 (Li and Dewey 2011).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Brain -VTA

extract_protocol:
Brain punches (n = 120) were homogenized in Trizol Reagent (Invitrogen, Cat, num. 15596018) and Zirconium Beads RNase Free (Next Advance, Cat. num. ZrOB05-RNA 0.5mm) using the Bullet Blender Blue (Next Advance, Model. num. BBX24B) at speed 6 for 1 min. RNA was then purified using the Direct-Zol kit (Zymo, Cat. num. R2052). RNA quality was assessed using the Agilent 2200 TapeStation system and samples with RIN above 7.5 were used for library preparations.
An average of 200ng of RNA was used for each sample to prepare the cDNA libraries. The NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs, Cat. Num. E7760S) was used following manufacturer’s instructions. A total of 119 libraries were sequenced on the Illumina NovaSeq 6000 system (2 x 100 bp reads)
polyA-enriched RNA-Seq

treatment_protocol: Vehicle or THC (10mg/kg) was administered daily to mice by intraperitoneal injections (i.p.) from postnatal day (PND) 28 to PND 48, which cover the whole adolescent period in mice (Laviola et al. 2003). To examine the long-term effects of chronic adolescent exposure to THC, mice were tested two weeks after a drug abstinence period, starting at PND 63.

value: Ventral tegmental area

value: THC

value: Male

value: 11 weeks


title: Male_VTA_THC FTL_379


title: Male_VTA_THC FTL_375


title: Male_VTA_THC FTL_374


title: Male_VTA_THC FTL_376


title: Male_VTA_THC FTL_377


title: A9-p2-NTG_232_mouse_Trem2_WT

description:
Sample181
mRNA expression in microglia


title: A9-p2-K1_243_human_TREM2_R47H_het

description:
Sample180
mRNA expression in microglia


title: A9-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample186
mRNA expression in microglia


title: Male_VTA_Veh FTL_372

value: Vehicle


title: Dppa2-4_cKO-x-HET_mating1_HOMc


title: A9-p2-K1_241_human_TREM2_R47H_het

description:
Sample179
mRNA expression in microglia


title: A9-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample178
mRNA expression in microglia


title: Dppa2-4_cKO-x-HET_mating1_HOMb


title: Female_VTA_THC FTL_367

value: Female


title: Male_VTA_Veh FTL_370


title: Dppa2-4_cKO-x-HET_mating1_HOMa


title: Female_VTA_THC FTL_368


title: Female_VTA_THC FTL_366


title: A9-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample177
mRNA expression in microglia


title: Dppa2-4_cKO-x-HET_mating1_HET2d


title: Dppa2-4_cKO-x-HET_mating1_HET2c


title: Male_VTA_Veh FTL_373


title: Female_VTA_THC FTL_364


title: A9-p1-NTG_233_mouse_Trem2_WT

description:
Sample175
mRNA expression in microglia


title: Male_VTA_Veh FTL_371


title: A9-p1-NTG_232_mouse_Trem2_WT

description:
Sample174
mRNA expression in microglia


title: Dppa2-4_cKO-x-HET_mating1_HET2a


title: Dppa2-4_cKO-x-HET_mating1_HET2b


title: scRNA-seq_sample5

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: University Medical Center Utrecht

description: single cell mRNA sequencing of mouse thyroid follicular cell organoids in early passage

data_processing:
Fastq files were trimmed with TrimGalore-0.4.3 and mapped with STAR-2.5.3a to the mouse reference genome (GRCm38). Introns and exons were extracted from the corresponding annotation files. Cells with raw transcript counts higher than 1.5 times the interquartile range above the upper quartile of the rest of the population were removed as potential doublets. Subsequently, clustering and single-cell analysis were performed with Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts normalized between samples.

