title: nt22B

city: Worcester

first: Ye

last: Duan

state: MASSACHUSETTS

address: 373 Plantation Street, Biotech Two, Suite 306

department: Program of Molecular Medicine

institute: Umass Medical School

description:
U22A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
22B

data_processing:
Adaptor removal by Cutadapt/1.9
Size filtered at 22nt (let-7) or 18-25 nt (total sRNA) by Cutadapt/1.9
Reads were initially mapped with Bowtie2/2.3.4.3 to C. elegans rRNA and tRNA sequences to remove tRNA and rRNA fragments
For let-7 counts, reads were mapped with Bowtie2/2.3.4.3 to either wild type or mutant let-7a sequences indexed with -c using parameters --end-to-end -N 0 --no-1mm-upfront -L 22
For total sRNA counts, mapped to C. elegans genome WBCel235 by Star/2.7.6a with default parameters.
small RNA abundance is counted by subread/1.6.2/featureCounts
Genome_build: WBCel235
Supplementary_files_format_and_content: single_nt.let7.reads.csv (sRNA counts (let-7 mut. And let-7(+)))
Supplementary_files_format_and_content: single_nt.miR.reads.csv (sRNA counts (miRNA annotations))

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C.elegans were cultured on nematode growth medium (NGM) and fed with E. coli HB101 unless specified. To obtain populations of synchronized developing worms, gravid adults were collected and washed twice with water. Pellets of centrifuged worms were treated with 5 ml 1N NaOH and 1% (v/v) sodium hypochlorite for 5 min with shaking to obtain embryos, and the embryos were rinsed with M9 buffer three times. The embryos were hatched in 10 ml M9 buffer at 20°C for 16-18 hrs with mild shaking. Hatched L1 larvae were transferred to plates at 30-50 worms per plate and replicate plates were cultured  for defined periods; samples of the population were examined by microscopy to confirm the developmental stage at the time of harvest.

extract_protocol:
Harvested worms were washed with M9 medium, centrifuged, and the worm pellets were flash-frozen in liquid nitrogen. The worm pellets were thawed and lysed by adding 4X volumes of QIAzol (Qiagen, Cat: 79306) and shaking vigorously at room temperature for 15 min. The total RNA was extracted by the addition of 0.85X volume chloroform, centrifugation, and recovery of the aqueous phase, which was then re-extracted with 1 volume phenol:chloroform:isoamyl alcohol (25:24:1, pH = 5.5). Total RNA was then precipitated by add 1 volume of isopropanol and 0.5 µl GlycoBlue (Invitrogen, Cat: AM9516), followed by incubation at -80oC for at least 30 min, and recovery by centrifugation at 25,000 rcf for 10 min at 4 °C. The supernatants were then removed, and the RNA pellets were subsequently washed twice by 70% (v/v) ethanol, dried in air for 5 min, dissolved in water, and stored at -80 °C. Worm samples for RNA-seq were aliquoted from the ribosome profiling harvests before the lysis step and frozen separately. The total RNA was extracted as described above. To enrich for mRNA, rRNA was depleted as described in detail elsewhere (Duan et al., 2020b). rRNA-depleted mRNA samples were then purified by RNA Clean & Concentrator-5 Kit (ZYMO, Cat: R1015)
Libraries were constructed using NEBNext multiplex small RNA library prep set (NEB, Cat:E7300)
small RNA seq

treatment_protocol: Synchronized populations of developing worms were cultured at 20 °C for 45 hrs after feeding. Harvested worms were washed with water three times and incubated at room temperature for 10 min to allow digestion of intestinal bacteria. Worms were then pelleted by centrifuge at 4,500 rcf for 2 min at room temperature and residual water was removed until the total volumes were twice as the worm pellets. The samples were then flashed frozen by liquid nitrogen and stored at -80 °C.

tag: Stage

value: mid L4

tag: temperature

value: 20 °C


title: nt22C

status: Public on Dec 06 2021

type: SRA

country: USA

description:
U22A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
22C

library_source: transcriptomic

molecule: total RNA

tag: genotype


title: v2-homecage-inhibitor1

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description:
10x genomics, v2
OR_swap_umi_counts.csv.gz
OR_swap_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.

organism: Mus musculus

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 %.

tag: strain

tag: tissue

value: whole olfactory mucosa

tag: age

value: 6-12 weeks


title: A6-p2-PS19_246_P301S_mouse_Trem2_WT

city: San Francisco

first: Lay

last: Kodama

state: CA

address: 1650 Owens St.

department: Gladstone Institute of Neurological Disease

institute: University of California San Francisco

description:
Sample140
mRNA expression in microglia

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.

source_name: FACS isolated adult microglia

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

tag: trem2 species

value: mouse

tag: p301s status

value: no

tag: brain region

value: hippocampus

tag: Sex

value: female

tag: gate

tag: cell type

value: microglia


title: A7-p1-K1_241_human_TREM2_R47H_het

description:
Sample141
mRNA expression in microglia

value: human


title: v2-homecage-inhibitor2


title: nt22A

description:
U22A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
22A


title: Male_NAc_THC FTL_327

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 -Nac

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: Nucleus accumbens

tag: treatment

value: THC

value: Male

value: 11 weeks


title: Male_NAc_Veh FTL_326

value: Vehicle


title: Male_NAc_Veh FTL_325


title: A6-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample139
mRNA expression in microglia

value: yes


title: v2-homecage-control2

value: 5 weeks


title: ACE24h-2

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


title: nt21C

description:
U21A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
21C

value: mid L4


title: Male_NAc_Veh FTL_324


title: A9-p1-K1_243_human_TREM2_R47H_het

description:
Sample173
mRNA expression in microglia


title: v2-homecage-WTMOE2


title: nt21B

description:
U21A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
21B

value: 20 °C


title: A6-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample138
mRNA expression in microglia


title: Male_NAc_THC FTL_328


title: A6-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample137
mRNA expression in microglia


title: ACE24h-1

value: whole olfactory mucosa


title: nt21A

description:
U21A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
21A


title: A7-p1-K1_243_human_TREM2_R47H_het

description:
Sample142
mRNA expression in microglia


title: A6-p2-NTG_233_mouse_Trem2_WT

description:
Sample136
mRNA expression in microglia


title: nt20C

description:
G20C
single_nt.miR.reads.csv
single_nt.let7.reads.csv
20C


title: v2-homecage-WTMOE1

value: 6-12 weeks


title: v2-homecage-WT20w2

value: 20 weeks


title: Male_NAc_Veh FTL_322


title: v2-homecage-control1


title: Female_NAc_THC FTL_320

value: Female


title: A6-p2-NTG_232_mouse_Trem2_WT

description:
Sample135
mRNA expression in microglia

value: mouse

value: no

value: hippocampus


title: nt20B

description:
G20C
single_nt.miR.reads.csv
single_nt.let7.reads.csv
20B


title: A6-p2-K1_243_human_TREM2_R47H_het

description:
Sample134
mRNA expression in microglia

value: human

value: female

value: microglia


title: v2-homecage-WT20w1


title: Male_NAc_Veh FTL_321

value: Nucleus accumbens

value: Male


title: A6-p2-K1_241_human_TREM2_R47H_het

description:
Sample133
mRNA expression in microglia


title: nt20A

description:
G20C
single_nt.miR.reads.csv
single_nt.let7.reads.csv
20A


title: Female_NAc_THC FTL_319

value: THC

value: 11 weeks


title: nt19C

description:
A19U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
19C


title: Female_NAc_THC FTL_318


title: v2-homecage-OMP-IRES-GFP-4

value: OMP-IRES-GFP


title: Male_NAc_Veh FTL_323

value: Vehicle


title: v2-homecage-OMP-IRES-GFP-3


title: nt19B

description:
A19U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
19B

value: mid L4

value: 20 °C


title: Female_NAc_THC FTL_317


title: A6-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample131
mRNA expression in microglia

value: yes


title: nt19A

description:
A19U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
19A


title: A6-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample132
mRNA expression in microglia


title: v2-homecage-OMP-IRES-GFP-2

value: whole olfactory mucosa

value: 6-12 weeks


title: Female_NAc_THC FTL_316

value: Female


title: v2-homecage-OMP-IRES-GFP-1


title: A6-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample130
mRNA expression in microglia


title: P2-IRES-GFP-2


title: nt18C

description:
U18A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
18C


title: Female_NAc_THC FTL_315


title: A6-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample129
mRNA expression in microglia


title: Female_NAc_Veh FTL_314


title: A6-p1-NTG_233_mouse_Trem2_WT

description:
Sample128
mRNA expression in microglia

value: no


title: nt18B

description:
U18A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
18B


title: nt18A

description:
U18A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
18A


title: Female_NAc_Veh FTL_313


title: P2-IRES-GFP-1


title: A6-p1-NTG_232_mouse_Trem2_WT

description:
Sample127
mRNA expression in microglia

value: mouse

value: hippocampus


title: Female_NAc_Veh FTL_312


title: M72inS50-IRES-GFP-2


title: M72inS50-IRES-GFP-1


title: nt17C

description:
A17U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
17C


title: nt17B

description:
A17U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
17B


title: A6-p1-K1_243_human_TREM2_R47H_het

description:
Sample126
mRNA expression in microglia

value: human

value: female


title: S50inM72-IRES-GFP-2

description:
10x genomics, v2
OR_swap_umi_counts.csv.gz
OR_swap_metadata.csv.gz


title: Female_NAc_Veh FTL_311

value: Nucleus accumbens


title: nt17A

description:
A17U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
17A


title: Female_NAc_Veh FTL_310


title: Female_NAc_Veh FTL_309


title: A5-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample123
mRNA expression in microglia

value: microglia


title: A5-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample124
mRNA expression in microglia


title: nt16B

description:
U16G
single_nt.miR.reads.csv
single_nt.let7.reads.csv
16B


title: nt16C

description:
U16G
single_nt.miR.reads.csv
single_nt.let7.reads.csv
16C


title: A5-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample122
mRNA expression in microglia


title: P1 molar mesenchyme

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v2.1.0 using default settings.
Secondary analysis was performed using Loupe Cell Browser v5 (10x Genomics, San Francisco, CA, USA). Clusters were defined by k-means clustering based on the PCA of the transcriptomic signature.

