title: A375_TADA2Bsg_CRISPRKO_day7_DMSO_rep2

description:
Library name: Sample 20
htseq_count_CRISPRKO.txt


title: A375_TADA2Bsg_CRISPRKO_day7_Vemu_rep3

status: Public on Apr 29 2026

type: SRA

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

country: USA

institute: Van Andel Institute

description:
Library name: Sample 24
htseq_count_CRISPRKO.txt

library_source: genomic

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq
Fastq files were trimed to 19bp (Epic) or 20bp (CRISPRa/CRISPRKO)
Trimmed reads were mapped to corresponding library built genomes by HISAT2
Guide RNA reads count tables were generated by HTSeq
Assembly: The full library sequence will be provided as a supplementary table in the associated manuscript
Supplementary files format and content: text files includes raw reads count
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The A375 cell line was purchased from ATCC and cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Genomic DNA was extracted using a phenol–chloroform method.
sgRNA sequences were amplified from the lentivirally integrated DNA using known universal primer sequences and prepared for sequencing through two sequential rounds of PCR.

treatment_protocol: A375 cells transduced with a whole-genome knockout library were treated with DMSO or vemurafenib (2 μM). A375 cells transduced with a homemade epigenetic library or a whole-genome activation library were treated with DMSO or vemurafenib (1 μM). Cells were split every 2–3 days.

tag: cell line

tag: cell type

value: Melanoma cell line

tag: genotype

value: TADA2B KO

tag: treatment

value: 2 uM Vemurafenib


title: ATACseq_Microglia_CD229PositiveCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep3_BC22_R2

city: Québec

first: David

last: Gosselin

state: Quebec

address: CRCHUL - 2705 Boulevard Laurier, Bloc T - 2-34

department: Molecular Medicine

country: Canada

institute: Université Laval

description:
Library name: Sample_20
R2 file used for alignment and analysis
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_Trem2KO_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt

data_processing:
Alignment: FASTQ files from sequencing experiments were mapped to the mouse mm10 reference genome. Bowtie2 (2.3.4.1) with default parameters was used to map ATAC-seq. HOMER was used to convert aligned reads into “tag directories” for further analyses.
Sequencing data analysis preprocessing Only R1 sequencing files were used for alignment and analyses, except for two ATAC-seq files for Trem2-/- CPZ 4 weeks CD229-CD11c- and CD229+CD11c- subsets – replicates 3 for which R2 files were used. For PE 150 sequencing files, 50 bp were first trimmed off the 3’ end of R1 (or R2) reads using fastp (fastp-0.20.0; command -t 50). Adapters were also removed off 5’ end of all R1 (or R2) reads using fastp in default mode. Then, R1 reads FASTQ sequencing files were mapped to the mouse GRCm38 - mm10 reference genome using Bowtie2 (2.3.4.1) with default parameters. HOMER was used to convert aligned reads into “tag directories” for further analyses.
ATAC-seq – Differential analyses Regions with accessible chromatin for each sample were first identified using their tag directory, using HOMER’s findPeaks.pl program with the -style factor parameter. For group comparison, a table of genomic coordinates containing all the regions identified across the relevant sample replicates was generated using HOMERS’s mergePeaks.pl program, with -size given parameter. Then, the regions from the mergePeak file were annotated with sequencing tags from ATAC-seq tag directories from relevant sample replicates using HOMER’s annotatePeak.pl program with mm10 -noadj parameters. Then, regions with differential chromatin accessibility were identified using HOMER’s getDiffExpression.pl program, which leveraged R/DESeq2 to assess differential enrichment with the following parameters: -AvsA -log2fold 0 -fdr 0.05 -simpleNorm. The resulting file is a read count normalized to 10 million total reads and with differential enrichment results. For data interpretation and plotting, differentially enriched distal CREs, defined as beyond 1000 bp upstream and 500 bp downstream of a TSS, with a LFC of 1 and at least 16 normalized reads were considered.
ATAC-seq data visualization: the UCSC genome browser was used to visualize ATAC-seq sequencing data. Bedgraph.gz files were generated using HOMER?s makeUCSCfile.pl.
Assembly: mm10
Supplementary files format and content: *R1.txt or *R2.txt: Tab-delimited text files of ATAC-seq peak coordinates, identified in associated microglia subset
Supplementary files format and content: *_RawData.txt: Tab-delimited text files of raw read counts at ATAC-seq peaks for associated conditions

organism: Mus musculus

extract_protocol:
Mice were euthanized with an overdose of ketamine-xylazine solution (90 ml/kg & 10 ml/kg) injected intraperitoneally and subsequently perfused transcardially with ice-cold 0.9% NaCl saline solution (Sigma-Aldrich, S5886-1K6). Brains were extracted and placed in ice-cold base buffer (BB) solution (HBSS 1X (Life Technologies, 14175-095), 1% BSA (Sigma-Aldrich, A9647), 1mM EDTA (Thermo Fisher Scientific, 15575020), 1 mM sodium butyrate (Sigma-Aldrich, B5887), 1 mM Flavoperidol (Sigma-Aldrich, F3055))35. For flow cytometry, brains were cut into smaller pieces in BB solution before adding Accutase solution (Sigma-Aldrich, A6964) to enzymatically dissociate the brain. After 1 hour of incubation, brains were further homogenized on ice using a cut P1000 tip, then an uncut tip and finally a P200 tip. For FACS, brains from 2-6 mice were from same conditions were pooled and homogenized in BB solution by gentle mechanical dissociation on ice using a 7 ml polytetrafluoroethylene pestle (Duran Wheaton Kimble, 357542) and filtered through a 100 µm cell strainer (ThermoFisher 22-363-549).  Following brain homogenization, homogenates were resuspended in 37% Percoll (Thermo Fisher Scientific (Cytivia) 17089101; 8 ml/brain, in 15 ml tubes (1 tube/brain), which were then centrifuged at 600 x g for 20 min at 20°C, with medium acceleration and no deceleration. Pellets were then recovered and washed once in with BB solution, centrifuged at 300 RCF at 4°C for 7 min, resuspended in 4 ml HBSS 1X and then centrifuged at 300 RCF at 4°C for 7 min to remove proteins. Cells were resuspended in 100 µl HBSS1x and incubated on ice in the dark for 10 min with 1:100 anti-CD16/CD32 receptor unconjugated antibody (BioLegend 101302, clone 93). Then, cells were incubated on ice in the dark for 10 min with 1:1000 Live/Dead yellow stain (Thermo Fisher Scientific L34959) and conjugated antibodies directed against cell surface proteins: 1:167 anti-Ace-Alexa 750 (R&D Systems FAB15131S, clone 230214), 1:100 anti-CD11b-Brilliant Violet 421 (BioLegend 101251, clone M1/70), 1:100 anti-CD44-APC/Cy7 (BioLegend 103027, clone IM7), 1:200 anti-CD45-BB700 (BD Biosciences 566439, clone 30-F11), 1:100 anti-CD229-Alexa 647 (BD Biosciences 566689, clone Ly9.7.144), 1:133 anti-CD11c-PE (BioLegend 117308, clone N418) and 1:100 anti-Clec7a-PE/Cy7 (Thermo Fisher Scientific 25-5859-80, clone bg1fpj). After incubation, cells were washed in HBSS1x and centrifuged at 300 RCF at 4°C for 7 min. Then, cell pellets were either 1) resuspended in BB and filtered through a 35 µm cell strainer and sorted for RNA-seq and ATAC samples, or 2) underwent cross-linking for ChIP-seq samples. For cross-linking, cell pellets were resuspended in HBSS 1x and fixed with 1% PFA at RT in the dark for 10 min, after which 1/20th volume of 2.625 M glycine (Thermo Fisher Scientific BP381-500) was added for quenching for 10 min. Cells were washed in BB, centrifuged at 1000 RCF at 4°C for 10 min and filtered through a 35 µm cell strainer using BB and then sorted. Flow cytometry data was acquired with a BD FACSymphonyA1 instrument. Data was analyzed with FlowJo (v10.10.0). Microglia were sorted with BD FACSAria Fusion instrument (100 µm nozzle).
Assay for Transposase-Accessible Chromatin-sequencing (ATAC-seq) Immediately after sorting, aliquot of 80,000 microglia were centrifuged (350 RCF at 4°C for 10 min) and cell pellets were lysed in 50 µl lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in molecular grade water) on ice and nuclei were pelleted by centrifugation at 500 RCF for 10 min. Nuclei were then gently resuspended on ice in 50 µl transposase reaction mix (1x Tagment DNA buffer (Illumina 15027866), 2.5 µl Tagment DNA enzyme I (Illumina 15027865), in molecular grade water) and incubated at 37C for 30 min on a PCR cycler. DNA was then purified with Zymo ChIP DNA concentrator columns (Zymo Research D5205) and eluted with 10 µl of elution buffer. DNA was then amplified with PCR mix (1.25 µM for each of i5- and i7-indexed primers, from Mezger et al 2018, 0.6x SYBR Green I (Thermo Fisher Scientific S7563), 1x NEBNext High-Fidelity 2x PCR MasterMix, (NEB M0541)) for 9 cycles, run on gel for size selection of fragments (160-280 bp) as detailed above, and paired-end sequenced for 100 or 150 cycles on an Illumina NovaSeq X Plus or NovaSeq 6000 (Illumina, San Diego, CA) according to manufacturer’s instruction.  Illumina sequencing Sequencing for ATAC-seq samples was performed on NovaSeq X Plus at the IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA, or NovaSeq 6000 at The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children, Toronto, ON, Canada.