growth_protocol: The complete or part of the thyroid was chopped into small pieces of approximately 1 mm using a scalpel. Epithelial tissue pieces were enzymatically digested in 5 mL collagenase (Sigma-Aldrich, C9407, 1 mg/mL) with 10 μM ROCK inhibitor Y-27632 (Abmole, M1817) and 100µg/mL Primocin (Invivogen, ant-pm-1) in AdDMEM/F12 (GIBCO) for about 25-30 minutes shaking (120 RPM) at 37°C. The homogeneous cell suspension was pelleted and washed with AdDMEM/F12. The tissue was resuspended in 1mL Red blood cell lysis buffer (Roche, 11814389001) and incubated at RT for 5 min. Fragments were mechanically dissociated using narrowed glass pipette. Cells from a single murine thyroid were plated in approximately 100 uL Cultrex Pathclear Reduced Growth Factor Basement Membrane Extract (BME) (3533-001, Amsbio). After BME solidification, complete expansion medium was added.  Mouse expansion medium consisted in AdDMEM/F12 (GIBCO) supplemented with B27 supplement (Gibco, 17504044), Glutamax, HEPES, 100 U/mL Penicillin-Streptomycin (all Thermo Fisher scientific), 1.25 mM N-acetylcysteine (Sigma-Aldrich, A9165), 10 mM nicotinamide (Sigma-Aldrich, N0636) and the following growth factors: 1% R-spondin 3 conditioned medium (U-Protein Express), 0.5 μM A83-01 (Tocris, 2939), 1 μM FSK (Tocris, 1099), 500ng/mL EGF (Preprotech, AF-100-15-1mg) and 100 ng/mL FGF10 (Peprotech, 100-26)

extract_protocol:
For single-cell sequencing of the tissue, mouse thyroid was dissociated with collagenase I (Sigma-Aldrich) as described above and subsequently resuspended in TrypLE Express (GIBCO) pre-heated to 37°C and dissociated under repeated pipetting. For single-cell sequencing of TFCOs, organoid droplets were incubated in Cell Recovery solution (354253, Corning) for 30 minutes in order to dissolve the BME. Then, organoids were pelleted and resuspended in TrypLE Express (GIBCO) pre-heated to 37°C and dissociated under repeated pipetting. When the gland and the organoids were fully dissociated into single cells, samples were pelleted, washed, resuspended in FACS buffer (advanced DMEM/F12, 10 μM Y-27632 and DAPI) and strained (35 μm). DAPI-negative cells were immediately sorted into 384-well plates containing ERCC spike-ins (Agilent), RT primers and dNTPs (Promega) using a FACSFusion (BD Biosciences). Plates were prepared using Mosquito HTS (TTPlabtech).
Single-cell RNA sequencing libraries were prepared following the SORT-seq protocol (Muraro et al., 2016) which is based on the CEL-seq2 method (Grün et al., 2015). In short, cells were first lysed for 5 minutes at 65 °C, and RT and second-strand mixes were dispensed by the Nanodrop II liquid handling platform (GC Biotech). Single-cell double-stranded cDNAs were pooled together and in vitro transcribed for linear amplification. Illumina sequencing libraries were prepared using the TruSeq small RNA primers (Illumina) and these DNA libraries were sequenced paired-end, respectively, on the Illumina NextSeq

treatment_protocol: No treatment was used in this study

value: Wild type

value: Thyroid

tag: passage stage

value: Early passage


title: Male_VTA_Veh FTL_369


title: Female_VTA_Veh FTL_360


title: JFP169-T50-Rep-4

city: Richmond

first: Todd

last: Kitten

state: VA

address: 521 N. 11th Street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth University

data_processing:
Individual libraries were pooled equimolarly and the final pool was sequenced on an Illumina MiSeq with 2 x 75-bp paired-end reads. Demultiplexing was performed on the Illumina MiSeq’s on-board computer. The Virginia Commonwealth University Genomics Core Facility completed all RNA-seq library preparation and sequencing.
Reads were paired in Geneious Prime v.2021.1.1 and trimmed using the BBDuk Trimmer plugin with recommended settings.
Paired reads were then aligned to the respective reference genome and expression levels calculated for each using Geneious Prime with default settings.
Genome_build: NC_009009.1
Supplementary_files_format_and_content: Tab-delimited txt file containing Gene Name, Minimum coordinate, Maximum coordinate, Length, Direction, FPKM, Raw read count, Raw transcript count, RPKM, TPM, and Locus_tag