source_name: P1 molar

extract_protocol:
Molars were dissected with sharp tweezers from seven littermates of P7 Krt14-RFP mice. Single cell dissociation was essentially performed as previously described (Li et al. 2015). Briefly, dissected incisors were incubated in 4 mg/ml Dispase II (Roche) for 14 min at 37°C. Then incisors were placed in cold DMEM/F12 and dental epithelium and mesenchyme were separated under microscope. The tissues are then placed in Accutase (Sigma) for 30min at 37°C. After pipetting up and down using 1000 μm tips, single cell suspension was further produced through a 70 μm sterile cell strainer. The cells were resuspended with 0.04% BSA containing cold PBS.
Single-cell suspensions were loaded onto a 10X Chromium Controller (10X Genomics) and library preparation was performed according to the manufacturer’s instructions for the 10X Chromium Next GEM Single Cell Library kit v3 (10X Genomics).  Libraries were then pooled and sequenced on 4 lanes on a NextSeq500 sequencer (Illumina) using 10X Genomics recommended reads configuration.

value: molar mesenchyme


title: S50inM72-IRES-GFP-1


title: P1 molar epithelium

value: molar epithelium


title: A6-p1-K1_241_human_TREM2_R47H_het

description:
Sample125
mRNA expression in microglia


title: A5-p2-NTG_233_mouse_Trem2_WT

description:
Sample120
mRNA expression in microglia


title: Male_DMS_THC FTL_306

source_name: Brain -DMS

value: Dorsolateral striatum

value: THC

value: Male

value: 11 weeks


title: Male_DMS_THC FTL_307


title: A5-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample121
mRNA expression in microglia

value: yes


title: Male_DMS_THC FTL_305


title: nt15B

description:
G15A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
15B

value: mid L4

value: 20 °C


title: nt15A

description:
G15A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
15A


title: nt16A

description:
U16G
single_nt.miR.reads.csv
single_nt.let7.reads.csv
16A


title: nt14C

description:
U14A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
14C


title: Male_DMS_THC FTL_304


title: A5-p2-K1_243_human_TREM2_R47H_het

description:
Sample118
mRNA expression in microglia


title: Male_DMS_THC FTL_308


title: pK27R_2_EpiLC_rep3

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore Version 0.6.5, then mapped to mm10 whole genome using HISAT 2.2.0 with default parameters
FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads at gene level.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are in Microsoft Excel worksheets with DeSeq2 comparisions between mutant and control mESC transcriptomes, mutant EpiLCs vs control mESC transcriptomes and quantification of relevant ChIP signals of unchanged, down or upregulated genes at the transcriptomic levels
ChIP_RNA_integrated_mESCs.xlsx
DeSeq2_all samples_EpiLC_vs_ABE7_10_mESCs.xlsx  DeSeq2_all_samples_mESCs.xlsx

source_name: EpiLCs

growth_protocol: mESCs were grown in feeder-free standard naïve pluripotent growth conditions including LIF and 2i (GSK3 and MEK1 inhibitors)

extract_protocol:
Total RNA was extracted from fresh cell pellet using Qiagens Rneasy Plus mini kit (Catalog : 74136) and quantified using Nanodrop. 1 microgram total RNA was used as input for library preparation.
Libraries were constructed using SMARTer Stranded Total RNA Sample prep kit - High input (Catalog Number 634875) according to manufacturers guidelines.
Total RNA-Seq

treatment_protocol: For generation of EpiLCs, 250000 naïve pluripotent mESCs were plated in fibronectin coated 6-well plates in N2B27 media supplemented with Activin A, FGF and KOSR (knockout serum replacement) as outlined in Hayashi et al., Cell 2011 (PMID: 21820164) with daily media change. EpiLCs were harvested at 48 hours post plating and RNA was extracted from three independent replicates for each cell line.

value: EpiLCs


title: pK27R_1_EpiLC_rep2


title: A5-p2-NTG_232_mouse_Trem2_WT

description:
Sample119
mRNA expression in microglia

value: no


title: Male_DMS_THC FTL_303


title: A5-p2-K1_241_human_TREM2_R47H_het

description:
Sample117
mRNA expression in microglia


title: Male_DMS_Veh FTL_302

value: Vehicle


title: pK27R_2_EpiLC_rep2


title: pK27R_1_EpiLC_rep1


title: A5-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample116
mRNA expression in microglia

value: mouse

value: hippocampus


title: nt14B

description:
U14A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
14B


title: nt14A

description:
U14A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
14A


title: nt15C

description:
G15A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
15C


title: A5-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample115
mRNA expression in microglia

value: female


title: Male_DMS_Veh FTL_301


title: pK27R_1_EpiLC_rep3


title: Male_DMS_Veh FTL_300


title: nt13A

description:
U13A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
13A


title: nt13C

description:
U13A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
13C


title: cK27R_1_EpiLC_rep1


title: nt13B

description:
U13A
single_nt.miR.reads.csv
single_nt.let7.reads.csv
13B


title: Male_DMS_Veh FTL_299


title: cK27R_2_EpiLC_rep2


title: A5-p1-K1_241_human_TREM2_R47H_het

description:
Sample109
mRNA expression in microglia

value: human


title: nt11C

description:
G11U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
11C


title: cK27R_2_EpiLC_rep1


title: pK27R_2_EpiLC_rep1


title: A5-p1-NTG_233_mouse_Trem2_WT

description:
Sample112
mRNA expression in microglia

value: microglia


title: A5-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample113
mRNA expression in microglia


title: nt12C

description:
G12U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
12C


title: A5-p1-K1_243_human_TREM2_R47H_het

description:
Sample110
mRNA expression in microglia


title: Male_DMS_Veh FTL_298


title: cK27R_2_EpiLC_rep3


title: A5-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample114
mRNA expression in microglia


title: cK27R_1_EpiLC_rep2


title: nt12B

description:
G12U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
12B


title: Male_DMS_Veh FTL_297


title: A5-p1-NTG_232_mouse_Trem2_WT

description:
Sample111
mRNA expression in microglia


title: Female_DMS_THC FTL_295

value: Female


title: nt12A

description:
G12U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
12A


title: Female_DMS_THC FTL_296


title: SUZ12KO_EpiLC_rep2


title: SUZ12KO_EpiLC_rep3


title: A4-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample107
mRNA expression in microglia


title: nt11A

description:
G11U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
11A


title: Female_DMS_THC FTL_294


title: ABE_7_10_EpiLC_rep3

value: ABE


title: A4-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample106
mRNA expression in microglia


title: A4-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample105
mRNA expression in microglia


title: SUZ12KO_EpiLC_rep1


title: Female_DMS_THC FTL_293

value: Dorsolateral striatum


title: ABE_7_10_EpiLC_rep1


title: nt10B

description:
A10U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
10B


title: nt10C

description:
A10U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
10C


title: Female_DMS_THC FTL_292

value: THC


title: A4-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample108
mRNA expression in microglia


title: ABE_7_10_EpiLC_rep2


title: nt10A

description:
A10U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
10A


title: Female_DMS_Veh FTL_290


title: Female_DMS_Veh FTL_289


title: pK27R_2_mESC_rep2

source_name: mESCs

value: mESCs


title: A4-p2-NTG_232_mouse_Trem2_WT

description:
Sample103
mRNA expression in microglia


title: nt11B

description:
G11U
single_nt.miR.reads.csv
single_nt.let7.reads.csv
11B


title: Female_DMS_Veh FTL_288

value: 11 weeks


title: Female_DMS_THC FTL_291


title: nt09C

description:
U9G
single_nt.miR.reads.csv
single_nt.let7.reads.csv
09C


title: nt09B

description:
U9G
single_nt.miR.reads.csv
single_nt.let7.reads.csv
09b


title: pK27R_2_mESC_rep1


title: A4-p2-K1_241_human_TREM2_R47H_het

description:
Sample101
mRNA expression in microglia


title: nt09A

description:
U9G
single_nt.miR.reads.csv
single_nt.let7.reads.csv
09A


title: Female_DMS_Veh FTL_287


title: A4-p2-NTG_233_mouse_Trem2_WT

description:
Sample104
mRNA expression in microglia


title: cK27R_1_EpiLC_rep3


title: Female_DMS_Veh FTL_286


title: pK27R_1_mESC_rep2


title: pK27R_2_mESC_rep3


title: Female_DMS_Veh FTL_285


title: WT_A

description:
WT
single_nt.miR.reads.csv
single_nt.let7.reads.csv
WT_A


title: A4-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample99
mRNA expression in microglia

value: yes


title: A4-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample100
mRNA expression in microglia


title: pK27R_1_mESC_rep3


title: A4-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample98
mRNA expression in microglia


title: pK27R_1_mESC_rep1


title: Male_PFC_THC FTL_283

source_name: Brain -PFC

value: Prefrontal cortex

value: Male


title: A4-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample97
mRNA expression in microglia


title: cK27R_2_mESC_rep3


title: Male_PFC_THC FTL_284


title: A4-p2-K1_243_human_TREM2_R47H_het

description:
Sample102
mRNA expression in microglia


title: Male_PFC_THC FTL_282


title: A4-p1-NTG_233_mouse_Trem2_WT

description:
Sample96
mRNA expression in microglia


title: cK27R_2_mESC_rep2


title: cK27R_2_mESC_rep1


title: MV-V2

city: Richmond

first: Niels

middle: C.