tag: strain

tag: developmental stage

value: Adult

value: 0.2% Cuprizone diet for 4 weeks prior sacrifice


title: ATACseq_Microglia_CD229NegativeCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep3_BC25_R2

description:
Library name: Sample_17
R2 file used for alignment and analysis
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_Trem2KO_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_Cx3cr1Cre_Male_Adult_Basal_rep2_BC12_R1

description:
Library name: Sample_22
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_SamplesAnnotated_RawData.txt

value: None; Regular diet


title: A375_TADA2Bsg_CRISPRKO_day0_rep2

description:
Library name: Sample 17
htseq_count_CRISPRKO.txt


title: A375_TADA2Bsg_CRISPRKO_day0_rep1

description:
Library name: Sample 16
htseq_count_CRISPRKO.txt


title: ATACseq_Microglia_CD229PositiveCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep1_BC8_R1

description:
Library name: Sample_18
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_Trem2KO_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229NegativeCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep2_BC6_R1

description:
Library name: Sample_16
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_Trem2KO_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229NegativeCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep1_BC7_R1

description:
Library name: Sample_15
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_Trem2KO_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day8_DMSO_rep2

description:
Library name: Sample 11
htseq_count_epic.txt

value: WT

value: DMSO


title: ATACseq_Microglia_Trem2KO_Male_Adult_Basal_rep1_BC1_R1

description:
Library name: Sample_13
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_Trem2KO_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day8_DMSO_rep3

description:
Library name: Sample 12
htseq_count_epic.txt


title: ATACseq_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep3_BC3_R1

description:
Library name: Sample_12
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day14_DMSO_rep3

description:
Library name: Sample 6
htseq_count_epic.txt


title: ATACseq_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep2_BC11_R1

description:
Library name: Sample_11
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day8_DMSO_rep1

description:
Library name: Sample 10
htseq_count_epic.txt


title: ATACseq_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC10_R1

description:
Library name: Sample_8
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC2_R1

description:
Library name: Sample_9
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day14_Vemu_rep3

description:
Library name: Sample 9
htseq_count_epic.txt

value: 1 uM Vemurafenib


title: ATACseq_Microglia_Trem2KO_Male_Adult_Basal_rep2_BC20_R1

description:
Library name: Sample_14
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_Trem2KO_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day8_Vemu_rep1

description:
Library name: Sample 13
htseq_count_epic.txt


title: A375_Epic_day14_Vemu_rep2

description:
Library name: Sample 8
htseq_count_epic.txt


title: ATACseq_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC12_R1

description:
Library name: Sample_7
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep1_BC8_R1

description:
Library name: Sample_10
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day0_rep3

description:
Library name: Sample 3
htseq_count_epic.txt


title: A375_Epic_day14_Vemu_rep1

description:
Library name: Sample 7
htseq_count_epic.txt


title: A375_Epic_day0_rep1

description:
Library name: Sample 1
htseq_count_epic.txt


title: A375_Epic_day14_DMSO_rep1

description:
Library name: Sample 4
htseq_count_epic.txt


title: ATACseq_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC17_R1

description:
Library name: Sample_5
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC1_R1

description:
Library name: Sample_6
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_Epic_day0_rep2

description:
Library name: Sample 2
htseq_count_epic.txt


title: ATACseq_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC5_R1

description:
Library name: Sample_4
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_WT_Male_Adult_Basal_rep3_BC24_R1

description:
Library name: Sample_3
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_GCN5PCAFsg_DMSO_rep2

description: Library name: Sample 10

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig file, ChIP density profiles for genome browser.

extract_protocol:
DNA was extracted by ATAC-Seq Kit (Active Motif, Cat. 53150).
Libraries were constructed using Illumina standard protocols.

treatment_protocol: Non-targeting control cells, TADA2B KO cells, or GCN5 PCAF double KO cells were treated with DMSO or vemurafenib (1 μM) for 24h.

value: GCN5 PCAF double KO


title: ATACseq_Microglia_WT_Male_Adult_Basal_rep2_BC6_R1

description:
Library name: Sample_2
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: A375_GCN5PCAFsg_Vemu_rep2

description: Library name: Sample 12


title: A375_Epic_day14_DMSO_rep2

description:
Library name: Sample 5
htseq_count_epic.txt


title: A375_GCN5PCAFsg_Vemu_rep1

description: Library name: Sample 11


title: ATACseq_Microglia_WT_Male_Adult_Basal_rep1_BC23_R1

description:
Library name: Sample_1
Peaks_ATACseq_Microglia_WT_Adult_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
Peaks_ATACseq_Microglia_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt


title: RNA_dUTP_Microglia_Whole_Cx3cr1Egr2KO_Male_Adult_Cuprizone_5w_rep1_BC153_R1

description:
Library name: Sample_80
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_TPMnormalization.txt

library_source: transcriptomic

data_processing:
Sequencing data analysis preprocessing For all PE 150 sequencing files, 50 bp were first trimmed off the 3’ end of R1 reads using fastp (fastp-0.20.0; command -t 50). R1 reads FASTQ sequencing files were mapped to the mouse mm10 reference genome. STAR (2.7.0f) with default parameters was used to align RNA-seq experiments to the GRCm38 -mm10 mouse genome. HOMER was used to convert aligned reads into “tag directories” for further analyses.
RNA-seq – Differential analysis For differential expression analyses, a table read count including relevant group replicates was first created using the analyzeRepeats.pl program of HOMER (v4.11; http://homer.ucsd.edu/homer/) with the following parameters: rna -noadj -condenseGenes -count exons -pc 3. The resulting read count dataset was used to produce input files for pairwise comparisons using R package DESeq2. A Wald test was performed with DESeq2 to identify differentially enriched transcripts between groups of interest, using the following parameters: lfcThreshold = 0, alpha = 0.05. For data plotting and interpretation purposes and functional enrichment analyses with Metascape, only protein-coding mRNAs that have a Transcript Per Million (TPM)-normalized value of 16 or greater in at least one condition were retained. The base-2 logarithm of the TPM values was taken after adding a pseudocount of 1 TPM to each transcript. TPM datasets were generated using HOMER’s analyzeRepeats.pl program with parameters rna -condenseGenes -count exons -pc 3 -tpm.
RNA-seq data visualization: The UCSC genome browser was used to visualize RNA-seq. Bedgraph.gz files were generated using HOMER's makeUCSCfile.pl; -strand parameter was specified for RNA-seq files.
Assembly: mm10
Supplementary files format and content: *_RawData.txt; abundance measurements; raw counts for all samples (*_1, *_2, *_3, etc are biological replicates)
Supplementary files format and content: *_TPMnormalization.txt; abundance measurements; Transcript per million normalization (*_1, *_2, *_3, etc are biological replicates)