organism: Streptococcus sanguinis

source_name: bacterial cells

growth_protocol: A BIOSTAT® B bioreactor (Sartorius Stedim) with a 1.5-L capacity UniVessel® glass vessel was used for growth of 800-mL cultures at 37°C. Cultures were stirred at 250 rpm and pH was maintained by the automated addition of 2 N KOH (Fisher Chemical). A 40 mL overnight pre-culture of S. sanguinis strain JFP169 was grown in BHI media and centrifuged for 10 minutes at 3,740 x g in an Allegra X-142 centrifuge at 4°C (Beckman-Coulter). The supernatant was discarded and the cells were resuspended in BHI prior to inoculation. The air flow was maintained at 0.03 Lpm for the entire experiment. At the peak OD, input flow of fresh BHI was set to 17% (~700 mL h-1) and output flow of waste was set to 34%. Cells were allowed to acclimate to the new conditions for 1 h. The T-20 sample was aseptically removed for total RNA isolation.

extract_protocol:
For each RNA sample, 2 mL of fermentor culture was added to 4 mL RNAprotect Bacteria Reagent (Qiagen) and immediately vortexed for 10 sec. The sample was then incubated at room temperature for 5-90 min. The samples were then centrifuged for 10 min at 3,740 x g at 4°C. The supernatant was discarded and the samples stored at -80°C. RNA isolation and on-column DNase treatment were completed using the RNeasy Mini Kit and RNase-Free DNase Kit, respectively (Qiagen). RNA was eluted in 50 µL RNase-Free water (Qiagen). A second DNase treatment was then performed on the samples (Invitrogen).
Total RNA quantity and integrity were determined using an Agilent Bioanalyzer RNA Pico assay.  All samples passed quality control assessment with RNA Integrity Numbers (RIN) above 8.  Two sequential rounds of ribosomal reduction were then performed on all samples using RiboMinus™ Transcriptome Isolation Kit (ThermoFisher).  The resulting depleted RNA was assessed using an Agilent Bioanalyzer RNA Pico assay to confirm efficient rRNA removal.  Stranded RNA-seq library construction was then performed on the rRNA-depleted RNA using the Kapa RNA HyperPlus kit for Illumina (Roche) following manufacturer’s specifications for library construction and multiplexing. Final Illumina libraries were assessed for quality using an Agilent Bioanalyzer DNA High Sensitivity Assay and qPCR quantification was performed using Kapa Library Quantification kit for Illumina (Roche).

treatment_protocol: Twenty minutes later, HCl was injected into the vessel (T0) in sufficient quantity to bring the pH to 6.2. Samples were taken for each post-HCl time point (T10, T25, T50) 10, 25 and 50 min after HCl addition.

value: ssaACB

tag: ph

tag: timepoint


title: Female_VTA_Veh FTL_362

tag: age


title: A9-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample176
mRNA expression in microglia

tag: trem2 species

value: human

value: hippocampus


title: Female_VTA_Veh FTL_359


title: Female_VTA_THC FTL_363


title: JFP169-T25-Rep-4


title: A9-p1-K1_241_human_TREM2_R47H_het

description:
Sample172
mRNA expression in microglia

tag: p301s status

value: no

value: female

value: microglia


title: JFP169-T10-Rep-4


title: A8-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample171
mRNA expression in microglia

value: mouse

tag: brain region


title: Female_VTA_Veh FTL_357

tag: Sex


title: scRNA-seq_sample3

description: single cell mRNA sequencing of mouse thyroid follicular cell organoids in late passage

value: Late passage


title: scRNA-seq_sample4


title: scRNA-seq_sample2


title: Female_VTA_Veh FTL_358

value: Ventral tegmental area


title: Female_VTA_THC FTL_365

value: THC


title: A8-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample170
mRNA expression in microglia

value: yes

tag: gate


title: A9-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample183
mRNA expression in microglia

