title: A375_TADA2Bsg2_SOX10OE_rep2

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 17

library_source: transcriptomic

data_processing:
Element AVITI uses onboard AVITI Control Software with integrated primary analysis/basecalling to convert raw electrical sequencing signals into base calls and Phred quality scores
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

molecule: total RNA

organism: Homo sapiens

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

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

tag: cell line

tag: cell type

value: Melanoma cell line

tag: genotype

value: TADA2B knockout plus SOX10 overexpression


title: A375_TADA2Bsg2_SOX10OE_rep1

description: Library name: Sample 16


title: A375_TADA2Bsg2_SOX10OE_rep3

description: Library name: Sample 18


title: A375_TADA2Bsg2_rep3

description: Library name: Sample 15

value: TADA2B knockout


title: A375_TADA2Bsg1_SOX10OE_rep3

description: Library name: Sample 12


title: A375_TADA2Bsg1_SOX10OE_rep2

description: Library name: Sample 11


title: A375_TADA2Bsg1_SOX10OE_rep1

description: Library name: Sample 10


title: A375_TADA2Bsg1_rep1

description: Library name: Sample 7


title: A375_TADA2Bsg2_rep1

description: Library name: Sample 13


title: A375_TADA2Bsg1_rep3

description: Library name: Sample 9


title: A375_GFPsg_SOX10OE_rep2

description: Library name: Sample 5

value: SOX10 overexpression


title: A375_GFPsg_SOX10OE_rep1

description: Library name: Sample 4


title: A375_GFPsg_SOX10OE_rep3

description: Library name: Sample 6


title: A375_GFPsg_rep2

description: Library name: Sample 2

value: WT


title: A375_GFPsg_rep1

description: Library name: Sample 1


title: A375_SOX10sg_rep2

description: Library name: Sample 5

data_processing:
Element AVITI uses onboard AVITI Control Software with integrated primary analysis/basecalling to convert raw electrical sequencing signals into base calls and Phred quality scores
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: raw reads count

value: SOX10 knockout


title: A375_SOX10sg_rep1

description: Library name: Sample 4


title: A375_mCherrysg_rep3

description: Library name: Sample 3


title: A375_TADA2Bsg1_rep2

description: Library name: Sample 8


title: A375_mCherrysg_rep2

description: Library name: Sample 2


title: A375_TADA2Bsg2_rep2

description: Library name: Sample 14


title: A375_mCherrysg_rep1

description: Library name: Sample 1


title: A375_GFPsg_rep3

description: Library name: Sample 3


title: A375_Tram_Persisters3_Withdraw

description: Library name: Sample 9

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

molecule: polyA RNA

treatment_protocol: A375 parental cells were treated with 2 nM trametinib for 8 weeks or subjected to continuous drug withdrawal for 4 weeks prior to RNA extraction.

tag: treatment

value: Withdraw


title: A375_Tram_Persisters2_Withdraw

description: Library name: Sample 8


title: A375_Tram_Persisters4_Withdraw

description: Library name: Sample 10


title: A375_Tram_Persisters5_Withdraw

description: Library name: Sample 11


title: A375_SOX10sg_rep3

description: Library name: Sample 6


title: A375_Tram_Persisters5

description: Library name: Sample 6

value: 2 nM Trametinib


title: A375_Tram_Persisters2

description: Library name: Sample 3


title: Rat number12, Right hemisphere, HIP

city: Tehran

first: Ashkan

last: Veysi

state: Tehran

address: 16 Azar avenue

department: Cell and molecular biology

country: Iran

institute: University of Tehran

description: Library name: Sample 120

data_processing:
The sequence-ready libraries were normalized to a concentration of 1.5 nM and pooled
Trimmed reads were aligned to the rat reference genome (mRatBN7.2) with Star v2.7.10. To remove true PCR duplicates, the UMIs were used to deduplicate aligned reads with UMI-tools v1.1.2 and the remaining reads per gene were counted implementing HTSeq v2.0.1
Assembly: mRatBN7.2
Supplementary files format and content: TXT files ( text file format), containing non-normalized genecount of mRNA genes

organism: Rattus norvegicus

source_name: Hippocampus

growth_protocol: A total of 24 male Wistar rats were group-housed (2 per cage) and kept under standard laboratory conditions until their treatment.