molecule: polyA RNA

extract_protocol:
Mice were euthanized with an overdose of ketamine-xylazine solution (90 ml/kg & 10 ml/kg) injected intraperitoneally and subsequently perfused transcardially with ice-cold 0.9% NaCl saline solution (Sigma-Aldrich, S5886-1K6). Brains were extracted and placed in ice-cold base buffer (BB) solution (HBSS 1X (Life Technologies, 14175-095), 1% BSA (Sigma-Aldrich, A9647), 1mM EDTA (Thermo Fisher Scientific, 15575020), 1 mM sodium butyrate (Sigma-Aldrich, B5887), 1 mM Flavoperidol (Sigma-Aldrich, F3055))35. For flow cytometry, brains were cut into smaller pieces in BB solution before adding Accutase solution (Sigma-Aldrich, A6964) to enzymatically dissociate the brain. After 1 hour of incubation, brains were further homogenized on ice using a cut P1000 tip, then an uncut tip and finally a P200 tip. For FACS, brains from 2-6 mice were from same conditions were pooled and homogenized in BB solution by gentle mechanical dissociation on ice using a 7 ml polytetrafluoroethylene pestle (Duran Wheaton Kimble, 357542) and filtered through a 100 µm cell strainer (ThermoFisher 22-363-549).  Following brain homogenization, homogenates were resuspended in 37% Percoll (Thermo Fisher Scientific (Cytivia) 17089101; 8 ml/brain, in 15 ml tubes (1 tube/brain), which were then centrifuged at 600 x g for 20 min at 20°C, with medium acceleration and no deceleration. Pellets were then recovered and washed once in with BB solution, centrifuged at 300 RCF at 4°C for 7 min, resuspended in 4 ml HBSS 1X and then centrifuged at 300 RCF at 4°C for 7 min to remove proteins. Cells were resuspended in 100 µl HBSS1x and incubated on ice in the dark for 10 min with 1:100 anti-CD16/CD32 receptor unconjugated antibody (BioLegend 101302, clone 93). Then, cells were incubated on ice in the dark for 10 min with 1:1000 Live/Dead yellow stain (Thermo Fisher Scientific L34959) and conjugated antibodies directed against cell surface proteins: 1:167 anti-Ace-Alexa 750 (R&D Systems FAB15131S, clone 230214), 1:100 anti-CD11b-Brilliant Violet 421 (BioLegend 101251, clone M1/70), 1:100 anti-CD44-APC/Cy7 (BioLegend 103027, clone IM7), 1:200 anti-CD45-BB700 (BD Biosciences 566439, clone 30-F11), 1:100 anti-CD229-Alexa 647 (BD Biosciences 566689, clone Ly9.7.144), 1:133 anti-CD11c-PE (BioLegend 117308, clone N418) and 1:100 anti-Clec7a-PE/Cy7 (Thermo Fisher Scientific 25-5859-80, clone bg1fpj). After incubation, cells were washed in HBSS1x and centrifuged at 300 RCF at 4°C for 7 min. Then, cell pellets were either 1) resuspended in BB and filtered through a 35 µm cell strainer and sorted for RNA-seq and ATAC samples, or 2) underwent cross-linking for ChIP-seq samples. For cross-linking, cell pellets were resuspended in HBSS 1x and fixed with 1% PFA at RT in the dark for 10 min, after which 1/20th volume of 2.625 M glycine (Thermo Fisher Scientific BP381-500) was added for quenching for 10 min. Cells were washed in BB, centrifuged at 1000 RCF at 4°C for 10 min and filtered through a 35 µm cell strainer using BB and then sorted. Flow cytometry data was acquired with a BD FACSymphonyA1 instrument. Data was analyzed with FlowJo (v10.10.0). Microglia were sorted with BD FACSAria Fusion instrument (100 µm nozzle).
RNA-seq library preparation: Isolation and fragmentation of poly(A) and cDNA synthesis RNA-seq library preparation was performed similarly as previously described. Following sorting, 100,000 to 200,000 microglia were centrifuged (350 RCF at 4°C for 10 min), and resuspended into 100 µl lysis/Oligo d(T) Magnetic Beads binding buffer (Thermo Fisher Scientific A33562, or 100 mM Tris-HCl pH 7.5, 500 mM LiCl, 10 mM EDTA pH 8.0, 1% LiDS, 5 mM DTT, in molecular grade water) and stored at -80°C until processing. For isolation and enrichment of polyA mRNA, samples were thawed at RT and incubated with 20 µl Oligo d(T) Magnetic Beads (NEB S1419S) as follows: 2 min at 65°C on a PCR cycler and then 10 min at room temperature (RT). Samples were then placed on a collection magnet at RT and washed serially with 180 µl of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in molecular grade water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in molecular grade water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 µl of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by incubation at 80°C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.  A second round of poly(A) RNA selection was then performed. Eluted Oligo d(T) beads were first washed on a magnet with 150 µl EB and then 150 µl 2X Oligo d(T) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100, in molecular grade water) and resuspended in 50 µl of 2x DTBB. Resuspended Oligo d(T) beads were then added to isolated RNA and incubated at 65°C and at RT as described above. Beads were then placed on a magnet and washed once with 180 µl of RNA-WB1, then once with 180 µl of RNA-WB3, and then resuspended in 30 µl of 1x First-Strand buffer (made from 5x stock Thermo Fisher Scientific 18080-044 with molecular grade water) transferred in a new PCR strip. Beads were collected on a magnet and resuspended in 10 µl of 2x SuperScript III buffer (made from 5x stock Thermo Fisher Scientific 18080-044 supplemented with 10 mM DTT, in molecular grade water). Resuspended beads were then incubated at 94°C for 9 min to fragment poly(A) RNA. Beads were then placed back on a magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  Collected poly(A) mRNA in 2X SuperScript III buffer was then incubated for 1 min at 50°C on a PCR cycler with 2.5 µl of the following mix: 1.5 µg Random Primer (Thermo Fisher Scientific 48190-011), 10 µM Oligo d(T)20 primer (Thermo Fisher Scientific 18418020), 10 units SUPERase•In RNase Inhibitor (Thermo Fisher Scientific A32694), 4.0 mM dNTP mix (Thermo Fisher Scientific 18427088). Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25°C for 10 min and 50°C for 50 min on a PCR cycler with 7.6 µl of the following mix: 0.2 µg actinomycin D (Sigma-Aldrich A1410; stock at 2 µg/µl in DMSO), 13.15 mM DTT (Thermo Fisher Scientific 361045836), 0.026% Tween-20 (from 10% stock Enzo 80-1929, in molecular grade water), 100 units SuperScript III Reverse Transcriptase (Thermo Fisher Scientific 18080-044), in molecular grade water. After incubation, RNA/DNA complexes were isolated by adding 36 µl of RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on a magnet and beads were washed twice with 150 µl of 75% EtOH. Following washings, beads were air-dried at RT for 6-10 min and eluted with 10 µl of water.  Second-strand synthesis was then performed. RNA/DNA samples, in 10 µl of water, were incubated for 2.5 hours at 16°C with 5 µl of the following mix: 3x NEB Buffer 2 (10x stock New England Biolabs B7002S), 1.0 µl PCR mix (stock of 10 mM solution for each dATP, dCTP, dGTP, and dUTP from Thermo Fisher Scientific, in molecular grade water), 2.0 mM dUTP (Thermo Fisher Scientific, R0133), 1 unit RNAse H (Enzymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in molecular grade water). DNA was then purified by addition of 1.5 µl Sera-Mag SpeedBeads Carboxyl Magnetic Beads (Thermo Fisher Scientific (Cytivia) 45152105050250), resuspended in 30 µl 20% PEG 8000/2.5 M NaCl (PEG 8000 from Sigma-Aldrich P2139; 5M NaCl from Thermo Fisher Scientific AM9759), incubated at RT for 15 min and placed on a magnet for two rounds of bead washing with 80% EtOH. Beads were then air dried for 6-10 min and DNA was eluted from the beads by adding 40 µl of water. Supernatant was then collected on a magnet and placed on ice or stored at -20°C until DNA blunting, poly(A)-tailing, and adapter ligation (see below).  RNA-seq final library preparation Sequencing libraries were prepared from generated cDNA by blunting, A-tailing, and adapter ligation using barcoded adapters (NEXTflex Unique Dual Index Barcodes (Set B)(Bioo Scientific NOVA-514151), as described in Gosselin et al. 2014. Libraries were PCR-amplified for 14 cycles and size selected for fragments (200-400 bp for ChIP-seq) by gel extraction (10% TBE gels, Thermo Fisher Scientific Technologies EC62752BOX).  RNA-seq libraries were paired-end sequenced for 100 or 150 cycles on an Illumina NovaSeq X Plus or NovaSeq 6000 (Illumina, San Diego, CA) according to manufacturer’s instruction.  Illumina sequencing Sequencing for RNA-seq samples was performed on NovaSeq X Plus at the IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA, or NovaSeq 6000 at The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children, Toronto, ON, Canada.

value: 0.2% Cuprizone diet for 5 weeks prior sacrifice


title: RNA_dUTP_Microglia_Whole_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep1_BC152_R1

description:
Library name: Sample_78
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_TPMnormalization.txt


title: A375_GCN5PCAFsg_DMSO_rep1

description: Library name: Sample 9


title: RNA_dUTP_Microglia_Whole_Cx3cr1Egr2KO_Male_Adult_Cuprizone_5w_rep2_BC141_R1

description:
Library name: Sample_81
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_Whole_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep2_BC140_R1

description:
Library name: Sample_79
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_WholePopulation_Cuprizone5w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg_Vemu_rep2

description: Library name: Sample 8


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep3_BC127_PE150_R1

description:
Library name: Sample_77
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt

value: 0.2% Cuprizone diet for 6 weeks prior sacrifice


title: A375_TADA2Bsg_Vemu_rep1

description: Library name: Sample 7


title: A375_TADA2Bsg_DMSO_rep2

description: Library name: Sample 6


title: A375_TADA2Bsg_DMSO_rep1

description: Library name: Sample 5


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep3_BC126_PE150_R1

description:
Library name: Sample_74
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep1_BC111_R1

description:
Library name: Sample_75
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep2_BC124_PE150_R1

description:
Library name: Sample_76
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep2_BC121_PE150_R1

description:
Library name: Sample_70
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_DSG_Vemu_HA-TADA2B_rep3

description: Library name: Sample 39

extract_protocol:
Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).
Libraries were constructed using Illumina standard protocols.

treatment_protocol: A375 control cells or KO cells were treated with DMSO or vemurafenib (1 μM) for 24h.