last: Asmussen

state: VA

address: 601 W. Main St. Room 392

institute: Virginia Commonwealth University

data_processing:
miARma-Seq v 1.6
Quality: prefix=pre
Aligner: bowtie2, bowtielength=17, bowtieparameters = -N 1
ReadCount: seqid=product, featuretype=miRNA
Genome_build: NCBI Rnor_6.0
Supplementary_files_format_and_content: files were generated using miARma-Seq

organism: Rattus norvegicus

source_name: Growth Zone Chondrocyte Matrix Vesicles

growth_protocol: chondrocytes were grown out to fourth passage in T-175 flasks using Dulbecco's modified Eagle's medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Life Technologies), 50 parts/mL penicillin/streptomycin and 50 mg/mL ascorbic acid (Sigma-Aldrich). Cell culture medium was changed 24hrs after plating and then at 72hr intervals.

extract_protocol:
MVs were isolated from chondrocyte cultures by differential centrifugation of the trypsin digested cell layer (briefly: after trypsinization - 0.25% Trypsin-EDTA - for 10 min, 1xDPBS containing 10% exosome-free FBS was added to stop the reaction. The MVs were isolated by sequential centrifugation at 500 g for 5min, 24,000 g for 20 min and 100,000 g for 70 min. The MV pellets were washed with 0.9% NaCl and recentrifuged at 100,000 g for 70 min.)
NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) RiboZero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre, an Illumina Company) NEB Multiplex Small RNA Library Prep Set for Illumina Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following  steps:  1) 3’-adaptor ligation;  2) 5’-adaptor ligation;  3) cDNA synthesis;  4) PCR amplification;  5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).  The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in  situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq per the manufacturer’s instructions.

treatment_protocol: confluent fourth passage chondrocytes were treated for 24 hours with either vehicle (EtOH) or 1α,25-dihydroxyvitamin D3

value: Growth Zone Matrix Vesicle

tag: passage

tag: cell source

value: costochondral cartilage

value: 4 hour vehicle (EtOH)

tag: molecule subtype

value: small RNA


title: A4-p1-NTG_232_mouse_Trem2_WT

description:
Sample95
mRNA expression in microglia

value: mouse

value: no

value: hippocampus


title: Male_PFC_THC FTL_281


title: WT_B

description:
WT
single_nt.miR.reads.csv
single_nt.let7.reads.csv
WT_B

value: mid L4

value: 20 °C


title: A4-p1-K1_243_human_TREM2_R47H_het

description:
Sample94
mRNA expression in microglia

value: human

value: female

value: microglia


title: WT_C

description:
WT
single_nt.miR.reads.csv
single_nt.let7.reads.csv
WT_C


title: MV-V1


title: MV-D3

value: 1α,25-dihydroxyvitamin D3


title: Male_PFC_THC FTL_280

value: THC

value: 11 weeks


title: A4-p1-K1_241_human_TREM2_R47H_het

description:
Sample93
mRNA expression in microglia


title: Male_PFC_THC FTL_279

value: Prefrontal cortex


title: Male_PFC_Veh FTL_278

value: Vehicle

value: Male


title: MV-D2

value: Growth Zone Matrix Vesicle

value: costochondral cartilage


title: Suz12KO_mESC_rep3

value: mESCs


title: MV-D1

value: small RNA


title: Male_PFC_Veh FTL_277


title: cK27R_1_mESC_rep1


title: A3-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample90
mRNA expression in microglia

value: yes


title: cK27R_1_mESC_rep2


title: Suz12KO_mESC_rep2


title: Male_PFC_Veh FTL_276


title: A3-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample91
mRNA expression in microglia

value: mouse

value: hippocampus


title: Suz12KO_mESC_rep1


title: A3-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample92
mRNA expression in microglia

value: no


title: Male_PFC_Veh FTL_275


title: A3-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample89
mRNA expression in microglia

value: human


title: MV-V3

value: 4 hour vehicle (EtOH)


title: cK27R_1_mESC_rep3


title: ExoFBS-1

source_name: Commercial FBS Vesicles

value: Commercial FBS


title: Male_PFC_Veh FTL_274


title: Cell-V3

source_name: Growth Zone Chondrocyte Cells

value: Growth Zone Chondrocyte


title: A3-p2-NTG_233_mouse_Trem2_WT

description:
Sample88
mRNA expression in microglia

value: female

value: microglia


title: ABE_7_10_mESC_rep2

value: ABE


title: Cell-V2


title: A3-p2-NTG_232_mouse_Trem2_WT

description:
Sample87
mRNA expression in microglia


title: Male_PFC_Veh FTL_273

value: Prefrontal cortex

value: Vehicle

value: 11 weeks


title: Cell-V1

value: costochondral cartilage


title: ABE_7_10_mESC_rep3

value: mESCs


title: ABE_7_10_mESC_rep1


title: Female_PFC_THC FTL_271

value: THC

value: Female


title: Cell-D3

value: 1α,25-dihydroxyvitamin D3

value: small RNA


title: Female_PFC_THC FTL_272


title: A3-p2-K1_241_human_TREM2_R47H_het

description:
Sample85
mRNA expression in microglia

value: no

value: hippocampus


title: Cell-D2


title: Female_PFC_THC FTL_270


title: A3-p2-K1_243_human_TREM2_R47H_het

description:
Sample86
mRNA expression in microglia

value: human


title: A3-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample83
mRNA expression in microglia

value: mouse

value: yes


title: Cell-D1

value: Growth Zone Chondrocyte


title: Female_PFC_THC FTL_269


title: ExoFBS-2

value: Commercial FBS


title: A3-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample84
mRNA expression in microglia

value: female

value: microglia


title: A3-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample82
mRNA expression in microglia


title: Female_PFC_THC FTL_268

value: Prefrontal cortex


title: A3-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample81
mRNA expression in microglia


title: Female_PFC_THC FTL_267

value: 11 weeks


title: Female_PFC_Veh FTL_266

value: Vehicle


title: A3-p1-NTG_233_mouse_Trem2_WT

description:
Sample80
mRNA expression in microglia


title: Female_PFC_Veh FTL_265


title: A3-p1-NTG_232_mouse_Trem2_WT

description:
Sample79
mRNA expression in microglia


title: Female_PFC_Veh FTL_263


title: A3-p1-K1_241_human_TREM2_R47H_het

description:
Sample77
mRNA expression in microglia


title: Female_PFC_Veh FTL_262


title: A2-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample75
mRNA expression in microglia


title: A2-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample76
mRNA expression in microglia


title: A2-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample74
mRNA expression in microglia


title: Female_PFC_Veh FTL_261


title: home-home-1

description:
10x genomics, v3.1
envA_bidirectional_switch_umi_counts.csv
envA_bidirectional_switch_metadata.csv

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 %.
single cell 3' end RNA-seq

value: whole olfactory mucosa

value: 6-12 weeks


title: envA-home-2


title: home-home-2


title: LS174T, sample 2, batch 2

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.54.1).

label: biotin

organism: Homo sapiens

source_name: LS174T cells, grown for 15 days on a regular 12-well cell culture plate under static conditions

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: HT29-MTX-E12 cells (ECACC) were obtained from Sigma-Aldrich (Darmstadt, Germany). Caco-2 (ATCC HTB-37) and LS174T (ATCC CL-188) cells were purchased at LGC Standards (Wesel, Germany). All cell types were cultured in Dulbecco's Modified Eagle Medium with 4.5g/L glucose, 110 mg/L sodium pyruvate and 584 mg/L L-glutamine (Corning, NY, USA) supplemented with 10% Fetal Bovine Serum and 1% penicillin/streptomycin. When cells reached 80-90% confluency, they were counted and seeded. Passage numbers between 15 and 27 were used for Caco-2 cells and between 3 and 21 for HT29-MTX-E12 cells. LS174T cells were used between passage 17 and 19.