extract_protocol:
RNA extraction was carried out using the Fatty Tissue RNA Purification Kit according to the manufacturer’s instructions manual.
Sequencing libraries from the isolated total RNA were generated using the QuantSeq 3′ mRNA-Seq Library Prep Kit in combination with unique dual indexes (UDI) and UMI according to the manufacturer’s protocol

treatment_protocol: After the final handling of animals, they were injected subcutaneously with either saline or psilocybin (2 mg/kg) dissolved in 0.9% saline.

tag: tissue

value: Hippocampus

value: Psilocybin

tag: concentration (ng/ul)

tag: rqn

tag: total number_of_reads_(m)


title: Rat number11, Right hemisphere, HIP

description: Library name: Sample 118

value: Saline


title: Rat number9, Left hemisphere, HIP

description: Library name: Sample 113


title: Rat number10, Right hemisphere, HIP

description: Library name: Sample 116


title: A375_Parental cell

description: Library name: Sample 1

value: No treatment


title: Rat number8, Left hemisphere, HIP

description: Library name: Sample 111


title: Rat number12, Left hemisphere, HIP

description: Library name: Sample 119


title: A375_Tram_Persisters1

description: Library name: Sample 2


title: Rat number6, Right hemisphere, HIP

description: Library name: Sample 108


title: Rat number8, Right hemisphere, HIP

description: Library name: Sample 112


title: Rat number5, Right hemisphere, HIP

description: Library name: Sample 106


title: Rat number11, Left hemisphere, HIP

description: Library name: Sample 117


title: Rat number7, Left hemisphere, HIP

description: Library name: Sample 109


title: A375_Tram_Persisters3

description: Library name: Sample 4


title: A375_Tram_Persisters1_Withdraw

description: Library name: Sample 7


title: Rat number4, Right hemisphere, HIP

description: Library name: Sample 104


title: Rat number9, Right hemisphere, HIP

description: Library name: Sample 114


title: A375_Tram_Persisters4

description: Library name: Sample 5


title: Rat number4, Left hemisphere, HIP

description: Library name: Sample 103


title: Rat number5, Left hemisphere, HIP

description: Library name: Sample 105


title: Rat number3, Left hemisphere, HIP

description: Library name: Sample 101


title: Rat number7, Right hemisphere, HIP

description: Library name: Sample 110


title: Rat number6, Left hemisphere, HIP

description: Library name: Sample 107


title: Rat number1, Right hemisphere, HIP

description: Library name: Sample 98


title: Rat number1, Left hemisphere, HIP

description: Library name: Sample 97


title: Rat number12, Right hemisphere, AMG

description: Library name: Sample 96

source_name: Amygdala

value: Amygdala

tag: rin

tag: %reads >=_phred_30


title: Rat number11, Right hemisphere, AMG

description: Library name: Sample 94


title: Rat number2, Left hemisphere, HIP

description: Library name: Sample 99


title: Rat number11, Left hemisphere, AMG

description: Library name: Sample 93


title: Rat number10, Left hemisphere, AMG

description: Library name: Sample 91


title: Rat number10, Right hemisphere, AMG

description: Library name: Sample 92


title: Rat number7, Right hemisphere, AMG

description: Library name: Sample 86


title: Rat number6, Left hemisphere, AMG

description: Library name: Sample 83


title: Rat number8, Right hemisphere, AMG

description: Library name: Sample 88


title: Rat number8, Left hemisphere, AMG

description: Library name: Sample 87


title: Rat number9, Right hemisphere, AMG

description: Library name: Sample 90


title: Rat number5, Right hemisphere, AMG

description: Library name: Sample 82


title: Rat number9, Left hemisphere, AMG

description: Library name: Sample 89


title: Rat number4, Left hemisphere, AMG

description: Library name: Sample 79


title: Rat number7, Left hemisphere, AMG

description: Library name: Sample 85


title: Rat number3, Right hemisphere, AMG

description: Library name: Sample 78


title: Rat number2, Right hemisphere, AMG

description: Library name: Sample 76


title: Rat number3, Left hemisphere, AMG

description: Library name: Sample 77


title: Rat number2, Right hemisphere, HIP