title: A375_DSG_Vemu_HA-TADA2B_rep2

description: Library name: Sample 38


title: A375_Ctrl_DMSO_rep2

description: Library name: Sample 2


title: A375_Ctrl_Vemu_rep2

description: Library name: Sample 4


title: A375_Ctrl_Vemu_rep1

description: Library name: Sample 3


title: A375_DSG_DMSO_HA-TADA2B_rep2

description: Library name: Sample 35


title: A375_DSG_DMSO_HA-TADA2B_rep1

description: Library name: Sample 34


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep1_BC109_R1

description:
Library name: Sample_69
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep1_BC110_R1

description:
Library name: Sample_72
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep2_BC123_PE150_R1

description:
Library name: Sample_73
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Cx3cr1Egr2KO_Male_Adult_Cuprizone_6w_rep3_BC125_PE150_R1

description:
Library name: Sample_71
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_Ctrl_DMSO_rep1

description: Library name: Sample 1


title: A375_DSG_Vemu_HA-TADA2B_rep1

description: Library name: Sample 37


title: A375_DSG_DMSO_HA-TADA2B_rep3

description: Library name: Sample 36


title: A375_DSG_TADA2Bsg2_GCN5_rep2

description: Library name: Sample 31


title: RNA_dUTP_Microglia_Cx3cr1Egr2KO_Male_Adult_Basal_rep1_BC139_PE150_R1

description:
Library name: Sample_67
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep1_BC106_R1

description:
Library name: Sample_61
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Cx3cr1Egr2KO_Male_Adult_Basal_rep2_BC107_PE150_R1

description:
Library name: Sample_68
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep3_BC131_PE150_R1

description:
Library name: Sample_63
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_DSG_GFPsg_GCN5_rep3

description: Library name: Sample 29


title: A375_DSG_TADA2Bsg2_GCN5_rep3

description: Library name: Sample 32


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep3_BC135_PE150_R1

description:
Library name: Sample_66
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep2_BC119_PE150_R1

description:
Library name: Sample_65
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_DSG_GFPsg_GCN5_rep2

description: Library name: Sample 28


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep2_BC116_PE150_R1

description:
Library name: Sample_62
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_DSG_TADA2Bsg2_GCN5_rep1

description: Library name: Sample 30


title: A375_DSG_EV

description: Library name: Sample 33


title: A375_DSG_input

description: Library name: Sample 26


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep1_BC105_R1

description:
Library name: Sample_58
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep3_BC130_PE150_R1

description:
Library name: Sample_60
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep1_BC146_R1

description:
Library name: Sample_55
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_GCN5PCAFsg_Vemu_H3K9ac_rep2

description: Library name: Sample 24


title: A375_GCN5PCAFsg_Vemu_H3K9ac_rep3

description: Library name: Sample 25


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep2_BC115_PE150_R1

description:
Library name: Sample_59
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_GCN5PCAFsg_Vemu_H3K9ac_rep1

description: Library name: Sample 23


title: A375_GCN5PCAFsg_DMSO_H3K9ac_rep2

description: Library name: Sample 21


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep2_BC156_R1

description:
Library name: Sample_53
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep2_BC157_R1

description:
Library name: Sample_56
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep3_BC139_R1

description:
Library name: Sample_57
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep3_BC138_R1

description:
Library name: Sample_54
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_GCN5PCAFsg_DMSO_H3K9ac_rep1

description: Library name: Sample 20


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_6w_rep1_BC107_R1

description:
Library name: Sample_64
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_DSG_GFPsg_GCN5_rep1

description: Library name: Sample 27


title: A375_TADA2Bsg2_Vemu_H3K9ac_rep3

description: Library name: Sample 19


title: A375_GCN5PCAFsg_DMSO_H3K9ac_rep3

description: Library name: Sample 22


title: RNA_dUTP_Microglia_Clec7aPositiveCD229NegativeCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep3_BC137_R1

description:
Library name: Sample_51
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg2_Vemu_H3K9ac_rep1

description: Library name: Sample 17


title: RNA_dUTP_Microglia_Clec7aPositiveCD229NegativeCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep2_BC155_R1

description:
Library name: Sample_50
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep1_BC145_R1

description:
Library name: Sample_52
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aNegativeCD229NegativeCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep1_BC142_R1

description:
Library name: Sample_47
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229NegativeCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep1_BC143_R1

description:
Library name: Sample_49
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg2_DMSO_H3K9ac_rep2

description: Library name: Sample 15


title: RNA_dUTP_Microglia_CD229Positive_Cx3cr1Mef2aKO_Male_Adult_Basal_rep2_BC101_PE150_R1

description:
Library name: Sample_46
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg2_DMSO_H3K9ac_rep3

description: Library name: Sample 16


title: A375_TADA2Bsg2_DMSO_H3K9ac_rep1

description: Library name: Sample 14


title: A375_TADA2Bsg2_Vemu_H3K9ac_rep2

description: Library name: Sample 18


title: RNA_dUTP_Microglia_Clec7aNegativeCD229NegativeCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep2_BC154_R1

description:
Library name: Sample_48
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg1_Vemu_H3K9ac_rep1

description: Library name: Sample 11


title: RNA_dUTP_Microglia_CD229Negative_Cx3cr1Mef2aKO_Male_Adult_Basal_rep2_BC117_PE150_R1

description:
Library name: Sample_43
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229Positive_Cx3cr1Mef2aKO_Male_Adult_Basal_rep1_BC116_R1

description:
Library name: Sample_45
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_Vemu_H3K9ac_rep2

description: Library name: Sample 12


title: RNA_dUTP_Microglia_CD229Negative_Cx3cr1Mef2aKO_Male_Adult_Basal_rep1_BC115_R1

description:
Library name: Sample_42
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_DMSO_H3K9ac_rep1

description: Library name: Sample 8


title: RNA_dUTP_Microglia_Cx3cr1Mef2aKO_Male_Adult_Basal_rep2_BC147_R1

description:
Library name: Sample_40
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_Ctrl_Vemu_H3K9ac_rep2

description: Library name: Sample 6


title: A375_Ctrl_Vemu_H3K9ac_rep1

description: Library name: Sample 5


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep2_BC151_R1

description:
Library name: Sample_37
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229Negative_Cx3cr1Mef2aKO_Male_Adult_Basal_rep3_BC100_PE150_R1

description:
Library name: Sample_44
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_Vemu_H3K9ac_rep3

description: Library name: Sample 13


title: A375_Ctrl_DMSO_H3K9ac_rep3

description: Library name: Sample 4


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep3_BC134_R1

description:
Library name: Sample_38
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg1_DMSO_H3K9ac_rep3

description: Library name: Sample 10


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep1_BC138_R1

description:
Library name: Sample_36
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg1_DMSO_H3K9ac_rep2

description: Library name: Sample 9


title: RNA_dUTP_Microglia_Cx3cr1Mef2aKO_Male_Adult_Basal_rep3_BC100_R1

description:
Library name: Sample_41
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_Ctrl_DMSO_H3K9ac_rep2

description: Library name: Sample 3


title: RNA_dUTP_Microglia_Cx3cr1Mef2aKO_Male_Adult_Basal_rep1_BC139_R1

description:
Library name: Sample_39
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg2_Vemu_rep3

description: Library name: Sample 27

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq
Fastq files were mapped to hg38 human genome by HISAT2
Gene reads count tables were generated by HTSeq
Assembly: hg38
Supplementary files format and content: text files includes raw reads count

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Plus Mini Kit according to the manufacturer’s instructions.
KAPA Stranded mRNA-Seq Kit

treatment_protocol: Non-targeting control cells or TADA2B KO cells were treated with DMSO, vemurafenib (1 μM), or trametinib (20 nM) for 24h before RNA extraction.


title: A375_Ctrl_Vemu_H3K9ac_rep3

description: Library name: Sample 7


title: RNA_dUTP_Microglia_Clec7aPositiveCD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep3_BC132_R1

description:
Library name: Sample_32
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep1_BC137_R1

description:
Library name: Sample_33
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep2_BC150_R1

description:
Library name: Sample_34
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_Ctrl_DMSO_H3K9ac_rep1

description: Library name: Sample 2


title: A375_TADA2Bsg2_Vemu_rep2

description: Library name: Sample 26


title: A375_TADA2Bsg2_Vemu_rep1

description: Library name: Sample 25


title: RNA_dUTP_Microglia_Clec7aPositiveCD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep1_BC136_R1

description:
Library name: Sample_30
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_input

description: Library name: Sample 1


title: RNA_dUTP_Microglia_Clec7aNegativeCD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep3_BC131_R1

description:
Library name: Sample_29
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aPositiveCD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep2_BC149_R1

description:
Library name: Sample_31
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg2_Tram_rep3

description: Library name: Sample 24

value: 20 nM Trametinib


title: A375_TADA2Bsg2_Tram_rep2

description: Library name: Sample 23


title: RNA_dUTP_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep3_BC133_R1

description:
Library name: Sample_35
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Clec7aNegativeCD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep2_BC148_R1

description:
Library name: Sample_28
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: A375_TADA2Bsg2_Tram_rep1

description: Library name: Sample 22


title: A375_TADA2Bsg2_DMSO_rep2

description: Library name: Sample 20


title: RNA_dUTP_Microglia_Clec7aNegativeCD229NegativeCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep1_BC135_R1

description:
Library name: Sample_27
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Cx3cr1Cre_Male_Adult_Basal_rep3_BC130_R1

description:
Library name: Sample_26
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Cx3cr1Cre_Male_Adult_Basal_rep2_BC117_R1

description:
Library name: Sample_25
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: RNA_dUTP_Microglia_Cx3cr1Cre_Male_Adult_Basal_rep1_BC115_R1

description:
Library name: Sample_24
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamlesAnnotated_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_CD229Subset_SamplesAnnotated_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_Cuprizone5w_TPMnormalization.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_RawData.txt
RNA_Cx3cr1CreERT2WT_Cx3cr1Egr2_Basal_Cuprizone6w_TPMnormalization.txt


title: A375_TADA2Bsg1_Vemu_rep2

description: Library name: Sample 17


title: A375_TADA2Bsg1_Vemu_rep3

description: Library name: Sample 18


title: A375_TADA2Bsg2_DMSO_rep1

description: Library name: Sample 19


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep3_BC114_R1

description:
Library name: Sample_22
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep4_BC141_R1

description:
Library name: Sample_23
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep2_BC156_R1

description:
Library name: Sample_21
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg2_DMSO_rep3

description: Library name: Sample 21


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep1_BC136_R1

description:
Library name: Sample_20
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_Tram_rep2

description: Library name: Sample 14


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep2_BC155_R1

description:
Library name: Sample_17
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_Tram_rep3