extract_protocol: RNA was isolated using the Maxwell 16 LEV simplyRNA Cells Kit (Promega, cat. no. AS1270) and the Maxwell 16 MDx Instrument (Promega), following the manufacturer’s instructions. Total RNA yield (Nanodrop ND-1000, Nanodrop Products, Maarssen, The Netherlands) and RNA integrity (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) were assessed. Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Caco-2 and HT29MTX-E21 cells were seeded (day 0) at a density of 273,000 cells/mL in 275 µL per well on 12 mm 0.4 µm-pore polyester Transwell membranes (Corning 3460). A volume of 1 mL medium was added to the basolateral compartment. One day after seeding (day 1), media of all Transwells was refreshed and Semi-Wet conditions with Mechanical Stimulation (SWMS) were applied (PMID: 23869232,  29156489). To these Transwells, 75 µL and 850 µL of medium was added to the apical and basolateral compartments, respectively, and plates were put on a CO2-resistant shaker (Thermo Fisher Scientific, Breda, The Netherlands) at 65 rpm. Media volumes of Transwells grown under static conditions were unchanged. LS174T cells were seeded at similar seeding density on regular 12-well cell culture plates. This cell line was cultured under static conditions in a regular wells plate only, since these cells do not form a continuous monolayer of cells, but grow in a rather irregular manner (PMID: 23869232). Medium was refreshed every Monday, Wednesday and Friday and cells were harvested 15 days after seeding (t = 15 days). Each experiment was replited using multiple batches.

tag: cell line

tag: growth condition

value: static

tag: culture system

value: 22.1 mm regular 12-well tissue culture (TC) treated surface treatment cell culture plates (Corning 3512)

tag: culture time

value: 15 days

tag: experiment batch


title: LS174T, sample 3, batch 3


title: LS174T, sample 3, batch 1


title: A2-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample73
mRNA expression in microglia


title: A2-p2-NTG_233_mouse_Trem2_WT

description:
Sample72
mRNA expression in microglia

value: no


title: A2-p2-NTG_232_mouse_Trem2_WT

description:
Sample71
mRNA expression in microglia

value: hippocampus


title: Female_PFC_Veh FTL_264

tag: strain

tag: tissue

value: Female


title: HT29MTX, SWMS, sample 2, batch 3

source_name: HT29MTX-E21 cells, grown for 15 days on a Transwell membrane under semi-wet conditions with mechanical stimulation (SWMS)

value: 12 mm 12-well 0.4 µm-pore polyester Transwell membranes (Corning 3460)


title: HT29MTX, Stat, sample 1, batch 3

source_name: HT29MTX-E21 cells, grown for 15 days on a Transwell membrane under static conditions


title: HT29MTX, SWMS, sample 2, batch 2

value: semi-wet conditions with mechanical stimulation (SWMS)


title: A3-p1-K1_243_human_TREM2_R47H_het

description:
Sample78
mRNA expression in microglia

tag: trem2 species

value: human


title: HT29MTX, Stat, sample 2, batch 2


title: envA-home-1

tag: age


title: envA-envA-2


title: Caco2, SWMS, sample 1, batch 3

source_name: Caco-2 cells, grown for 15 days on a Transwell membrane under semi-wet conditions with mechanical stimulation (SWMS)


title: HT29MTX, Stat, sample 3, batch 1


title: A2-p2-K1_243_human_TREM2_R47H_het

description:
Sample70
mRNA expression in microglia

tag: p301s status

tag: brain region


title: A2-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample68
mRNA expression in microglia

value: mouse

tag: Sex

tag: gate


title: envA-envA-1


title: 1ON-envA5d-2

description:
10x genomics, v3.1
envA_timecourse_umi_counts.csv.gz
envA_timecourse_metadata.csv.gz


title: 1ON-envA2w-1


title: A2-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample66
mRNA expression in microglia

value: yes

value: female

tag: cell type


title: HT29MTX, SWMS, sample 3, batch 1


title: Caco2, Stat, sample 2, batch 3

source_name: Caco-2 cells, grown for 15 days on a Transwell membrane under static conditions


title: Caco2, SWMS, sample 2, batch 2


title: Caco2, Stat, sample 1, batch 2


title: Caco2, Stat, sample 3, batch 1


title: 1ON-envA5d-1


title: Caco2, SWMS, sample 2, batch 1


title: A2-p1-NTG_233_mouse_Trem2_WT

description:
Sample64
mRNA expression in microglia

value: microglia


title: 1ON-envA3d-1


title: A2-p2-K1_241_human_TREM2_R47H_het

description:
Sample69
mRNA expression in microglia


title: 1ON-envA3d-2


title: A2-p1-NTG_232_mouse_Trem2_WT

description:
Sample63
mRNA expression in microglia


title: 1ON-envA2w-2


title: normal replicate 5

city: Chengdu

first: Di

last: Cao

state: Sichuan

address: No.37 Guoxue Alley, Wuhou District

department: Department of Hematology

country: China

institute: Sichuan University

description: Gene expression difference between lymphoma patients and healthy individuals

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual. a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon).

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner and GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing:
A),The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged. B),We use Median Normalization Method to obtain “Normalized Data”. C),After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test. D),Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.
Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.

source_name: Peripheral blood serum

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps: a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: diagnosis

value: healthy

value: serum

tag: gender

value: male


title: A2-p1-K1_243_human_TREM2_R47H_het

description:
Sample62
mRNA expression in microglia


title: A2-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample67
mRNA expression in microglia


title: normal replicate 3


title: 1ON-envA24h-2

source_name: whole olfactory mucosa

value: whole olfactory mucosa

value: 6-12 weeks


title: 1ON-envA24h-1


title: A2-p1-K1_241_human_TREM2_R47H_het

description:
Sample61
mRNA expression in microglia

source_name: FACS isolated adult microglia


title: normal replicate 4


title: patient replicate 9

value: DLBCL


title: normal replicate 2


title: A2-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample65
mRNA expression in microglia


title: patient replicate 10


title: normal replicate 1


title: 1ON-envA12h-1


title: A12-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample59
mRNA expression in microglia


title: 1ON-envA4h-2


title: 1ON-envA12h-2


title: 1ON-envA4h-1


title: patient replicate 8


title: A12-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample57
mRNA expression in microglia


title: A12-p2-NTG_232_mouse_Trem2_WT

description:
Sample56
mRNA expression in microglia


title: 1ON-envA2h-1


title: 1ON-envA2h-2


title: 1ON-envA45m-2


title: A12-p2-K1_243_human_TREM2_R47H_het

description:
Sample55
mRNA expression in microglia


title: A12-p2-K1_241_human_TREM2_R47H_het

description:
Sample54
mRNA expression in microglia


title: A12-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample60
mRNA expression in microglia


title: A12-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample53
mRNA expression in microglia


title: A12-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample52
mRNA expression in microglia


title: 1ON-envA45m-1


title: baseline-ON-4


title: A12-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample58
mRNA expression in microglia


title: IMX606 replicate 2

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

institute: Delft University of Technology

data_processing:
RNA-seq reads were aligned to the CEN.PK113-7D reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
raw counts normalized with RPKM from edgeR
For differential analysis the raw counts were processed with DESeq2
Genome_build: CEN.PK113-7D ASM257140v2
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cell culture

growth_protocol: RNA from strains IMX605 and IMX606 was sampled from the biological duplicate aerobic SMD bioreactor cultures run by Kuijpers et al (2016).

extract_protocol:
RNA was extracted with hot-phenol method as described by Schmitt et al. (1990)
cDNA libraries were prepared using the TruSeq stranded mRNA kit (illumina) and sequenced on HISeq 2500 (illumina) at Macrogen

treatment_protocol: Cultures were sampled into liquid nitrogen and processed as described by Piper et al. (2002)

tag: replicate

value: Replicate 2

tag: glycolytic gene location

value: single locus on chromosome IX


title: baseline-ON-3


title: MG aerobic replicate 1

description: GEO sample accession GSM1559297

value: Replicate 1

value: native loci


title: DPG-5d-2

description:
10x genomics, v3.1
chronic_ACE_umi_counts.csv.gz
chronic_ACE_metadata.csv.gz


title: IMX606 replicate 1


title: A12-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample50
mRNA expression in microglia

value: hippocampus


title: MG aerobic replicate 2

description: GEO sample accession GSM1559298


title: IMX605 replicate 2

value: single locus on chromosome V


title: A12-p1-NTG_233_mouse_Trem2_WT

description:
Sample49
mRNA expression in microglia

value: human

value: no


title: DPG-5d-1


title: patient replicate 2


title: ACE1p-5d-2


title: patient replicate 1


title: IMX605 replicate 1


title: A12-p1-NTG_232_mouse_Trem2_WT

description:
Sample48
mRNA expression in microglia

value: mouse


title: A12-p1-K1_243_human_TREM2_R47H_het

description:
Sample47
mRNA expression in microglia

value: female


title: A12-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample51
mRNA expression in microglia

value: yes

value: microglia


title: patient replicate 3

value: serum


title: A12-p1-K1_241_human_TREM2_R47H_het

description:
Sample46
mRNA expression in microglia


title: sw480

city: Nanning

first: Weizhong

last: Tang

state: State...

address: Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region 530021 P.R. China.