description: Library name: Sample 100


title: Rat number1, Right hemisphere, AMG

description: Library name: Sample 74


title: Rat number4, Right hemisphere, AMG

description: Library name: Sample 80


title: Rat number2, Left hemisphere, AMG

description: Library name: Sample 75


title: Rat number5, Left hemisphere, AMG

description: Library name: Sample 81


title: Rat number11, Right hemisphere, STR

description: Library name: Sample 70

source_name: Striatum

value: Striatum


title: Rat number12, Right hemisphere, STR

description: Library name: Sample 72


title: Rat number12, Left hemisphere, STR

description: Library name: Sample 71


title: Rat number1, Left hemisphere, AMG

description: Library name: Sample 73


title: Rat number8, Right hemisphere, STR

description: Library name: Sample 64


title: Rat number9, Left hemisphere, STR

description: Library name: Sample 65


title: Rat number6, Right hemisphere, AMG

description: Library name: Sample 84


title: Rat number10, Left hemisphere, STR

description: Library name: Sample 67


title: Rat number11, Left hemisphere, STR

description: Library name: Sample 69


title: Rat number9S, Right hemisphere, STR

description: Library name: Sample 66


title: Rat number4, Right hemisphere, STR

description: Library name: Sample 56


title: Rat number8, Left hemisphere, STR

description: Library name: Sample 63


title: Rat number3, Right hemisphere, STR

description: Library name: Sample 54


title: Rat number7, Right hemisphere, STR

description: Library name: Sample 62


title: Rat number6, Right hemisphere, STR

description: Library name: Sample 60


title: Rat number1, Right hemisphere, STR

description: Library name: Sample 50


title: Rat number2, Left hemisphere, STR

description: Library name: Sample 51


title: Rat number5, Left hemisphere, STR

description: Library name: Sample 57


title: Rat number12, Left hemisphere, CIN

description: Library name: Sample 47

source_name: Cingulate cortex

value: Cingulate cortex


title: Rat number6, Left hemisphere, STR

description: Library name: Sample 59


title: Rat number10, Right hemisphere, CIN

description: Library name: Sample 44


title: Rat number5, Right hemisphere, STR

description: Library name: Sample 58


title: Rat number7, Left hemisphere, STR

description: Library name: Sample 61


title: Rat number9, Right hemisphere, CIN

description: Library name: Sample 42


title: Rat number4, Left hemisphere, STR

description: Library name: Sample 55


title: Rat number3, Left hemisphere, STR

description: Library name: Sample 53


title: Rat number2, Right hemisphere, STR

description: Library name: Sample 52


title: Rat number11, Right hemisphere, CIN

description: Library name: Sample 46


title: Rat number6, Right hemisphere, CIN

description: Library name: Sample 36


title: Rat number1, Left hemisphere, STR

description: Library name: Sample 49


title: Rat number5, Right hemisphere, CIN

description: Library name: Sample 34


title: Rat number10, Left hemisphere, CIN

description: Library name: Sample 43


title: Rat number11, Left hemisphere, CIN

description: Library name: Sample 45


title: Rat number7, Left hemisphere, CIN

description: Library name: Sample 37


title: Rat number9, Left hemisphere, CIN

description: Library name: Sample 41


title: Rat number8, Left hemisphere, CIN

description: Library name: Sample 39


title: Rat number8, Right hemisphere, CIN

description: Library name: Sample 40


title: Rat number12, Right hemisphere, CIN

description: Library name: Sample 48


title: Rat number7, Right hemisphere, CIN

description: Library name: Sample 38


title: Rat number1, Right hemisphere, CIN

description: Library name: Sample 26


title: Rat number6, Left hemisphere, CIN

description: Library name: Sample 35


title: Rat number1, Left hemisphere, CIN

description: Library name: Sample 25


title: Rat number12, Left hemisphere, mPFC

description: Library name: Sample 23

source_name: mPFC

value: mPFC


title: Rat number9, Right hemisphere, mPFC

description: Library name: Sample 18


title: Rat number9, Left hemisphere, mPFC

description: Library name: Sample 17


title: Rat number10, Left hemisphere, mPFC