description: Library name: Sample 15


title: A375_TADA2Bsg1_DMSO_rep3

description: Library name: Sample 12


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep1_BC135_R1

description:
Library name: Sample_16
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep3_BC113_R1

description:
Library name: Sample_18
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_DMSO_rep1

description: Library name: Sample 10


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep4_BC140_R1

description:
Library name: Sample_19
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_DMSO_rep2

description: Library name: Sample 11


title: RNA_dUTP_Microglia_Trem2KO_Male_Adult_Basal_rep3_BC106_R1

description:
Library name: Sample_15
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_Vemu_rep1

description: Library name: Sample 16


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep3_BC100_R1

description:
Library name: Sample_12
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_GFPsg_Vemu_rep3

description: Library name: Sample 9


title: A375_GFPsg_Vemu_rep1

description: Library name: Sample 7


title: A375_GFPsg_Vemu_rep2

description: Library name: Sample 8


title: RNA_dUTP_Microglia_Trem2KO_Male_Adult_Basal_rep1_BC100_R1

description:
Library name: Sample_13
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_GFPsg_Tram_rep3

description: Library name: Sample 6


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep2_BC97_R1

description:
Library name: Sample_11
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_Trem2KO_Male_Adult_Basal_rep2_BC101_R1

description:
Library name: Sample_14
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_TADA2Bsg1_Tram_rep1

description: Library name: Sample 13


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC99_R1

description:
Library name: Sample_9
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC149_R1

description:
Library name: Sample_7
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: A375_GFPsg_DMSO_rep1

description: Library name: Sample 1


title: A375_GFPsg_Tram_rep2

description: Library name: Sample 5


title: matched AC-PC pair patient-derived organoid (PDO) cells, originating donor KG236, GEX

city: New York

first: Jura

last: Pintar

email: pintarj1@mskcc.org, ganeshk@mskcc.org

state: NY

address: 1275 York Avenue

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: KG236_GEX
scRNA-seq of matched AC-PC pair patient-derived organoids (PDOs), GEX

library_source: transcriptomic single cell

data_processing:
FASTQ files from organoid samples were processed with the SEQC pipeline using the GRCh38 human genome reference, default parameters, and platform set to 10x Genomics v3 3′ scRNA-seq kit. The SEQC pipeline performs read demultiplexing, alignment and unique molecular identifier (UMI) and cell barcode correction, producing a preliminary count matrix of cells by unique transcripts.
CellBender (v.0.3.0), an unsupervised method for removing ambient RNA from scRNA-seq data, was used to generate a denoised (i.e., ambient-RNA-corrected) count matrix, as well as the probability that each droplet contains a cell. Droplets with a cell-probability less than 0.5 were discarded. CellBender-corrected counts were used for all downstream analysis.
Cells were designated as outliers if they satisfied at least two of the following five conditions: 1) their log1p(total counts) were either more than 3 median absolute deviations (MADs) below or 5 MADs above the median of their organoid line; 2) their log1p(number of genes expressed) was either more than 3 MADs below or 5MADs above the median; 3) their percent of genes expressed in the top 20% of most highly expressed genes was more than 5 MADs below or above the median; 4) their feature-count distance (the difference between the value of log1p(number of genes expressed) observed, and the value predicted from the regression of log1p(number of genes expressed) on log1p(total counts)) was more than 5 MADs below or above the median; 5) their percentage of mitochondrial counts was both more than 2.5 MADs above the median and above the absolute threshold of 8%. Same-sample doublets were detected using scDblFinder (v.1.16.0). Both outliers and same-sample doublets were discarded.
Multiple integration methods were tested on the data set and evaluated using the scIB pipeline fast metrics, which measure both batch correction and preservation of biological variance. The overall best performer was scANVI, a semi-supervised variant of scVI, a deep-learning method that uses a variational autoencoder network. First, a hyperparameter grid search was performed and a scVI model with 3 hidden layers of 64 nodes per layer and 40 latent dimensions selected, with dispersion allowed to differ between batches. The default number of epochs with early stopping based on reconstruction loss validation was used for all training. The trained scVI model was then used to generate a scANVI model supplied with sample type labels (primary tumor vs. metastasis). The scANVI model was trained for an additional 71 epochs after which it showed no further improvement. The trained model was used to generate an integrated 40-dimensional embedding of the data.
The k-nearest-neighbor graph based on the scANVI embedding and the correlation metric was computed using Scanpy (v.1.10.0), with otherwise default parameter settings. The Uniform Manifold Approximation and Projection (UMAP) was then computed using Scanpy with default parameter settings.
Assembly: GRCh38
Supplementary files format and content: H5AD file containing CellBender-corrected and raw counts for all samples (only cells passing QC included), HTO counts, organoid line assignments, sample type annotation, scANVI embedding, kNN graph, and UMAP; description of all elements included in unstructured metadata (uns) under the key "manifest".
Supplementary files format and content: 10x MEX-formatted (*barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz) CellBender-corrected GEX counts for cells passing QC
Supplementary files format and content: 10x MEX-formatted (*barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz) HTO counts for cells passing QC
Supplementary files format and content: Compressed Tab-Separated Values file (.tsv.gz) containing hashtag assignments to cells passing QC

molecule: total RNA

source_name: patient-derived organoid

growth_protocol: AC and PC organoids were cultured in WRENAFI (Advanced DMEM/F12 (AdDF12; Thermo Fisher Scientific), GlutaMAX (2 mM, Thermo Fisher Scientific), HEPES (10 mM, Thermo Fisher Scientific), N-acetyl-l-cysteine (1 mM, Sigma-Aldrich), B27 supplement with vitamin A (Thermo Fisher Scientific), primocin (100 μg ml-1, InvivoGen), EGF (50 ng ml-1, Peprotech), Noggin (50X, IPA), A83-01 (500 nM, Sigma-Aldrich), FGF2 (50 ng ml-1, Peprotech), IGF-I (100 ng ml-1, Peprotech), 1% R-pondin1-conditioned medium (media collected from HEK293 cell lines expressing recombinant R-spondin 1), NGS-Wnt (0.5 M, ImmunePrecise N001). Cells processed as described above were suspended at 2,000 cells per 40 μL and plated in 40 μL domes of 1:1 Matrigel:WRENAFI mixture (Corning) in suspension culture plates. After Matrigel domes solidified at 37 °C for 30-60 minutes, WRENAFI supplemented with Y-27632 (MedChemExpress) was added to the well.

extract_protocol:
Organoids were harvested from Matrigel 3mM EDTA in DPBS then dissociated into single cells using TrypLE (Thermo Fisher Scientific) for 5–10 min at 37 °C and serially filtered through a 40-μm then 20-μm cell strainers to generate single cell suspensions. For multiplexing, cells were incubated with TotalSeq-B hash-tagging antibodies in FACS buffer (10 mM HEPES, 0.1 mM EDTA, 0.1% FBS) for 45 min then washed 3X with FACS buffer. Cells were then incubated with DAPI in FACS buffer sorted to enrich for live cells then equal numbers of cells from each of two paired samples were combined into a single suspension. FACS-sorted cells were washed once with DPBS containing 0.04% BSA and resuspended to a final concentration of 700–1,300 cells per microlitre. Cell viability was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II).
scRNA-seq was performed on the Chromium instrument (10x Genomics) according to the 3′ RNA v3.1 user manual. Cells were captured in droplets and subjected to reverse transcription and cell barcoding; emulsions were then broken and cDNA was purified using Dynabeads MyOne SILANE followed by PCR amplification according to the manual instructions. Up to 10,000 cells were targeted for each sample. Final libraries were sequenced on the Illumina NovaSeq S4 platform (R1, 28 cycles; i7, 8 cycles; R2, 90 cycles).

tag: tissue

value: patient-derived organoid

value: KG236Ap, KG236Om, two additional lines excluded from downstream analysis (mixture)

value: primary appendiceal adenocarcinoma (AC) PDO, peritoneal carcinomatosis (PC) PDO (mixture)

value: primary tumor PDO (AC), metastatic tumor PDO (PC)


title: matched AC-PC pair patient-derived organoid (PDO) cells, originating donor KG236, HTO

description:
Library name: KG236_HTO
scRNA-seq of matched AC-PC pair patient-derived organoids (PDOs), HTO

library_source: other

molecule: protein

tag: hto

value: TotalSeq-B0251 anti-human Hashtag 1 (KG236Ap), TotalSeq-B0252 anti-human Hashtag 2 (KG236Om), TotalSeq-B0253 anti-human Hashtag 3 (sample excluded from downstream analysis), TotalSeq-B0254 anti-human Hashtag 4 (sample excluded from downstream analysis)