institute: Guangxi Medical University Cancer Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colorectal cancer cell line

extract_protocol:
Centrifuge cell suspension, place the collected cells on the surface of the omentum and remove them, freeze them quickly on dry ice, and use Trizol reagent to obtain RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: sw620


title: A11-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample45
mRNA expression in microglia


title: RKO

description: RKO

value: RKO


title: patient replicate 7


title: A11-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample44
mRNA expression in microglia


title: lovo

description: lovo

value: lovo


title: A11-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample43
mRNA expression in microglia


title: patient replicate 5

value: male


title: CRLF2 IL7RAins 2

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the human genome (hg19) using STAR
Counting proceeded over genes annotated in Ensembl using htseq-count
Normalization and differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Processed file include DESeq2 normalized counts

source_name: transduced engrafted human cells sorted from spleen of engrafted mouse

growth_protocol: CB human cells from several batches were transduced with CRLF2-IL7RAins or BB control lenti viruses.

extract_protocol:
total RNA was extracted from trizol ccording to manufacturer's protocol
cDNA libraries were prepared using SMARTer v3 kit (Clontech Laboratories, Inc. A Takara Bio Company, Mountain View, CA, USA)
Nextera-XT indexing protocols (Illumina, CA, USA).

treatment_protocol: After engraftment, 4000-20000 human non T (hCD45+CD3-) transduced (GFP+/CRLF2+) cells were sorted from engrafted mice spleensdirectly into TRIzol .

value: hCD45+ CRLF2+ sorted cells

tag: source

value: Human (sorted from mouse)


title: BB-control for IG-32

value: hCD45+ GFP+ sorted cells


title: CRLF2 IL7RAins 1


title: BB-control for IG-14 and IG-17


title: CRLF2 IL7RAins 4


title: BB-control for IG-6


title: CRLF2 IL7RAins 3


title: BB-control for IG-9


title: HCT116


title: BB-control for IG-2


title: CRLF2 IL7RAins 5


title: CRLF2 IL7RAins 6


title: A11-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample42
mRNA expression in microglia


title: DLD_1


title: A11-p2-NTG_233_mouse_Trem2_WT

description:
Sample41
mRNA expression in microglia


title: ACE10p-5d-2

value: whole olfactory mucosa

value: 6-12 weeks


title: ACE1p-5d-1


title: ACE10p-5d-1


title: ACE0_1p-5d-2


title: MS2h-2

description:
10x genomics, v3.1
ActSeq_conc_analog_umi_counts.csv.gz
ActSeq_conc_analog_metadata.csv.gz


title: ACE0_1p-5d-1


title: A11-p2-NTG_232_mouse_Trem2_WT

description:
Sample40
mRNA expression in microglia

value: hippocampus


title: MS2h-1


title: homecage-DPG30m-4


title: homecage-DPG30m-3


title: A11-p2-K1_243_human_TREM2_R47H_het

description:
Sample39
mRNA expression in microglia


title: A11-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample38
mRNA expression in microglia


title: hThy24N_tissue_thyroid_tissue

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

description: Bulk RNA sequencing of human thyroid 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: hg38
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 thyroid gland were plated in Cultrex Pathclear Reduced Growth Factor Basement Membrane Extract (BME) (3533-001, Amsbio). The volume of BME was determined based on the size of the final pellet. After BME solidification, complete expansion medium was added. After BME solidification, complete expansion medium was added. Human expansion medium contained AdDMEM/F12 (GIBCO) supplemented with B27 supplement (Gibco, 17504044), Glutamax, HEPES, 100 U/mL Penicillin-Streptomycin (all Thermo Fisher scientific), 100 µg/mL Primocin (Invivogen), 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), 100 ng/mL FGF10 (Peprotech, 100-26), 3mM p38 inhibitor (Sigma-Aldrich, S7067), 1:1000 Wnt surrogate (U-Protein Express) and 100ng/mL TSH (Sigma-Aldrich, T8931).

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.

treatment_protocol: No treatment was used in this study

tag: genotype

value: Wild type

value: Thyroid tissue

tag: passage stage

value: Tissue


title: A11-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample37
mRNA expression in microglia

value: mouse


title: A11-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample36
mRNA expression in microglia

value: human

value: female


title: patient replicate 4

value: DLBCL


title: patient replicate 6

value: serum


title: A11-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample35
mRNA expression in microglia

value: yes

value: microglia


title: A11-p1-NTG_232_mouse_Trem2_WT

description:
Sample33
mRNA expression in microglia

value: no


title: A11-p1-NTG_233_mouse_Trem2_WT

description:
Sample34
mRNA expression in microglia


title: hThy20N_tissue_thyroid_tissue


title: hThy23N_P4_organoid

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

value: TFC organoids

value: Late passage


title: hThy23N_tissue_thyroid_tissue


title: hThy20N_P4_organoid_2


title: A11-p1-K1_241_human_TREM2_R47H_het

description:
Sample32
mRNA expression in microglia


title: hThy20N_P4_organoid_1


title: A10-p2-PS19_246_P301S_mouse_Trem2_WT

description:
Sample31
mRNA expression in microglia


title: hThy20N_P2_organoid

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

value: Early passage


title: A10-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample30
mRNA expression in microglia


title: hThy23N_P1_organoid_2


title: hThy23N_P1_organoid_1


title: A10-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample28
mRNA expression in microglia


title: A10-p2-NTG_233_mouse_Trem2_WT

description:
Sample27
mRNA expression in microglia


title: aHiChIP PR T0

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description:
HiChIP PR T0
HiChIP_T0_all.interactions_FitHiC_Q0.05_MergeNearContacts.bed

library_source: genomic

data_processing:
Library strategy: HI-ChIP
ChIP-seq and ATAC-seq Peak Calling Analysis of sequence data was carried out as previously described (Ferrari et al, 2020)  with minor modifications. Reads were aligned to the hg38 human genome reference  sequence (GRCh38) using Bowtie (Langmead et al, 2009) and aligning parameters of  uniqueness (-S –m1 –v2 –t –q). p values for the significance of ChIP-seq counts  compared to input DNA were calculated as described (Pellegrini & Ferrari, 2012) using  a threshold of 10-8 and a false discovery rate (FDR) < 1%.
HiCHIP experiments were performed as described (Mumbach et al., 2016) using PR  specific antibody (Santa Cruz, H190). Analysis was performed using dovetail HiChIP  pipeline (https://hichip.readthedocs.io/en/latest/).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig or bed

molecule: genomic DNA

source_name: HiChIP PR T0

growth_protocol: T47D breast cancer cells were routinely grown in RPMI 1640 medium supplemented with  10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100μg/ml streptomycin.  For the experiments, cells were plated in RPMI medium without phenol red  supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later  medium was replaced by fresh medium without serum.  MCF10A cells were routinely grown in DMEM/F12 medium with 5% Horse Serum, 20  ng/ml EGF, 100 U/ml penicillin and 100mg/ml streptomycin, 0.5 mg/mL Hydrocortisone,  100 ng/ml Cholera Toxin and 10 mg/ml Insulin.  T47Dwhite cells  were routinely grown in RPMI medium without phenol red supplemented with 10%  dextran-coated charcoal treated FBS (DCC/FBS).

extract_protocol:
RNA was extracted from cells treated or not for 6hs with 50pM or 10nM  R5020 and submitted to massive sequencing using the Solexa Genome Analyzer.
RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and  dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer  and RNA subjected to Bioanalyzer for quality control. Libraries were prepared using 1 μg of polyA+ RNA by PCR amplification of cDNA with bar-coded primers using the Illumina  TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-  2500 to obtain pair-ended (PE) 100-base-long reads.
ChIP assays were performed as described (Strutt and Paro, 1999)

treatment_protocol: After 24h in serum-free  conditions, cells were incubated with R5020 or Progesterone at different concentrations  ranging from 0.01, 0.05, 0.5, 0.1, 1 and 10nM for different times at 37 C.


title: A10-p2-NTG_232_mouse_Trem2_WT

description:
Sample26
mRNA expression in microglia


title: aHiChIP PR5020 T30

description:
HiChIP PR T30
HiChIP_T30_all.interactions_FitHiC_Q0.05_MergeNearContacts.bed

source_name: HiChIP PR T30


title: A10-p2-K1_243_human_TREM2_R47H_het

description:
Sample25
mRNA expression in microglia


title: ND538.Day28_Continuous [scTCR-seq]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Library strategy: 10X single cell TCR-Seq
Alignment: 10X v2 sequencing data were aligned to the vdj-GRCh38-alts-ensembl-3.1.0 genome and processed using the cellranger vdj command in Cell Ranger v3.1.0.
Genome_build: vdj-GRCh38-alts-ensembl-3.1.0
Supplementary_files_format_and_content: We include filtered coverage annotation files (FCA) which detail the VDJ peptides recovered in each cell (maps unique cell barcodes to peptide sequences)

source_name: M5CAR T cells (PBMCs)

growth_protocol: Primary human CD4+ T and CD8+ T cells from normal donors were provided by University of Pennsylvania Human Immunology Core. CAR T cells were generated as previously described (Carpenito et al., 2009). Briefly, CD4+ and CD8+ T at 1:1 ratio at 1 x 10e6 cells/ml were activated with Dynabeads CD3/CD28 CTSTM (Gibco, Life Technologies) at a 3:1 bead-to-cell ratio. Approximately after 24 hours, T cells were transduced at a multiplicity of infection (MOI) of 5. At day 5 beads were removed from cultures. T cell cultures were maintained at 8 x 10e5 cells/ml. Cell number and volume were monitored daily using Multisizer 4 Coulter Counter (Beckmanwaslter). Transduced T cells were cryopreserved when reached the resting state, as determined by cell size.