description: Library name: Sample 19


title: Rat number4, Right hemisphere, CIN

description: Library name: Sample 32


title: Rat number11, Right hemisphere, mPFC

description: Library name: Sample 22


title: Rat number3, Left hemisphere, CIN

description: Library name: Sample 29


title: Rat number8, Right hemisphere, mPFC

description: Library name: Sample 16


title: Rat number2, Left hemisphere, CIN

description: Library name: Sample 27


title: Rat number3, Right hemisphere, CIN

description: Library name: Sample 30


title: Rat number5, Left hemisphere, CIN

description: Library name: Sample 33


title: Rat number12, Right hemisphere, mPFC

description: Library name: Sample 24


title: Rat number11, Left hemisphere, mPFC

description: Library name: Sample 21


title: Rat number10, Right hemisphere, mPFC

description: Library name: Sample 20


title: Rat number8, Left hemisphere, mPFC

description: Library name: Sample 15


title: Rat number7, Right hemisphere, mPFC

description: Library name: Sample 14


title: Rat number6, Left hemisphere, mPFC

description: Library name: Sample 11


title: Rat number5, Left hemisphere, mPFC

description: Library name: Sample 9


title: Rat number5, Right hemisphere, mPFC

description: Library name: Sample 10


title: Rat number4, Right hemisphere, mPFC

description: Library name: Sample 8


title: Rat number2, Left hemisphere, mPFC

description: Library name: Sample 3


title: Rat number6, Right hemisphere, mPFC

description: Library name: Sample 12


title: Rat number3, Right hemisphere, mPFC

description: Library name: Sample 6


title: Rat number7, Left hemisphere, mPFC

description: Library name: Sample 13


title: Rat number2, Right hemisphere, mPFC

description: Library name: Sample 4


title: Rat number1, Right hemisphere, mPFC

description: Library name: Sample 2


title: Rat number4, Left hemisphere, mPFC

description: Library name: Sample 7


title: HD3, DIF-mut55, UMI-4C, rep2

city: Mexico City

first: Gustavo

last: Tapia

state: CDMX

address: Cto. Exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

description: Library name: Sample 8

library_source: genomic

data_processing:
Raw fastq files were processed and analysed using the R package UMI4Cats (https://github.com/Pasquali-lab/UMI4Cats) as described in Ramos-Rodríguez et al. (2021) https://doi.org/10.1093/bioinformatics/btab392
Assembly: galGal6
Supplementary files format and content: Raw UMI counts in a tabular delimited file

molecule: genomic DNA

organism: Gallus gallus

source_name: Hematopoietic

growth_protocol: HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cells were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lysed and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for targeted fragmentation with an average peak size at 500 bp. Proximity ligation products were enriched using Streptavidin-coated beads.
Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and ligation junctions for specific viewpoints were enriched using a nested PCR approach as described in Schwartzman et al. 2016. Viewpoint-specific downstream (DS) primers contained P5 sequence at their 5’ end and TruSeq Primer 2.0 (P7) was used to complement adapter sequences for pair-end sequencing.

treatment_protocol: Cells were treated with H7 (20 μM, Sigma) and 10 mM Hepes pH 8.0 in HD3 cell medium in 1% CO2 athmosphere at 42°C for 24 h

value: Hematopoietic

value: Chicken erythroblasts

value: 20μM H7 (Sigma), 10mM Hepes pH 8, 42°C, 1% CO3


title: Rat number1, Left hemisphere, mPFC

description: Library name: Sample 1


title: HD3, DIF-WT, UMI-4C, rep1

description: Library name: Sample 3

value: 20μM H7 (Sigma), 10mM Hepes pH 8, 42°C, 1% CO2


title: HD3, WT, UMI-4C, rep1

description: Library name: Sample 1


title: HD3, DIF-mut55, ATAC, rep1

description: Library name: Sample 7

data_processing:
Sequencing reads were trimmed for adaptor sequence using Trim Galore
Trimmed sequencing reads were mapped to GRCg6a/galGal6 using Bowtie2
Read filtering and peak calling were performed using NGSUtils and MACS2, respectively
Assembly: galGal6
Supplementary files format and content: Peaks in a tabular-delimited file