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC159_R1

description:
Library name: Sample_5
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep1_BC150_R1

description:
Library name: Sample_10
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC148_R1

description:
Library name: Sample_4
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: matched AC-PC pair patient-derived organoid (PDO) cells, originating donor KG208, HTO

description:
Library name: KG208_HTO
scRNA-seq of matched AC-PC pair patient-derived organoids (PDOs), HTO

value: KG208Ap, KG208PW (mixture)

value: TotalSeq-B0251 anti-human Hashtag 1 (KG208Ap), TotalSeq-B0252 anti-human Hashtag 2 (KG208PW)


title: RNA_dUTP_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC98_R1

description:
Library name: Sample_6
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt

value: Adult


title: A375_GFPsg_Tram_rep1

description: Library name: Sample 4

value: Melanoma cell line


title: RNA_dUTP_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC160_R1

description:
Library name: Sample_8
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt

value: 0.2% Cuprizone diet for 4 weeks prior sacrifice


title: A375_GFPsg_DMSO_rep3

description: Library name: Sample 3

value: WT


title: E. coli W, narQXLP deletion with empty vector, Rep1

city: Pohang-si

first: Junyeong

middle: Yeol

last: Sung

state: Gyeongsangbuk-do

address: 77, Cheongam-ro, Nam-gu, Pohang-si, Gyeongsangbuk-do, Republic of Korea, POSTECH

country: South Korea

institute: POSTECH

description: Library name: narQXLP deletion_Empty_1

data_processing:
Sequencing reads were mapped to the reference genome by Tophat (v2.0.13). The aligned results were added to Cuffdiff (v2.2.0) to report differentially expressed genes
Assembly: Escherichia_coli_W (GCA_000184185.1)
Supplementary files format and content: csv files including fpkm value

organism: Escherichia coli

source_name: prokaryotic cell

growth_protocol: For cell cultivation, a modified M9 minimal medium with 100 mM glycerol, 0.5 g L−1 MgSO4·7H2O, 2.0 g L−1 NH4Cl, 2.0 g L−1 NaCl, 1.0 g L−1 yeast extract (Seok et al., 2018), and 100 mM potassium phosphate buffer (pH 7.0) was used. Appropriate antibiotics were added for plasmid maintenance: 50 mg L−1 ampicillin, 34 mg L−1 chloramphenicol, and 50 mg L−1 streptomycin. All cultures were incubated at 37 °C with 200 rpm agitation.

extract_protocol:
Total RNA was extracted after cell disruption using the APA Stranded RNA-Seq Library Preparation Kit (Illumina, San Diego, CA).
RNA purity was determined by assaying 1 µl of total RNA extract on a NanoDrop8000 spectrophotometer (Thermofisher, Waltham, MA). Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with an RNA Integrity Number (RIN) value. RNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded total RNA library prep kit)

value: prokaryotic cell

value: narQXLP deletion (E. coli W)

value: Empty vector control


title: E. coli W, narQXLP deletion with NarQ overexpression, Rep1

description: Library name: narQXLP deletion_NarQ_1

value: NarQ overexpression


title: A375_GFPsg_DMSO_rep2

description: Library name: Sample 2

value: DMSO


title: RNA_dUTP_Microglia_C57_Male_Adult_Basal_rep2_BC104_R1

description:
Library name: Sample_2
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt

value: None; Regular diet


title: 5723-OP-2

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 5723-OP-2

data_processing:
The CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: hg19
Supplementary files format and content: cell ranger output format

source_name: placenta and chorioamniotic membranes

extract_protocol:
Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE [https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf]
Tissue Sections;  https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: placenta and chorioamniotic membranes

value: mixed (single cell)

value: placenta cells

value: gHTN


title: RNA_dUTP_Microglia_C57_Male_Adult_Basal_rep3_BC128_R1

description:
Library name: Sample_3
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: RNA_dUTP_Microglia_C57_Male_Adult_Basal_rep1_BC98_R1

description:
Library name: Sample_1
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_RawData.txt
RNA_WT_Trem2KO_Basal_Cuprizone4w_SamplesAnnotated_TPMnormalization.txt


title: matched AC-PC pair patient-derived organoid (PDO) cells, originating donor KG215, GEX

description:
Library name: KG215_GEX
scRNA-seq of matched AC-PC pair patient-derived organoids (PDOs), GEX

value: patient-derived organoid

value: KG215Ap, KG215Om (mixture)

value: primary appendiceal adenocarcinoma (AC) PDO, peritoneal carcinomatosis (PC) PDO (mixture)

value: primary tumor PDO (AC), metastatic tumor PDO (PC)


title: matched AC-PC pair patient-derived organoid (PDO) cells, originating donor KG215, HTO

description:
Library name: KG215_HTO
scRNA-seq of matched AC-PC pair patient-derived organoids (PDOs), HTO

value: TotalSeq-B0251 anti-human Hashtag 1 (KG215Ap), TotalSeq-B0252 anti-human Hashtag 2 (KG215Om)


title: E. coli W, narQXLP deletion with NarQ overexpression, Rep2

description: Library name: narQXLP deletion_NarQ_2


title: matched AC-PC pair patient-derived organoid (PDO) cells, originating donor KG208, GEX

description:
Library name: KG208_GEX
scRNA-seq of matched AC-PC pair patient-derived organoids (PDOs), GEX

value: KG208Ap, KG208PW (mixture)


title: E. coli W, Wild type with NarQ overexpression, Rep2

description: Library name: WT_NarQ_2

value: Wild type (E. coli W)


title: E. coli W, Wild type with NarQ overexpression, Rep1

description: Library name: WT_NarQ_1

value: prokaryotic cell


title: 5109-OP-1

description: Library name: 5109-OP-1


title: E. coli W, narQXLP deletion with empty vector, Rep2

description: Library name: narQXLP deletion_Empty_2

value: narQXLP deletion (E. coli W)


title: 5065-OP-2

description: Library name: 5065-OP-2

value: Control


title: E. coli W, Wild type with empty vector (Control), Rep1

description: Library name: WT_Empty_1

value: Empty vector control


title: 5065-OP-3

description: Library name: 5065-OP-3


title: E. coli W, Wild type with empty vector (Control), Rep2

description: Library name: WT_Empty_2


title: 3804-OP-1

description: Library name: 3804-OP-1


title: 6015-OP-1

description: Library name: 6015-OP-1


title: YUMM1.7 -2

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

country: Germany

institute: University Hospital Mannheim

description: Library name: Unknown_CE192-ZX01-010005

data_processing:
The cell calling and gene counting were done using the Cell Ranger software v8.0.1
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
Lymph nodes were collected and digested using collagenase to yield a single cell suspension. Positive enrichment of stromal cells was achieved using CD45 magnetic beads.
Approx. 10000 cells / condition were subjected to GEM generation using the Chromium GEM-X Single Cell 3' Kit v4

value: lymph node

value: de-enriched for CD45

value: YUMM1.7 bearing mice


title: 5300-OP-1

description: Library name: 5300-OP-1

value: placenta and chorioamniotic membranes

value: mixed (single cell)


title: 5009-OP-1

description: Library name: 5009-OP-1

value: placenta cells


title: 3723-OP-1

description: Library name: 3723-OP-1

value: gHTN


title: Subject 23

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

description: Library name: J8

data_processing:
Raw sequence files were demultiplexed into FASTQ format using the Cell Ranger mkfastq command (v6, 10x Genomics). Reads were aligned to the human GRCh38 reference genome, including intronic regions, and gene counts were quantified as UMI (Unique Molecular Identifier) counts using Cell Ranger count (v6, 10x Genomics).
Ambient RNA contamination was removed by processing all samples with CellBender (v0.2), using the raw_feature_bc_matrix.h5 output file from Cell Ranger as input, with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and h5 files

source_name: Brain: Amygdala

extract_protocol:
Post-mortem frozen samples of brains were obtained from the Harvard Brain Tissue Resource Center (HBTRC)/NIH NeuroBioBank and the Massachusetts Alzheimer’s Disease Research Center (ADRC) neuropathology core and stored at -80ºC. Frozen samples of the amygdala gray matter were dissected and dissociated to prepare nuclei suspensions as previously described (Limone, Mordes et al. 2024). Aliquots (10 µl) of each preparation were stained with diluted Hoechst 33342 dye and examined on a Countess III FL with brightfield and fluorescence to verify the presence of nuclei.
Nuclei were processed on a 10x chromium controller, and libraries were prepared using the 10X genomics single cell 3’ V3.1 kit. Reactions were sequenced on a NovaSeq (Illumina) at the UCSF IHG.

tag: Sex

value: Female

tag: age

tag: disease state

value: PD

tag: cohort

value: Cohort 03

tag: pathology

value: Lewy body limbic/transitional

tag: braak and_braak_nft_stage

value: Braak stage 1


title: 3716-OP-1

description: Library name: 3716-OP-1


title: 3658-OP-1

description: Library name: 3658-OP-1


title: Naïve

description: Library name: Unknown_CE192-ZX01-010004

value: tumor-free mice


title: SP_SPF_2

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

description:
Library name: SP-SPF2
scRNA-Seq (10x Genomics)

data_processing:
[Gene counting] Alignment of sequencing reads and gene counting with single-cell resolution were performed with 10x Genomics Cell Ranger v6.0.1, using the default parameters and the pre-built mouse reference v2020-A (10x Genomics, Inc) based on mm10 GRCm38.p6 (release 98) and annotation from GENCODE Release M23. The algorithm was run using a different number of expected cells for each sample as indicated on the column "expected cells" from the sample description.
[Filtering] Only cells with more than 1200 genes detected, less than 10% of mitochondrial genes and with UMI counts less than 3 standard deviations above the mean were kept for downstream analysis. Only data for genes detected in at least 3 cells in one of the samples were kept for further analysis. Contaminating cells were filtered out based on the average cluster expression of the marker genes Cd14, Lyz2, Fcgr3, Ms4a7, Fcer1g, Cst3, H2-Aa, Ly6d, Ms4a1, Ly6d, Cd19, Cd3e, Cd8a and mitochondrial genes.
[Normalization] Downstream analysis was performed with the R package Seurat v4.0.1. Raw read counts data from different tissues of the same donor were merged and normalized together using the R package sctransform v0.3.2 (with glmGamPoi method).
[Integration] After exclusion of contaminating clusters, anchors between replicates were identified on top 1000 highly variable genes and integration performed on first 20 dimensions.
[Visualization] PCA was calculated on the top 1000 highly variable genes, KNN graph and UMAP were computed on the 30 nearest neighbors and first 20 PCA dimensions.
[Clustering] The shared nearest neighbor (SNN) modularity optimization-based algorithm was used at resolutions 0.36 for identification of Louvain clusters.
Assembly: GRCm38.p6 (release 98) - GENCODE Release M23
Supplementary files format and content: Cellranger compressed files contain the filtered UMI counts matrix (Market Exchange Format for sparse matrices) and TSV files with genes and barcode sequences (corresponding to row and column indices respectively) as output by 10x Genomics Cell Ranger.