tag: cell type


title: JFP169-T-20-Rep-4


title: Male_Amy_THC FTL_356

source_name: Brain -Amy

value: Amygdala

value: Male

value: 11 weeks


title: Female_VTA_Veh FTL_361

value: Vehicle

value: Female


title: JFP169-T50-Rep-3


title: scRNA-seq_sample1

value: Wild type

value: Thyroid


title: A8-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample169
mRNA expression in microglia

value: human


title: Male_Amy_THC FTL_355


title: scRNA-seq_mThyroidTissue2

description: single cell mRNA sequencing of mouse thyroid tissue

value: Tissue


title: A8-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample168
mRNA expression in microglia

value: hippocampus


title: Male_Amy_THC FTL_354


title: scRNA-seq_mThyroidTissue1


title: JFP169-T25-Rep-3

value: ssaACB


title: JFP169-T-20-Rep-3


title: Male_Amy_THC FTL_353


title: JFP169-T10-Rep-3


title: Male_Amy_THC FTL_352


title: A8-p2-NTG_233_mouse_Trem2_WT

description:
Sample167
mRNA expression in microglia

value: no

value: female

value: microglia


title: Lung_tissue_tissue1

description:
Bulk RNA sequencing of mouse lung tissue
Lung_tissue

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg38. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: mm10
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts normalized between samples.

source_name: Lung tissue

extract_protocol:
Total RNA was extracted using the standard RNeasy Kit (Qiagen) protocol and used for library preparation and sequencing.
mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq (Hashimshony et al., 2016; Simmini et al., 2014). In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers.

value: Lung


title: JFP169-T50-Rep-2


title: Lung_tissue_tissue2


title: A8-p2-K1_243_human_TREM2_R47H_het

description:
Sample165
mRNA expression in microglia


title: Thyroid_tissue_tissue2

description:
Bulk RNA sequencing of mouse thyroid tissue
Thyroid_tissue

source_name: Thyroid tissue


title: A8-p2-K1_241_human_TREM2_R47H_het

description:
Sample164
mRNA expression in microglia


title: JFP169-T10-Rep-2


title: Male_Amy_Veh FTL_350


title: JFP169-T25-Rep-2


title: Male_Amy_THC FTL_351

value: THC


title: A8-p2-NTG_232_mouse_Trem2_WT

description:
Sample166
mRNA expression in microglia

value: mouse


title: A8-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample163
mRNA expression in microglia


title: JFP169-T-20-Rep-2


title: mThy16_late_organoid

description:
Bulk RNA sequencing of mouse thyroid follicular cell organoids in late passage
TFC_organoid_late

source_name: TFC organoids

value: Late passage


title: Male_Amy_Veh FTL_349

value: Amygdala

value: Male


title: Thyroid_tissue_tissue1


title: JFP169-T50-Rep-1


title: Male_Amy_Veh FTL_348

value: Vehicle

value: 11 weeks


title: A8-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample162
mRNA expression in microglia

value: yes


title: A8-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample161
mRNA expression in microglia


title: mThy14_late_organoid

value: Wild type

value: Thyroid


title: Male_Amy_Veh FTL_347


title: mThy16_early_organoid

description:
Bulk RNA sequencing of mouse thyroid follicular cell organoids in early passage
TFC_organoid_early

value: Early passage


title: mThy14_early_organoid


title: A8-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample160
mRNA expression in microglia

value: human

value: hippocampus


title: JFP169-T10-Rep-1

value: ssaACB


title: Male_Amy_Veh FTL_345


title: Male_Amy_Veh FTL_346


title: A8-p1-NTG_233_mouse_Trem2_WT

description:
Sample159
mRNA expression in microglia

value: no

value: female


title: A8-p1-NTG_232_mouse_Trem2_WT

description:
Sample158
mRNA expression in microglia

value: microglia


title: A8-p1-K1_241_human_TREM2_R47H_het

description:
Sample157
mRNA expression in microglia


title: Female_Amy_THC FTL_343

value: THC

value: Female


title: Female_Amy_THC FTL_344


title: Female_Amy_THC FTL_342


title: A7-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample156
mRNA expression in microglia