extract_protocol:
Nuclei extraction of 50,000 cells was treated with the Tn5 enzyme for 30 min. Following tagmentation, DNA was extracted using MinElute columns (Qiagen).
Preparation of ATAC-seq libraries was performed as described in Buenrostro et al., (2015)


title: Rat number3, Left hemisphere, mPFC

description: Library name: Sample 5


title: HD3, DIF-mut55, UMI-4C, rep1

description: Library name: Sample 7


title: HD3, DIF-WT, ATAC, rep1

description: Library name: Sample 3


title: HD3, DIF-WT, UMI-4C, rep2

description: Library name: Sample 4


title: HD3, mut55, UMI-4C, rep1

description: Library name: Sample 5


title: HD3, WT, ATAC, rep2

description: Library name: Sample 2


title: HD3, mut55, ATAC, rep1

description: Library name: Sample 5


title: HD3, mut55, UMI-4C, rep2

description: Library name: Sample 6


title: HD3, mut55, ATAC, rep2

description: Library name: Sample 6


title: HD3, DIF-WT, ATAC, rep2

description: Library name: Sample 4


title: HD3, DIF-mut55, ATAC, rep2

description: Library name: Sample 8


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, replicate 1, ORF library

city: Cambridge

first: Adam

middle: J

last: Rubin

state: Massachusetts

address: 415 Main St.

institute: Broad Institute

description: Library name: Primary_Experiment_1_ATAC_replicate_1_ORF

data_processing:
Raw Illumina outupt files were processed into fastq files filtered using the Cumulus V2.1.1 Cell Ranger workflow on the Terra platform. The Cumulus workflow operated on the fastq files to generate processed data files for single-cell ATAC libraries (filtered aligned fragments, single cell calls, peak calls). In the associated raw data fastq files, R1 corresponds to the forward genomic DNA read, R2 corresponds to the 10x cell barcode, and R3 corresponds to the reverse genomic DNA read.
For ORF barcode libraries, a custom Python script (shared in the linked manuscript, called process_ATAC_ORF_barcode.py) was used to process fastq files into a matrix of cell barcodes versus ORF barcodes, with counts of each ORF barcode observed in each cell. In the associated raw data fastq files, R2 corresponds to the 10x cell barcode, and R3 corresponds to the ORF barcode read. As described in feature_reference.csv, the ORF barcode is found in positions 19-28 of the R3 read.
Signac v1.9.0 was used to merge single-cell ATAC library processed data from multiple channels and perform final analyses.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files: *fragments.tsv.gz, *fragments.tsv.gz.tbi, *peaks.bed, and *singlecell.csv files can be loaded directly into Signac.

source_name: Primary CD4 T cell

growth_protocol: Jurkat T cells were grown in RPMI supplemented 10% FBS and 1% penicillin/streptomycin. Primary human CD4 T cells were grown in the same media with the addition of 50 U/ml IL-2.

extract_protocol:
Cells were subjected to the 10x Genomics single-cell ATAC-seq protocol with modifications for the Spear-ATAC (Pierce et al., Nature Communications 2021) amplification of genetic barcodes.
ATAC chromatin accessibility libraries were generated following the protocol from 10x Genomics. ORF barcode libraries were generated using the final ATAC libraries as input, as described in the Spear-ATAC protocol, with modifications described in detail in Rubin et al. 2024 bioRxiv.

treatment_protocol: Cells were stimulated by the addition of anti-CD3 and anti-IgG antibodies for specified times. For the screen experiment using Jurkat T cells, one sample of cells were stimulated for each time point and these cells were split to be loaded onto separate channels in 10x Genomics controller. For experiments using primary human CD4 T cells, cells were stimulated in biological replicate samples, and each replicate was loaded separately into a channel in the 10x Genomics controller.