source_name: Spleen

extract_protocol:
Gene expression libraries for single cell RNA sequencing were prepared by using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 and the 10x Chromium Controller (10x Genomics).
cDNA synthesis and library preparation were performed following the manufacturer’s protocol (CG000206 Rev D). Single Index Kit T Set A was used for multiplexing (i7 index read, 8bp).

treatment_protocol: 3x103 splenic CD45.1+ SMARTA cells were transferred i.v. into CD45.2+ recipients one day prior to infection with LCMV Armstrong or Docile (3 mice per group). Lymphocytes were isolated from spleens and liver on days 10 and 28 post infection CD45.1+ SMARTA cells were enriched by positive selection using biotin-labeled anti-CD45.1 and anti-biotin microbeads combined with magnetic MACS cell separation and subsequently sorted on a FACS ARIA III sorter. Sorted cells were collected in culture medium containing 10%FCS and 2mM EDTA and stored at 4°C until all samples were ready for further processsing. Cells were centrifuged, media was removed and cells were resupended in BD satining buffer.

value: Spleen

value: CD8 T cells

tag: mouse background

tag: time point

value: day 16 post infection

tag: infection

value: LCMV Docile

tag: replicate

tag: expected cells


title: SP_GF_5

description:
Library name: SP-GF5
scRNA-Seq (10x Genomics)

tag: cell type


title: Subject 21

description: Library name: J6

value: Control

value: mild ADNC

value: Braak stage 3


title: SP_SPF_4

description:
Library name: SP-SPF4
scRNA-Seq (10x Genomics)


title: SP_GF_2

description:
Library name: SP-GF2
scRNA-Seq (10x Genomics)


title: Subject 18

description: Library name: J3

value: Lewy body diffuse/neocortical

value: Braak stage 4


title: Subject 20

description: Library name: J5

value: Male

value: Braak stage 2


title: SI_SPF_4

description:
Library name: SI-SPF4
scRNA-Seq (10x Genomics)

source_name: SI-LM

value: SI-LM


title: YUMMER1.7 -2

description: Library name: Unknown_CE192-ZX01-010006

value: lymph node

value: de-enriched for CD45

tag: genotype

tag: treatment

value: YUMMER1.7 bearing mice


title: Subject 22

description: Library name: J7

value: PD

value: Cohort 03

value: Lewy body limbic/transitional; had DBS

value: Braak stage 0


title: Subject 17

description: Library name: J2

value: Lewy body diffuse/neocortical; mild ADNC


title: SI_SPF_1

description:
Library name: SI-SPF1
scRNA-Seq (10x Genomics)

value: CD8 T cells

value: day 16 post infection

value: LCMV Docile


title: SH1000 pEPSA5::sroA 3hr/3hr

city: Washington, DC

first: Karl

last: Thompson

address: 2201 Georgia Ave, NW

institute: Howard University

description:
Library name: SH1000 pEPSA5::sroA
FPKM and Fold Change

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen CLC Genomics Workbench as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were caculated using RNA-Seq Analysis function with experimental fold change feature in Qiagen CLC Genomics Workbench
Expression values and fold change were normalized by quantile normalization
Normalized expression values and fold change comparisons were exported in excel format
Assembly: Data was aligned to the NCTC 8325 reference genome (NC_007795.1)
Supplementary files format and content: Comparisons were carried out following quantile normalization via the Qiagen Bioinformatics experimental fold change feature.

organism: Staphylococcus aureus

source_name: bacterial cells, pelleted

growth_protocol: Overnight S. aureus cultures were used to inoculate fresh TSB broth and grown for 3 hours. After which these cultures were used to seed fresh TSB at an OD600 of 0.05 Samples were then grown to an OD600 of 0.3 before being induced with xylose for 3 hours, then 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria.
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were pelleted and stored at -80°C prior to RNA extraction.

value: bacterial cells, pelleted

tag: strain

value: sroA overexpression strain

tag: growth medium

value: TSB

tag: growth conditions

value: Xylose


title: Nse2-12Pk_Input

city: Wroclaw

first: Karol

last: Kramarz

address: Kanonia 6/8

department: Faculty of Biological Sciences

country: Poland

institute: University of Wrocław

description: Library name: Nse2-12Pk_INP

data_processing:
Following an initial quality control assessment (Q30), raw sequencing reads were processed with Cutadapt to trim adapter sequences and remove low-quality reads.
The resulting filtered reads were mapped to the target S. pombe genome (assembly ASM294v3) and the spike-in S. cerevisiae S288C genome (assembly SacCer3) using Bowtie2.
Unmapped reads and duplicates were filtered out using SAMtools.
SAMtools was used to count reads uniquely mapped to each reference genome, and these values were used to calculate the occupancy ratio value.
The local bias was estimated using MACS3 by selecting the maximum background signal from the surrounding 1kb, 10kb, the fragment length d, and the whole-genome background.
The downsampling normalization method was used to scale down all the samples to the minimum number of spike-in reads in the dataset.
Enriched regions (peaks) were identified using the bdgpeakcall function in MACS3.
Assembly: Schizosaccharomyces pombe assembly ASM294v3
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: The growth of relevant mutants was done in rich medium (YES), relevant for S. pombe.

extract_protocol:
Logarithmic fission yeast cultures of untagged control, Pli1-12Pk or Nse2-12Pk were mixed with a calibrator – an aliquot of logarithmic budding yeast culture Ku70-cMyc. Immunoprecipitation of Pli1-12Pk- or Nse2-12Pk-bound DNA was then performed. Obtained samples were subjected to next generation sequencing (NGS) and signals from the IP/INPUT ratio were normalized to the budding yeast calibrator. In details, 100 mL of exponential culture (OD600 ~1) of untagged strain, Pli1-12Pk and Nse2-12Pk were mixed with 10 mL of budding yeast exponential culture Ku70-cMyc, used as a calibrator and then crosslinked with 1% formaldehyde (Sigma-Aldrich, F-8775) for 15 min. Formaldehyde crosslinking was quenched with 2.5 M glycine and cells were washed with 1x TBS. Next, samples were frozen in liquid nitrogen and cells were lysed by bead beating in FA-lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA with 1 mM PMSF and protease inhibitors (Sigma-Aldrich, P8215)). Chromatin sonication was done in a Bioruptor Pico (Diagenode) using Easy mode 10 cycles of 30 s ON and 30 s OFF. Immunoprecipitation was carried out overnight: 300  µL of extract was incubated on the wheel with anti-Pk antibody (Bio-Rad, MCA1360G) at 1:150 concentration. 20 µL of extract was preserved as INPUT fraction. Next morning Protein G Dynabeads (Invitrogen, 10003D) were added for 1 h, stringency washes to remove unspecific proteins were done and immunoprecipitated complexes were decrosslinked overnight at 65° C. Then samples were digested with RNAse A (Thermo Scientific, EN0531) for 30 min at 37oC and subsequently with proteinase K at 65oC for 1h. The associated DNA was then precipitated with isopropanol/glycogen/3M potassium acetate for 1h at -20oC. Precipitated DNA was centrifuged for 20 min at 4oC and then washed with cold 70% ethanol. Finally, DNA pellet was resuspended in 30 µL of Nuclease-Free Water (Sigma-Aldrich, W4502). DNA concentration was determined by Qubit4 Fluorometer (Invitrogen) using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and quality control qPCR was done on 10x dilution of obtained DNA suspension with SsoAdvanced Universal SYBR® Green Supermix (Bio-Rad, 1725274, primers listed in Table S2). Samples were then send for DNA libraries preparation and next generation sequencing (Novogene).
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina E7645L

value: yeast


title: Subject 19

description: Library name: J4

tag: tissue

tag: Sex

value: Female

value: Braak stage 4


title: SP_GF_1

description:
Library name: SP-GF1
scRNA-Seq (10x Genomics)

value: Spleen


title: Nse2-12Pk_ChIP

description: Library name: Nse2-12Pk_IP

value: anti-Pk antibody (Bio-Rad, MCA1360G)


title: Subject 15

description: Library name: K8

value: Male

tag: age

tag: disease state

value: PD

value: Cohort 02

value: Lewy body limbic/transitional

value: Braak stage 2


title: SP_SPF_1

description:
Library name: SP-SPF1
scRNA-Seq (10x Genomics)

value: CD8 T cells


title: SI_GF_5

description:
Library name: SI-GF5
scRNA-Seq (10x Genomics)

value: SI-LM

value: day 16 post infection


title: SI_SPF_2

description:
Library name: SI-SPF2
scRNA-Seq (10x Genomics)