extract_protocol:
For flow cytometry and sorting assays of CAE, M5 CAR T cells were stained in fluorescence-activated cell sorting (FACS) buffer consisting of PBS (Gibco), 0.5% bovine serum albumin (BSA) (GEMINI), 2 mM EDTA (Invitrogen), and 100ug/ml DNase (Roche). CountBrightTM Absolute Counting Beads, (ThermoFisher) were used as an internal standard according to the manufacturer's instructions to calculate absolute cell counts in cell suspensions.  Antibodies specific for human CD45 (ref 304032, clone HI30), CD3 (317322, OKT3), CD4 (357412, A161A1 / 317440), CD56 (304608, MEM-188), EpCAM (324226/324238, 9C4), CD94 (305520, DX22), KLRB1 (339918, HP-3G10), TIGIT (372716, A15153G), TCR Va24-Ja18 (342922, 6B11), PD-1 (329928, EH12.2H7) were purchased from BioLegend. Antibodies specific for human CD8 (560179, SK1) was purchased from BD Pharmingen. Antibodies specific for human NKG2A (FAB1059P, 131411) and Methothelin (FAB32652P, 420411) were purchased from R&D Systems. Antibodies specific for human CTLA-4 (12-1529-42, 14D3) was purchased from eBioscience. Antibody specific for human NKG2C (130-103-636, REA205) was purchased from Miltenyi.  M5 CAR expression was assessed using biotinylated goat anti-human IgG F(ab’)2 (Jackson ImmunoResearch, 109-066-006) followed by streptavidin (FITC or APC) (BioLegend) or using an anti-idiotype antibody provided by Novartis Pharmaceuticals. Live/dead staining was performed using a Live/Dead Fixable Aqua Dead Cell Stain Kit (Life Technologies following manufacturer’s protocol followed by cell surface staining for 20 minutes at room temperature in the dark. Intracellular staining was performed with the Foxp3/Transcription Factor Staining Buffer set (Thermo Fisher) according to the manufacturer’s instructions. Samples were acquired on an LSRII Fortessa Cytometer (BD Bioscience) and analyzed with FlowJo v10 software (FlowJo, LLC). Sorting assays were performed using a FACS Aria Cytometer (BD Bioscience).    TCR libraries were generated using Chromium Single Cell V(D)J Reagent Kits (10x Genomics) according to the manufacturer’s protocol. Briefly, 16,000 CD8+ T cells were sorted by flow cytometry and washed with ice cold PBS + 0.04% BSA. After washing, cells were used to generate single cell gel beads in emulsion. Following reverse transcription, gel beads in emulsion were disrupted and barcoded complementary DNA was isolated and amplified by PCR for 13 cycles. Two uL of post amplified cDNA was used to generate TCR libraries. After fragmentation, end repair and poly A tailing, samples indexes were added and amplified following manufacturer’s protocol.
The libraries were sequenced on an Illumina NextSeq 500 with a 150 cycle kit with parameters Read 1: 26, Read 2: 130, Index 1: 8, Index 2: 0. One RNA library and one TCR library (8:1 ratio) were pooled and sequenced on one flow cell.

treatment_protocol: AsPC-1 cells were routinely seeded in 6-well plates at 1 x 10e6 cells/well the day preceding T cell seeding. M5 CAR T cells (30 - 50% of transduction efficiency) were thawed and rested at 1 x 10e6 cells/ml in T75 flasks with R10 media. After 24 hours, the T cell number (CD45+EpCAM-) was calculated and 2.5 x 10e5 T cells/well were transferred to the AsPC-1 plates. After 3 - 4 days, the cocultures were thoroughly suspended by frequent pipetting and 300 - 400µl of the cell suspension was used for T cell counting assessment and flow cytometry staining. The remaining cell suspension was spun down and the supernatant (conditioned media) was collected and filtered with a 0.45µm filter (Corning). The cells were resuspended in media containing equal amounts of conditioned and fresh R10. The resulting T cell suspension was transferred into AsPC-1-coated plates cells (2.5 x 10e5 T cells/well) for continuous co-culture. This process was repeated for 20-35 days.

tag: donor

tag: antigen exposure

value: Continuous


title: ND538.Day0_Control [scTCR-seq]

value: Control


title: A10-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample29
mRNA expression in microglia

tag: trem2 species

value: hippocampus


title: A10-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample23
mRNA expression in microglia


title: ND150.Day0_Control [scTCR-seq]


title: opto2h-stimH-2

description:
10x genomics, v3.1
opto_umi_counts.csv.gz
opto_metadata.csv.gz

tag: strain

tag: tissue

value: whole olfactory mucosa

tag: age

value: 6-12 weeks


title: 2HA0_1p2h-1


title: 2HA0_1p2h-2


title: 2HA2h-1


title: ACE1p2h-1


title: 4MA2h-1


title: ACE0_1p2h-2


title: ACE1p2h-2


title: 2HA2h-2


title: ACE0_01p2h-1


title: ACE0_1p2h-4


title: 4MA2h-2


title: ACE0_1p2h-1


title: ACE0_01p2h-2


title: 2HA0_01p2h-2


title: ACE0_1p2h-3


title: A10-p2-K1_241_human_TREM2_R47H_het

description:
Sample24
mRNA expression in microglia

tag: p301s status

tag: brain region

tag: Sex


title: transformed H9 cells 3

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

source_name: human transformed embryonic stem cell line

growth_protocol: Cells were growth on matrigel coated plates in MEF conditioned medium supplemented with 8ng/ml bFGF.

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: SSEA3 positive cells were sorted for gene expression analysis

tag: cell type

value: embryonic stem cell line with neoplastic characteristics


title: ND150.Day28_Continuous [scTCR-seq]


title: human induced pluripotent stem cells cord blood derived

description: hCBiPSC

source_name: induced pluripotent stem cell line derived from human cord blood

label_protocol: In accordance with manufacturer's protocols

value: human cord blood derived


title: 2HA0_01p2h-1


title: transformed H9 cells 1


title: opto2h-stimH-1


title: transformed H9 cells 2


title: H9 cells

description: hPSC

source_name: human embryonic stem cell line

value: embryo derived H9 cell line


title: A10-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample21
mRNA expression in microglia

value: human

value: female

tag: gate


title: A10-p1-NTG_232_mouse_Trem2_WT

description:
Sample18
mRNA expression in microglia

value: mouse


title: Hallikar_ Mock control_73

city: Bengaluru

first: Suresh

middle: H

last: Basagoudanavar

state: Karnataka

address: IVRI, Hebbal

department: FMD Research Laboratory

country: India

institute: Indian Veterinary Research Institute

data_processing:
Tophat-2.0.13
DESeq2
Genome_build: ARS UCD 1.2
Supplementary_files_format_and_content: Txt files with raw counts

organism: Bos indicus

source_name: Ventral soft palate

growth_protocol: Cattle calves were experimentally infected with FMDV serotype ‘O’ by intradermolingual inoculation. Ventral soft palate tissue biopsy was collected at 48 hours post infection. Transcript profile from the tissue biopsies  were analysed for differential gene expression.

extract_protocol:
RNA was isolated from tissue samples using RNAeasy kit (Qiagen, USA). The total RNA was used to enrich mRNA using NEB Magnetic mRNA Isolation Kit.
The transcriptome library was prepared using NEB ultraII RNA library prep kit and sequenced using Illumina HiSeq (151 nt, paired-end), technology

treatment_protocol: Experimental infection of 6-9 month old cattle calves with Foot and mouth Disease Virus serotype ‘O’ by intradermolingual inoculation.

tag: breed

value: Hallikar

tag: treatment

value: Uninfected

value: Ventral soft palate

value: Epithelial


title: A10-p1-K1_241_human_TREM2_R47H_het

description:
Sample17
mRNA expression in microglia

value: no

value: microglia


title: A10-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample20
mRNA expression in microglia

value: yes


title: RNAseq1

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

description: total RNA extracted from the same culture of Sample 1

data_processing:
Basecalls performed using CASAVA version 1.5 for Sample 5 (RNAseq1) and version 1.9 for all the other samples.
Adapters removal with cutadapt software version 1.15
Trimming of the reads using Sickle, with a quality threshold of 20 (-q 20). Reads shorter than 21 nucleotides were removed (-l 21)
Reads corresponding to the rRNA sequences are first removed using Bowtie and sequences of ribosomal RNA (rRNA) operons of Legionella pneumophila strain Paris (NC_006368.1). Remaining reads were aligned to the L. pneumophila strain Paris chromosome sequence (NCBI Acc.-No: NC_006368.1) using Bowtie 2 (verson 2.3.4.3) with --local option. BAM files are build, sorted and indexed with the Samtools suite version 1.3.
Reads count with featureCounts programm (from the Subreads package). We used --primary option and stranded counts (option -s 1)
Differential analysis performed with Sartools version 1.3.0 (DESeq2 methods and "median" option to compute size factors).
Genome_build: NC_006368.1
Supplementary_files_format_and_content: columns of this TSV result file are tabular separated. This analysis file contains reads count and normalized reads count (norm. ...) for each sample (column 1 to 17). In column 18 to the end, there are different calculations like fold change, log2 fold change, P-value, adjusted p-value for the comparison between the two conditions (MVseq versus RNAseq).

organism: Legionella pneumophila

source_name: bacterial cells

growth_protocol: Legionella strains were grown in liquid BYE medium until post-exponential phase (OD 4.2).