value: Primary CD4 T cell

value: TCR stimulation


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 2, ORF library

description: Library name: Jurkat_Screen_ATAC_90min_channel_2_ORF

source_name: Jurkat T cell

value: Jurkat T cell


title: HD3, WT, UMI-4C, rep2

description: Library name: Sample 2


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, replicate 2, ORF library

description: Library name: Primary_Experiment_1_ATAC_replicate_2_ORF


title: HD3, WT, ATAC, rep1

description: Library name: Sample 1


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 2, ORF library

description: Library name: Jurkat_Screen_ATAC_30min_channel_2_ORF


title: Primary human CD4 T cell, 25 ORF screen, 90 min stimulation, replicate 3, ORF library

description: Library name: Primary_Experiment_2_ATAC_replicate_3_ORF


title: Primary human CD4 T cell, 25 ORF screen, 90 min stimulation, replicate 2, ORF library

description: Library name: Primary_Experiment_2_ATAC_replicate_2_ORF


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 1, ORF library

description: Library name: Jurkat_Screen_ATAC_30min_channel_1_ORF


title: Donor 6 Control

city: Headington

first: Jian

last: Luo

state: Oxford

address: 69 Headley Way

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: B61

data_processing:
Gene count data were retrieved through FeatureCounts by inputing FASTQ file
Count data were filtered through edgeR::filterByExpr using min.count=40,min.prop=0.9
Filtered count data were passed to sva::ComBat_seq to adjust for batch effects
DEGs were identified using DESeq2
Assembly: GRCh38(hg38)
Supplementary files format and content: Excel files with raw count after filteration and adjustment of batch effects and sample information

source_name: Blood

extract_protocol:
RNA from basophils was extracted using the RNeasy Plus Mini kit
RAN libraries were prepared using Novogene NGS-RNA Library Prep Set

value: Blood

value: Basophil

value: Primary Basophil

value: WT

value: Control


title: Donor 6 PGD2

description: Library name: B62


title: Primary human CD4 T cell, 25 ORF screen, 90 min stimulation, replicate 1, ORF library

description: Library name: Primary_Experiment_2_ATAC_replicate_1_ORF


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 1, ORF library

description: Library name: Jurkat_Screen_ATAC_90min_channel_1_ORF


title: Donor 6 IgE

description: Library name: B64

value: IgE


title: Donor 6 PGD2+QAW039

description: Library name: B63


title: Donor 5 IgE

description: Library name: B54


title: Donor 5 PGD2

description: Library name: B52


title: Donor 4 IgE

description: Library name: B44


title: Donor 4 PGD2+QAW039

description: Library name: B43


title: Donor 3 PGD2

description: Library name: B32


title: Donor 5 PGD2+QAW039

description: Library name: B53


title: Donor 4PGD2

description: Library name: B42


title: Donor 4 Control

description: Library name: B41


title: Donor 3 PGD2+QAW039

description: Library name: B33


title: Donor 5 Control

description: Library name: B51


title: Donor 2 IgE

description: Library name: B24


title: Donor 2 Control

description: Library name: B21


title: Donor 1 PGD2+QAW039

description: Library name: B13


title: Donor 2 PGD2

description: Library name: B22


title: Donor 2 PGD2+QAW039

description: Library name: B23


title: Donor 3 Control

description: Library name: B31


title: Donor 1 IgE

description: Library name: B14


title: Donor 3 IgE

description: Library name: B34


title: A375_CRISPRKO_MED12KO_day14_Vemu_rep3

description: Library name: Sample 39

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 (CRISPRKO)
Trimmed reads were mapped to corresponding library built genomes by HISAT2
Guide RNA reads count tables were generated by HTSeq
Assembly: Other
Supplementary files format and content: text files includes raw reads count
Library strategy: CRISPR Screen

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 MED12 knockout cells transduced with a homemade epigenetic library or a whole-genome knockout library were treated with DMSO or vemurafenib (2 μM). A375 MED23 knockout cells transduced with a homemade epigenetic library were treated with DMSO or vemurafenib (1 μM). Cells were split every 2–3 days.