value: mouse


title: SK36-T50-Rep-4

value: Wild Type


title: A7-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample155
mRNA expression in microglia


title: SK36-T10-Rep-4


title: Female_Amy_THC FTL_341

value: Amygdala


title: A7-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample154
mRNA expression in microglia


title: JFP169-T-20-Rep-1

value: ssaACB deletion


title: Female_Amy_THC FTL_340

value: 11 weeks


title: JFP169-T25-Rep-1


title: SK36-T50-Rep-3


title: Female_Amy_THC FTL_339


title: Female_Amy_Veh FTL_338

value: Vehicle


title: A7-p2-NTG_233_mouse_Trem2_WT

description:
Sample152
mRNA expression in microglia


title: SK36-T25-Rep-3


title: SK36-T10-Rep-3


title: Female_Amy_Veh FTL_337


title: Female_Amy_Veh FTL_336


title: A7-p2-NTG_232_mouse_Trem2_WT

description:
Sample151
mRNA expression in microglia


title: SK36-T25-Rep-4


title: SK36-T-20-Rep-3


title: A7-p2-K1_243_human_TREM2_R47H_het

description:
Sample150
mRNA expression in microglia


title: Female_Amy_Veh FTL_335


title: A7-p2-K1_241_human_TREM2_R47H_het

description:
Sample149
mRNA expression in microglia


title: SK36-T25-Rep-2


title: A7-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample148
mRNA expression in microglia


title: SK36-T-20-Rep-4


title: Female_Amy_Veh FTL_334


title: Female_Amy_Veh FTL_333


title: A7-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample147
mRNA expression in microglia

value: yes


title: A7-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample153
mRNA expression in microglia


title: Male_NAc_THC FTL_332

source_name: Brain -Nac

value: Nucleus accumbens

value: Male


title: SK36-T-20-Rep-2


title: SK36-T50-Rep-1


title: A7-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample146
mRNA expression in microglia

value: human


title: A7-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample145
mRNA expression in microglia

value: hippocampus


title: SK36-T25-Rep-1


title: DPG24h-1

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description:
10x genomics, v2
ActSeq_24h_umi_counts.csv.gz
ActSeq_24h_metadata.csv.gz

data_processing:
Demultiplexed fastq files were generated by mkfastq function in Cell Ranger software. Demultiplexed fastq files were aligned to the mouse reference genome mm10 (Ensembl 93) and converted into bam files using the 10x Genomics Cell Ranger software (version 2.2.0 (v2 and v3 samples) or 4.0.0 (v3.1 samples))
multimapped reads were filtered out by removing any read in the possorted_genome_bam.bam file with a MM:i:1 tag. UMIs in which separate reads were uniquely mapped to different genes were removed. The gene expression matrix was then recomputed by counting the number of distinct UMIs for each cell barcode for each gene.
mature olfactory sensory neurons (OSNs) were identified via iterative subclustering in Scanpy, and any mature OSN expressing a single OR (detected in at least 2-3 UMIs) were kept
Genome_build: Ensembl Rel 93 (GRCm38.p6)
Supplementary_files_format_and_content: <EXPT>_umi_counts.csv.gz: UMI counts for each gene for each mOSN used (cells x genes)  <EXPT>_metadata.csv.gz: Metadata for each cell, including which OR was expressed  Dataset_raw_file_names.csv.gz: Description of each replicate, and name of raw bam file, as well as the corresponding counts and metadata files.  Table_S1_datasets.csv.gz: Summary of single cell RNA-seq datasets for mature olfactory sensory neurons used in this study.  Table_S2_nmf_loadings.csv.gz: Loadings of 1,350 highly variable genes for 16 gene expression programs identified by consensus non-negative matrix factorization of the home cage dataset.  Table_S3_ES_neuronal_genes.csv.gz: 117 environmental state genes that have putative neuronal functions, including 73 genes with putative functions that affect sensory responses.  Table_S4_delta_ES_neuronal_gene_expression.csv.gz: Changes in z-scored expression of 117 environmental state genes for each OSN subtype across conditions.  Table_S5_activation_genes.csv.gz: 472 acute odor response-dependent genes used to calculate activation score. 8 values that characterize 472 genes that were used to calculate activation score are shown. Columns are as follows: “activation_score_loading”: gene loading for calculating activation score. “ess_correlation”: Spearman's rho between normalized expression and environmental state score in the home cage dataset on OR-by-OR basis. “p_adj_ACE2h”: FDR corrected p-values for the differential expression (via Wilcoxon signed-rank test) between control and acetophenone 2h samples for acetophenone responsive ORs on OR-by-OR basis. “ctl_expr_ACE2h”: Normalized mean expression for OSNs expressing-acetophenone responsive ORs in the control data. “expression_ACE2h”: Normalized mean expression for OSNs expressing acetophenone responsive ORs in the acetophenone 2h data. “p_adj_OCT2h”, “ctl_expr_OCT2h”, “expression_OCT2h”: same as the previous 3 columns for acetophenone responsive ORs, but for OSNs expressing octanal-responsive ORs.