extract_protocol:
RNA of bacteria cell pellet and purified Lp-MVs were extracted using the miRNeasy®Mini kit (Qiagen). Bacterial RNA was rRNA depleted using the RiboZero rRNA Removal Kit for Gram-negative bacteria (Illumina) and metal‐catalyzed heat‐fragmented to a size around 100–200 nt using the RNA fragmentation kit (Ambion).
TruSeq small RNA library

treatment_protocol: Bacterial cells were harvested by centrifugation at 5.000xg, 4°C for 15 min and pellet was frozen at -80°C for further used as total bacterial control The supernatant was twice passed through a 0.2µm PES membrane Stericup® Quick Release (Millipore) and re-centrifuged for 15min at 15.000xg, 4°C. The supernatant was treated with RNaseA/T1 (Thermo Scientific) at a final concentration of 2µg/ml RNaseA for 1h at 37°C followed by centrifugation at 150.000xg for 2h at 4°C to pellet the MVs. The MV-pellet was washed, re-centrifuged and resuspended in PBS.

value: Paris

tag: growth phase

value: post-exponential growth phase (OD4,2)

tag: sample type

value: bacterial culture


title: R5 Day 16 CAR+ T2 [RNA-seq]

description:
CD8.D16.CAR+.R5.2
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt

data_processing:
Alignment: paired-end data were aligned to human genome assembly GRCh37/hg19 using STAR v2.5.2a with command-line parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Post-processing: SAM files were converted to BAM format using samtools v1.1 (samtools view -bS)
Sorting: BAM files were sorted by position using samtools sort
Pooling of resequenced libraries: for replicate R2, several resequenced libraries were pooled after alignment to enhance coverage. This was accomplished using samtools merge as below:    R2 Control Day 0 CAR+ T1 - 4-Day0-CD8-CARpos_S7 with 16-Day0-CD8-CARpos_S5    R2 Control Day 0 CAR- T1 - 3-Day0-CD8-CARneg_S2 with 15-Day0-CD8-CARneg_S6    R2 Other CAR+ T1 - 21-IS-CD8-CARpos-10-24-2018_S11 with 12-IS-CD8-CARpos_S12 and 24-IS-CD8-CARpos_S10    R2 Continuous CAR+ T1 - 8-CS-CD8-CARpos_S9 with 20-CS-CD8-CARpos_S12    R2 Continuous CAR- T1 - 7-CS-CD8-CARneg_S6 with 19-CS-CD8-CARneg_S3
Tag counts per gene model: HTSeq v0.6.0 was used to count aligned tags over gene features with command-line python -m HTSeq.scripts.count -f bam -r pos -s no -t exon -i gene_id BAM_FILE GTF. The gene model GTF was constructed from RefSeq transcripts and UCSC Genome Browser's annotation of RefSeq transcript IDs to gene symbols.
Library size adjustment and significance testing: for the antigen exposure and time series analysis, DESeq2 was used to adjust library size and estimate significant differences at an FDR of 0.05.    Antigen exposure analysis: the Wald test was used to assess differences between control day 0 samples and continuous exposure samples. For this analysis we considered only CAR+ samples including control day 0, "other," and continuous exposure, with no day 16 time points. "Other" samples were included to adjust dispersions and library sizes but were not used for the contrast.    Time series analysis: the LRT was used to assess differences along the time course from day 0 to day 16 to day 28, with a full model of ~Replicate+Time and a reduced model of ~Replicate. For this analysis we considered only CAR+ samples including control day 0 and continuous exposure, with no "other" exposure.
Additional filtering: for the antigen exposure analysis, we removed genes which register as significantly different but which we expect to be artifacts due to SMART-seq's library construction; such genes fall along the extreme ends of a parabola in a volcano plot of the data. To remove these, we interpolated a line on the plot between IL22 and WDR63 (negative side) and another between ALK and INBHE (positive side). Any gene with a perpendicular < 1 to the lines was removed.
TPM calculation: to contrast CAR+ and CAR- samples, we calculated TPMs for each gene using the bioinfokit.analys module in python. Gene lengths were calculated from the GTF used to run HTSeq, taking the max of all summed exon lengths across multiple isoforms to be the length of each gene.
Genome_build: hg19
Supplementary_files_format_and_content: We include three tables of adjusted count data and two companion tables with DESeq2 significance testing results. For the antigen exposure analysis, we include the DESeq2 adjusted counts and DESeq2 significance results after processing to flag genes we deemed to be artifacts ("Additional filtering" above). For the time series analysis, we include the DESeq2 adjusted counts and DESeq2 significance results. For the CAR+ / CAR- analysis, we include a table of TPMs for all genes.

extract_protocol:
For flow cytometry and sorting assays of CAE, M5 CAR T cells were stained in fluorescence-activated cell sorting (FACS) buffer consisting of PBS (Gibco), 0.5% bovine serum albumin (BSA) (GEMINI), 2 mM EDTA (Invitrogen), and 100ug/ml DNase (Roche). CountBrightTM Absolute Counting Beads, (ThermoFisher) were used as an internal standard according to the manufacturer's instructions to calculate absolute cell counts in cell suspensions.  Antibodies specific for human CD45 (ref 304032, clone HI30), CD3 (317322, OKT3), CD4 (357412, A161A1 / 317440), CD56 (304608, MEM-188), EpCAM (324226/324238, 9C4), CD94 (305520, DX22), KLRB1 (339918, HP-3G10), TIGIT (372716, A15153G), TCR Va24-Ja18 (342922, 6B11), PD-1 (329928, EH12.2H7) were purchased from BioLegend. Antibodies specific for human CD8 (560179, SK1) was purchased from BD Pharmingen. Antibodies specific for human NKG2A (FAB1059P, 131411) and Methothelin (FAB32652P, 420411) were purchased from R&D Systems. Antibodies specific for human CTLA-4 (12-1529-42, 14D3) was purchased from eBioscience. Antibody specific for human NKG2C (130-103-636, REA205) was purchased from Miltenyi.  M5 CAR expression was assessed using biotinylated goat anti-human IgG F(ab’)2 (Jackson ImmunoResearch, 109-066-006) followed by streptavidin (FITC or APC) (BioLegend) or using an anti-idiotype antibody provided by Novartis Pharmaceuticals. Live/dead staining was performed using a Live/Dead Fixable Aqua Dead Cell Stain Kit (Life Technologies following manufacturer’s protocol followed by cell surface staining for 20 minutes at room temperature in the dark. Intracellular staining was performed with the Foxp3/Transcription Factor Staining Buffer set (Thermo Fisher) according to the manufacturer’s instructions. Samples were acquired on an LSRII Fortessa Cytometer (BD Bioscience) and analyzed with FlowJo v10 software (FlowJo, LLC). Sorting assays were performed using a FACS Aria Cytometer (BD Bioscience).    Total RNA was extracted using Qiazol (Qiagen) from 300 cells for day 0, day 16 or day 28 for CD8+ T cells continuously stimulated with antigen (two sorted populations including surface CAR-positive and surface CAR-negative cells). Cells were recovered by RNA Clean and Concentrator spin columns (Zymo), followed by incubation with oligo-dT. The transcription reaction was carried out on 100pg of cDNA for 1min at 55°C.
RNA-seq libraries were made following the previously established SMARTseq2 protocol (Picelli et al., 2014). Libraries were uniquely barcoded (Buenrostro et al., 2013) and amplified for 14 cycles. Fragment size distribution was verified and paired-end sequencing (2 x 75 bp reads) was carried out on an Illumina NextSeq 500.

tag: replicate

tag: car presence

value: Present

value: Continuous

tag: time

value: Day 16


title: opto2h-stimL-1

city: Boston

first: David

last: Brann

address: 220 Longwood Ave

institute: Harvard Medical School

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.

value: whole olfactory mucosa

value: 6-12 weeks


title: opto2h-stimM-2


title: opto2h-stimL-2


title: HepG2_Cdc20 down regulated Rep2

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: 4, Raja S. C. Mullick Road

department: Cancer Biology and Inflammatory Disorder Division

institute: CSIR-Indian Institute of Chemical Biology

description: Cdc20 down regulated  Replicate 2

hyb_protocol: Purified biotin labelled cRNAs were hybridized to the BeadChip using Direct hybridisation Whole-Gene Expression assay, according to the manufacturer's protocol (Illumina Inc., San Diego, CA). Subsequently  washing, blocking, and streptavidin-Cy3 staining were done followed by serial nonstringent washing steps to remove unbound conjugate.

scan_protocol: An Illumina iScan Reader was used to read the Illumina bioarrays and the primary intensity data were acquired in standard file format, using Genome  Studio

data_processing: Raw average signal intensity  was background substracted in Genome Studio and imported to bioconductor Lumi Package for data transformation (Log2 transformed). Robust Spline method was used for normalization. Differential expression was performed in bioconductor package Limma. Up-regulated and down-regulated genes with adjusted p-value < 0.05, and fold change ≥ or ≤ 1.5  were considered for further analysis.

label: Biotin

label_protocol: Isolated mRNA was reverse-transcribed to cDNA followed by labelled cRNA preparation using Illumina® TotalPrep™ RNA Amplification Kit

growth_protocol: HepG2 cell line was  cultured in DMEM medium (Life Technologies, Thermo Fisher Scientific Inc., MA USA) supplemented with 10% fetal calf serum (Life Technologies, Thermo Fisher Scientific Inc., MA USA) .

extract_protocol: The RNA isolation was performed as per Qiagen RNeasy Mini Kit manufacturer’s protocol (Qiagen, Hilden, Germany). Briefly,  cells were lysed in RLT lysis buffer and subsequently mixed with equal volume of 70% ethanol. The mix was then passed through RNeasy Spin column  followed by on column DNase treatment. The  column was subsequently washed with wash buffer and the column-bound RNA were eluted in RNase free water.The quality of the isolated RNA was checked in Agilent Bioanalyzer (Santa Clara).

treatment_protocol: HepG2 cells were transfected either with Flag Tagged Cdc20 (gifted by Dr. Jonathon Pines, Gurdon Institute,Cambridge, UK) or with Cdc20 siRNA (Santa Cruz Biotechnology Santa Cruz, CA, USA) for 48 hr before harvesting

tag: cell line

tag: gender

value: Male

value: 15 years old

value: Liver

value: hepatoma derived cell line

tag: genotype/variation

value: Cdc20 down regulated


title: A1-p2-PS19_246_P301S_mouse_Trem2_WT

city: San Francisco

first: Lay

last: Kodama

address: 1650 Owens St.

institute: University of California San Francisco

description:
Sample16
mRNA expression in microglia

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.