value: Melanoma cell line

value: MED12 KO


title: A375_CRISPRKO_MED12KO_day14_Vemu_rep2

description: Library name: Sample 38


title: A375_CRISPRKO_MED12KO_day14_DMSO_rep3

description: Library name: Sample 36


title: A375_CRISPRKO_MED12KO_day14_Vemu_rep1

description: Library name: Sample 37


title: A375_CRISPRKO_MED12KO_day14_DMSO_rep1

description: Library name: Sample 34


title: A375_CRISPRKO_MED12KO_day8_Vemu_rep3

description: Library name: Sample 33


title: Donor 1 PGD2

description: Library name: B12


title: A375_CRISPRKO_MED12KO_day14_DMSO_rep2

description: Library name: Sample 35


title: Donor 1 Control

description: Library name: B11


title: A375_CRISPRKO_MED12KO_day8_Vemu_rep1

description: Library name: Sample 31


title: aCcr3_2

city: Qingdao

first: yunfeng

last: yang

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

country: China

institute: shandong university

description: Library name: aCcr3_2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: REY15A
Supplementary files format and content: bw

organism: Saccharolobus islandicus REY15A

source_name: Strain

growth_protocol: Strains  were cultured in MTSV medium

extract_protocol:
The cells were then resuspended in TBS-TT buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween-20, 0.1% Triton X-100, pH 7.5) and fragmented by sonication until the DNA fragments were of 200-500 bp. After centrifugation (10,000 g for 15 minutes), a 100 µl aliquot of the DNA-containing supernatant was kept apart to be uses as an input control and the remaining sample was divided into two aliquots. One aliquot was incubated with anti-aCcr1 antibody-coated protein A beads (Cytiva) and the other was incubated with pre-immune serum-coated protein A beads, which served as a nonspecific binding control (Mock control). After incubation at 60 °C for 10 hrs, the samples were collected and the captured DNA was purified by using the DNA Cycle-Pure Kit (Omega) according to the manufacturer's instruction. The input samples were treated as above without the addition of antiserum and beads. The purified DNA was used for ChIP-Seq library preparation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: the cells were collected 3 hours after synchronization, cross-linked by adding 1% formaldehyde for 15 minutes, and quenched with a final concentration of 125 mM glycine.

value: Strain

value: anti-aCcr3 antibody-coated protein A beads


title: aCcr2_2

description: Library name: aCcr2_2

value: anti-aCcr2 antibody-coated protein A beads


title: Input

description: Library name: Input

value: Input

value: DNA-containing supernatant was kept apart to be uses as an input control


title: aCcr2_1

description: Library name: aCcr2_1


title: aCcr3_1

description: Library name: aCcr3_1


title: A375_CRISPRKO_MED12KO_day8_DMSO_rep1

description: Library name: Sample 28


title: control 3

description:
Library name: Sample 9
empty plasmid

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 mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
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: REY15A
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: Strains of Sis/pSeSD(Cont) and Sis/pSeSD-aCcr2,aCcr3 were cultured in ATV medium

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For transcriptomic analysis, culture was inoculated with an initial OD600 of 0.05. The cells were pelleted at 6,000 g for 10 min after 12 h of cultivation when the OD600 reached approximately 0.2. The pellet was resuspended in 1 ml PBS buffer. The cells were pelleted again and stored at -80°C.