source_name: whole olfactory mucosa

extract_protocol:
The main olfactory epithelium was dissected and cleaned up in the Earle’s Balanced Salt Solution (EBSS, pre-treated with carbogen for at least 5 minutes before each use, Worthington), then transferred to a round-bottomed glass dish containing 750 µL of papain solution (one vial of Papain, (Worthington) dissolved in 5 mL of EBSS and then equilibrated 10 minutes at 37 °C) and 100 µL of DNase solution (one vial of DNase-I (Worthington) dissolved in 500 µL of EBSS). Bone was removed from the epithelium under a dissecting microscope and the resultant tissue was placed in a 5 mL tube (Becton Dickinson) with an additional 1.75 mL of Papain solution and 200 µL of DNase-I solution and rocked gently for ~60 minutes at 37 °C. The tissue was then gently triturated with a 5 mL pipette 10-15 times, passed through a 40 µm cell strainer (Becton Dickinson), and washed with 1 mL of Hibernate-A medium containing 10 % Fetal Bovine Serum (FBS, GIBCO). Filtered cells were transferred to a new 5 mL tube and centrifuged 5 minutes at 300 x g. The supernatant was decanted, the cells were washed once with 4 mL Hibernate-A containing 10 % FBS and resuspended in 1 mL Hibernate-A containing 0.2 % FBS. Each of the solutions above contained transcriptional inhibitors (5 µg/mL of Actinomycin D, 10 µg/mL of Anisomycin and 10 µM of Triptolide, all obtained from Sigma) for all experiments, except where noted (Table S1). Dissociated cells were stained with propidium iodide (final concentration 1.65 µg/mL), and subject to FACS to remove dead cells and obvious doublets. For GFP-expressing mouse lines (OMP-IRES-GFP, P2(P2 locus), M72(S50 locus) and S50(M72 locus)), GFP positive and negative cells were sorted separately using a FITC filter. Cells were sorted into Hibernate-A containing 5 % FBS (also include 0.1x of transcriptional inhibitors), centrifuged for 5 minutes at 300 g, and resuspended with PBS.
Prepared single cell suspensions were used to prepare single cell RNA-seq library with the chromium single cell gene expression system (chromium single cell 3’ reagents and GEM v2, v3 or v3.1 dual index, 10x genomics), using the default protocols provided by 10x genomics. Each of the replicates other than GFP-positive ones was aimed to have 10,000 cells. The expected multiplet rate is ~8.0 %.

value: whole olfactory mucosa

value: 6-12 weeks


title: A7-p1-NTG_233_mouse_Trem2_WT

description:
Sample144
mRNA expression in microglia

value: no

value: female


title: DPG24h-2


title: Male_NAc_THC FTL_331

value: THC


title: SK36-T10-Rep-1


title: SK36-T50-Rep-2


title: Male_NAc_THC FTL_329


title: Male_NAc_THC FTL_330


title: SK36-T-20-Rep-1


title: A7-p1-NTG_232_mouse_Trem2_WT

description:
Sample143
mRNA expression in microglia

value: microglia


title: SK36-T10-Rep-2