value: LCMV Docile


title: SH1000 pEPSA5 3hr/3hr

description:
Library name: SH1000 pEPSA5
FPKM and Fold Change

value: bacterial cells, pelleted

value: Vector control strain


title: Pli1-12Pk_ChIP

description: Library name: Pli1-12Pk_IP


title: Subject 14

description: Library name: K7

tag: cohort

tag: pathology

value: Braak stage 3


title: Subject 16

description: Library name: J1

value: Control

value: Cohort 03

value: mild ADNC

tag: braak and_braak_nft_stage


title: SI_GF_2

description:
Library name: SI-GF2
scRNA-Seq (10x Genomics)

tag: mouse background

tag: time point


title: Pli1-12Pk_Input

description: Library name: Pli1-12Pk_INP

value: yeast


title: SI_GF_1

description:
Library name: SI-GF1
scRNA-Seq (10x Genomics)

tag: infection

tag: replicate


title: SPE3

city: hangzhou

first: Qihang

last: Zhao

address: hangzhou huansha road 261

country: China

institute: Hangzhou First People's Hospital

description: Library name: SPE3

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Matrix table with raw gene counts for every gene and every cell
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each smple

source_name: one sample from serious PE placenta

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: placenta

tag: condition

value: severe eclampsia


title: Subject 13

description: Library name: K6

value: Male

value: Braak stage 1


title: SPE1

description: Library name: SPE1


title: Subject 12

description: Library name: K5

value: Cohort 02


title: SPE2

description: Library name: SPE2


title: Subject 11

description: Library name: K4

value: PD

value: Lewy body diffuse/neocortical


title: untagged strain_ChIP

description: Library name: untagged_IP

tag: cell type

value: anti-Pk antibody (Bio-Rad, MCA1360G)


title: Current smoker, COPD

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

country: Japan

institute: Tokyo Women's Medical University

description:
Library name: Sample 4
10x Genomics

data_processing:
The dataset were analyzed by CellRanger 8.0 (10x Genomics). Gene expression was visualized using Loupe Browser software (10x Genomics).
Assembly: Human hg39
Supplementary files format and content: Barcodes.tsv, features.tsv, matrix.mtx files for each sample

source_name: Bronchial epithelial cells

extract_protocol:
ALIcultured cells were washed and detached using TRIPLE. Viability of single cell suspension was measured.
The library was constructed with the Chromium Singl Cell 3' v3.1 kit (10x Genomics) and sequenced using an Illumina NovaSeq X plus.

treatment_protocol: Primary bronchial epithelial cells were cultured in air/liquid culture conditions for more than 4 weeks.  The patients were classified as never-smoker (healthy) with normal lung function, ex-smokers with COPD, or current smokers with COPD.

value: Bronchial epithelial cells

tag: treatment

value: Current smoker, COPD


title: untagged strain_Input

description: Library name: untagged_INP


title: KO; CD8+T; CD3/CD28+IFN-α+IL-4

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description: Library name: KO-a

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
Genomic DNA was extracted under gentle conditions to preserve R-loops. Briefly, cells were lysed in lysis buffer containing SDS and proteinase K and incubated at 37°C overnight. Genomic DNA was then purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA pellet was resuspended in TE buffer. Purified DNA was digested with a cocktail of restriction enzymes (EcoRI, BamHI, HindIII, BsrGI, and XbaI) to generate fragments of approximately 100-500 bp. DNA concentration was determined using a NanoDrop spectrophotometer, and samples were used for subsequent DRIP assays.
DNA libraries for DNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Primary CD8⁺ T cells isolated from lymph nodes of WT and  Dusp2-/- mice were resuspended in T cell medium (RPMI-1640 supplemented with 10% FBS, 1 × Pen-Strep, 1 mM sodium pyruvate and 0.05 mM 2-mercaptoethanol). Cells were seeded into 48-well plates at a density of 2 × 10^6 cells/mL and stimulated with anti-CD3/28 antibodies (1 μg/mL+1 μg/mL), anti-CD3/28 antibodies (1 μg/mL+1 μg/mL)+IFN-α (50 ng/mL)+IL-4 (20 ng/mL) or left untreated. Cells were harvested 18 hours after activation

tag: genotype


title: Ex smoker, COPD, rep-1

description:
Library name: Sample 2
10x Genomics

growth_protocol: Primary bronchial epithelial cells were cultured in air/liquid culture conditions for more than 4 weeks.

value: Ex smoker, COPD


title: Ex smoker, COPD, rep-2

description:
Library name: Sample 3
10x Genomics


title: Subject 09

description: Library name: K2

value: Female


title: KO; CD8+T; UT

description: Library name: KO-UT

value: UT


title: Subject 10

description: Library name: K3

value: Braak stage 2


title: KO; CD8+T; CD3/CD28

description: Library name: KO-328


title: Ex smoker, COPD, rep-1

description:
Library name: Sample 2
10x Genomics

data_processing:
The dataset were analyzed by Cell Ranger ATAC (10x Genomics). ATAC signal was visualized using Loupe Browser software (10x Genomics).
Assembly: Human hg39
Supplementary files format and content: Barcodes.tsv, features.tsv, matrix.mtx files for each sample

molecule: other

extract_protocol:
ALIcultured cells were washed and detached using TRIPLE. Viability of single cell suspension was measured.
The library was constructed with the Chromium Next GEM Singl Cell ATAC library & Gel beads kit  v2 (10x Genomics) and sequenced using an Illumina NovaSeq X plus.


title: Ex smoker, COPD, rep-2

description:
Library name: Sample 3
10x Genomics


title: Current smoker, COPD

description:
Library name: Sample 4
10x Genomics


title: Never smoker, healthy

description:
Library name: Sample 1
10x Genomics

value: Never smoker, healthy


title: WT; CD8+T; CD3/CD28

description: Library name: WT-328

value: WT


title: Subject 08

description: Library name: L8

value: Cohort 01

value: Lewy body limbic/transitional


title: WT; CD8+T; CD3/CD28+IFN-α+IL-4

description: Library name: WT-a


title: Never smoker, healthy

description:
Library name: Sample 1
10x Genomics


title: Germination_Transverse_24HAI_C

city: Bundoora

first: Marta

last: Peirats Llobet

state: Victoria

address: 5 Ring road

country: Australia

institute: La Trobe University

description: Library name: GTR_24HAI_C

data_processing:
Raw sequencing data was processed using 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to IBSC v2.51 genome to get gene expression counts using Space Ranger's default settings.
Assembly: Barley genome, ((International Barley Sequencing Consortium (IBSC) v2.51 served as a reference genome for aligning the sequencing reads.
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: spatial_enrichment.cvs: spatial autocorrelation coefficient table in csv format
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression matrix in h5 format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: high-res image of the tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of the tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

organism: Hordeum vulgare

source_name: grain

extract_protocol:
Fresh frozen tissue embedded in OCT and sectioned to 8 µm thick in the cryostat.
Spatial sequencing libraries were synthesized as described in 10x User guide (PN-1000190, CG000239_VisiumSpatialGeneExpression_UserGuide_RevD). Visium libraries were sequenced on an Illumina NextSeq 550 platform according to the 10x Genomics Visium manufacturer’s instructions (NextSeq 500/550 High Output kit v2.5 (150 cycles) 20024907, CG00023_VisiumSpatialGeneExpression_UserGuide_RevD), targeting 100 million reads using dual indexing kit TT set A (PN-1000215, 10x Genomics).

treatment_protocol: No treatments

value: grain

value: La Trobe

value: no


title: Subject 01-2

description: Library name: K1

value: Control

value: Cohort 02

value: Braak stage 1


title: Germination_Transverse_24HAI_D

description: Library name: GTR_24HAI_D


title: WT; CD8+T; UT

description: Library name: WT-UT


title: Germination_Transverse_24HAI_B

description: Library name: GTR_24HAI_B


title: Dusp2-/-,CD44hi, rep2

description:
Library name: KO-hi-2
10X Genomics

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: mm39
Supplementary files format and content: FPKM

source_name: CD44hi Tvm

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Primary CD8⁺ T cells isolated from lymph nodes of WT and Cd4-Cre Rpa1fl/fl mice were resuspended in T cell medium (RPMI-1640 supplemented with 10% FBS, 1 × Pen-Strep, 1 mM sodium pyruvate and 0.05 mM 2-mercaptoethanol). Cells were seeded into 48-well plates pre-coated with anti-CD3 antibody (1 μg/mL) at a density of 2 × 10^6 cells/mL and stimulated with anti-CD28 antibody (1 μg/mL), IFN-α (50 ng/mL) and IL-4 (20 ng/mL). Cells were harvested 18 hours after activation and sorted into CD44super-high and CD44lo CD8⁺ T cell subsets.

value: CD44hi Tvm

value: KO


title: Germination_Transverse_24HAI_A

description: Library name: GTR_24HAI_A


title: Subject 06

description: Library name: L6

value: Male

value: PD

value: Braak stage 3


title: Dusp2-/-,CD44hi, rep1

description:
Library name: KO-hi-1
10X Genomics


title: Germination_Transverse_6HAI_C

description: Library name: GTR_6HAI_C


title: Subject 04

description: Library name: L4


title: Germination_Transverse_6HAI_B

description: Library name: GTR_6HAI_B


title: Germination_Transverse_6HAI_D

description: Library name: GTR_6HAI_D


title: Dusp2-/-,CD44lo, rep1

description:
Library name: KO-low-1
10X Genomics

source_name: CD44lo Tvm

value: CD44lo Tvm