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

tag: trem2 species

value: mouse

value: hippocampus

value: female


title: opto2h-stimM-1

tag: strain

tag: tissue

tag: age


title: human induced pluripotent stem cells fibroblast derived

description: hiPSC

source_name: pluripotent stem cell line derived from human fibroblast

value: human dermal fibroblast derived


title: R5 Day 16 CAR+ T1 [RNA-seq]

description:
CD8.D16.CAR+.R5.1
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt

tag: antigen exposure


title: HepG2_Cdc20 down regulated Rep1

description: Cdc20 down regulated  Replicate 1

tag: cell type


title: A10-p1-NTG_233_mouse_Trem2_WT

description:
Sample19
mRNA expression in microglia

value: human

tag: p301s status

value: no

tag: brain region

tag: Sex

tag: gate

value: microglia


title: Hallikar_ Mock control_71

tag: breed

value: Hallikar

tag: treatment

value: Uninfected

value: Ventral soft palate

value: Epithelial


title: Hallikar_ Infected_69

value: FMDV infected


title: opto-cage-2

value: whole olfactory mucosa

value: 6-12 weeks


title: A1-p2-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample14
mRNA expression in microglia

value: yes


title: R5 Continuous CAR- T2 [RNA-seq]

description:
CD8.CS.CAR-.R5.2
TPMs_-_Presence.txt

tag: replicate

tag: car presence

value: Absent

value: Continuous

value: Day 28


title: opto2h-ctrl-1


title: A10-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample22
mRNA expression in microglia

value: mouse

value: hippocampus


title: HepG2_Cdc20 Over expressed Rep1

description: Cdc20 overexpressed  Replicate 1

tag: cell line

value: Male

value: 15 years old

value: Liver

value: hepatoma derived cell line

value: Cdc20 overexpressed


title: HepG2_Cdc20 Over expressed Rep2

description: Cdc20 overexpressed  Replicate 2

tag: gender


title: A1-p2-NTG_233_mouse_Trem2_WT

description:
Sample12
mRNA expression in microglia

value: human

value: no

value: female

value: microglia


title: opto-cage-1

value: whole olfactory mucosa


title: opto2h-ctrl-2

value: 6-12 weeks


title: A1-p2-NTG_232_mouse_Trem2_WT

description:
Sample11
mRNA expression in microglia


title: opto12h-stimM-1


title: A1-p2-PS19_245_P301S_mouse_Trem2_WT

description:
Sample15
mRNA expression in microglia

value: yes


title: HepG2_Control Rep1

description: Control Replicate 1

tag: genotype/variation

value: Control


title: R5 Other CAR+ T1 [RNA-seq]

description:
CD8.IS.CAR+.R5.1
Adjusted_Counts_-_Exposure.txt
DESeq2_Results_-_Exposure.txt

value: Present

value: Other

tag: time


title: A1-p1-PS19_246_P301S_mouse_Trem2_WT

description:
Sample8
mRNA expression in microglia

tag: trem2 species

value: mouse


title: HepG2_Control Rep2

description: Control Replicate 2

tag: tissue


title: Malnad Gidda_ Infected_101

value: Malnad Gidda

value: FMDV infected

value: Ventral soft palate

value: Epithelial


title: opto12h-stimM-PI

tag: strain

tag: age


title: R5 Continuous CAR+ T2 [RNA-seq]

description:
CD8.CS.CAR+.R5.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt

tag: antigen exposure

value: Continuous

value: Day 28


title: Malnad Gidda_ Mock control_99

value: Uninfected

tag: cell type


title: opto12h-stimM-2


title: A1-p1-PS19_245_P301S_mouse_Trem2_WT

description:
Sample7
mRNA expression in microglia

tag: p301s status

tag: brain region

value: hippocampus


title: R5 Continuous CAR- T1 [RNA-seq]

description:
CD8.CS.CAR-.R5.1
TPMs_-_Presence.txt

value: Absent


title: A1-p2-K1_241_human_TREM2_R47H_het

description:
Sample9
mRNA expression in microglia

value: human

value: no

tag: Sex

value: female

tag: gate

value: microglia


title: R5 Continuous CAR+ T1 [RNA-seq]

description:
CD8.CS.CAR+.R5.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: Malnad Gidda_ Mock control_96

tag: breed

tag: treatment


title: A1-p2-K1_243_human_TREM2_R47H_het

description:
Sample10
mRNA expression in microglia


title: opto12h-ctrl-2

value: whole olfactory mucosa

value: 6-12 weeks


title: Arrb2KO-1ON-2

description:
10x genomics, v3.1
Arrb2KO_umi_counts.csv.gz
Arrb2KO_metadata.csv.gz


title: R5 Control Day 0 CAR- T1 [RNA-seq]

description:
CD8.D0.CAR-.R5.1
TPMs_-_Presence.txt

tag: replicate

tag: car presence

value: Control

value: Day 0


title: Malnad Gidda_ Infected_100

value: Malnad Gidda


title: Hallikar_ Infected_68

value: Hallikar

value: FMDV infected


title: HEC108_ki91_postIP

city: Suita

first: Atsushi

last: Kumanogoh

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka University

data_processing:
The adapter sequence was trimmed by trim_galore. Remaining trimmed reads were aligned to the human genome hg19 by tophat (v.2.1.1). The m6A-enriched peaks were detected by the MetPeak R package (v1.0.0) with default parameters as previously described (DOI: 10.1093/bioinformatics/btw281).
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were created by MetPeak.

source_name: endometrial cancer cell

growth_protocol: The cells were cultured in Dulbecco's modified Eagle medium containing 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco). The cells were maintained at 37°C under a humidified atmosphere containing 5% CO2.

extract_protocol:
MeRIP-Seq was conducted as described previously (DOI: 10.1038/s41593-018-0173-6; 10.1016/j.cell.2012.05.003.) with some modifications. Briefly, total RNA was extracted with QIAZol Lysis Reagent (79306; QIAGEN) and purified using GenElute™ mRNA Miniprep Kits (MRN70, Sigma) twice. The recovered poly(A) RNA was fragmented with NEBNext Magnesium RNA Fragmentation Module (E6150S, NEB) with an incubation time of 11 min. Twenty micrograms of the fragmented RNA was incubated with 10 μg of anti-m6A antibody (202203, Synaptic Systems).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: genotype

tag: rip antibody

value: 202203, Synaptic Systems


title: A1-p2-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample13
mRNA expression in microglia

tag: trem2 species

value: yes


title: Arrb2KO-1ON-1

tag: tissue


title: opto12h-ctrl-1

tag: strain


title: R5 Control Day 0 CAR- T2 [RNA-seq]

description:
CD8.D0.CAR-.R5.2
TPMs_-_Presence.txt

tag: time


title: A1-p1-PS19K1_267_P301S_human_TREM2_R47H_het

description:
Sample6
mRNA expression in microglia


title: Arrb2KO-cage-2

tag: age


title: A1-p1-PS19K1_248_P301S_human_TREM2_R47H_het

description:
Sample5
mRNA expression in microglia

tag: cell type


title: R4 Continuous CAR- T2 [RNA-seq]

description:
CD8.CS.CAR-.R4.2
TPMs_-_Presence.txt

tag: antigen exposure

value: Continuous

value: Day 28


title: Arrb2KO-envA5d-2


title: R4 Day 16 CAR+ T2 [RNA-seq]

description:
CD8.D16.CAR+.R4.2
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt

value: Present

value: Day 16


title: R5 Control Day 0 CAR+ T2 [RNA-seq]

description:
CD8.D0.CAR+.R5.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: Malnad Gidda_Infected_98

value: Ventral soft palate

value: Epithelial


title: A1-p1-NTG_233_mouse_Trem2_WT

description:
Sample4
mRNA expression in microglia

value: human

tag: p301s status

value: no

tag: brain region

value: hippocampus

value: female


title: HEC108_ki64_preIP


title: Arrb2KO-cage-1

value: whole olfactory mucosa

value: 6-12 weeks