value: control 3

value: Arabinose induction


title: A375_CRISPRKO_MED12KO_day8_DMSO_rep2

description: Library name: Sample 29


title: A375_CRISPRKO_MED12KO_day8_Vemu_rep2

description: Library name: Sample 32


title: control 1

description:
Library name: Sample 7
empty plasmid

value: control 1


title: A375_CRISPRKO_MED12KO_day8_DMSO_rep3

description: Library name: Sample 30


title: control 2

description:
Library name: Sample 8
empty plasmid

value: control 2


title: aCcr3 overexpressed 2

description:
Library name: Sample 5
aCcr3 overexpressed

value: aCcr3 overexpressed 2


title: A375_CRISPRKO_MED12KO_day0_rep3

description: Library name: Sample 27


title: A375_CRISPRKO_MED12KO_day0_rep2

description: Library name: Sample 26


title: aCcr3 overexpressed 1

description:
Library name: Sample 4
aCcr3 overexpressed

value: aCcr3 overexpressed 1


title: A375_Epic_MED12KO_day14_Vemu_rep3

description: Library name: Sample 24


title: A375_Epic_MED12KO_day14_Vemu_rep2

description: Library name: Sample 23


title: aCcr2 overexpressed 3

description:
Library name: Sample 3
aCcr2 overexpressed

value: aCcr2 overexpressed 3


title: aCcr2 overexpressed 2

description:
Library name: Sample 2
aCcr2 overexpressed

value: aCcr2 overexpressed 2


title: aCcr3 overexpressed 3

description:
Library name: Sample 6
aCcr3 overexpressed

value: aCcr3 overexpressed 3


title: aCcr2 overexpressed 1

description:
Library name: Sample 1
aCcr2 overexpressed

value: aCcr2 overexpressed 1


title: BAP1,-IAA,-6,-rep2

city: Tianjin

first: Meihan

last: Gong

address: Qixiangtai Road

institute: Tianjin Medical University

description: Library name: BAP1-IAA-6-rep2

data_processing:
Sequencing data were aligned to the mm39 reference genome with Hisat2 (v2.2.1), and SAM files were converted to BAM files using Samtools (v1.19).
BigWig files were generated using deepTools (v3.5.4) and visualized via the Integrative Genomics Viewer (IGV).
Gene counts were calculated by Stringtie (v2.2.1)
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: ESC

extract_protocol:
RNA was harvested using TRIzol reagent, 1 μg of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using  oligo -dT beads.

value: ESC


title: A375_CRISPRKO_MED12KO_day0_rep1

description: Library name: Sample 25

value: Melanoma cell line

value: MED12 KO


title: BAP1,-IAA,-6,-rep1

description: Library name: BAP1-IAA-6-rep1


title: A375_Epic_MED12KO_day14_DMSO_rep1

description: Library name: Sample 19


title: A375_Epic_MED12KO_day14_DMSO_rep3

description: Library name: Sample 21


title: A375_Epic_MED12KO_day14_DMSO_rep2

description: Library name: Sample 20


title: A375_Epic_MED12KO_day14_Vemu_rep1

description: Library name: Sample 22


title: BAP1,-IAA,-3,-rep1

description: Library name: BAP1-IAA-3-rep1


title: A375_Epic_MED12KO_day8_Vemu_rep3

description: Library name: Sample 18


title: A375_Epic_MED12KO_day8_Vemu_rep1

description: Library name: Sample 16


title: BAP1,-IAA,-0,-rep2

description: Library name: BAP1-IAA-0-rep2


title: BAP1,-IAA,-3,-rep2

description: Library name: BAP1-IAA-3-rep2


title: BAP1,-IAA,-0,-rep1

description: Library name: BAP1-IAA-0-rep1


title: A375_Epic_MED12KO_day8_DMSO_rep2

description: Library name: Sample 14


title: BAP1,+IAA,-6,-rep1

description: Library name: BAP1+IAA-6-rep1


title: BAP1,+IAA,-3,-rep1

description: Library name: BAP1+IAA-3-rep1


title: BAP1,+IAA,-6,-rep2

description: Library name: BAP1+IAA-6-rep2


title: A375_Epic_MED12KO_day8_DMSO_rep3

description: Library name: Sample 15


title: BAP1,+IAA,-0,-rep2

description: Library name: BAP1+IAA-0-rep2


title: A375_Epic_MED23KO_day14_Vemu_rep2

description: Library name: Sample 8

value: MED23 KO


title: A375_Epic_MED12KO_day0_rep2

description: Library name: Sample 11


title: A375_Epic_MED12KO_day8_DMSO_rep1

description: Library name: Sample 13


title: BAP1,+IAA,-0,-rep1

description: Library name: BAP1+IAA-0-rep1


title: BAP1,+IAA,-3,-rep2

description: Library name: BAP1+IAA-3-rep2


title: A375_Epic_MED23KO_day14_Vemu_rep1

description: Library name: Sample 7


title: A375_Epic_MED12KO_day0_rep3

description: Library name: Sample 12


title: UTX,-IAA,-3,-rep1

description: Library name: UTX-IAA-3-rep1


title: UTX,-IAA,-0,-rep2

description: Library name: UTX-IAA-0-rep2


title: UTX,-IAA,-6,-rep1

description: Library name: UTX-IAA-6-rep1


title: UTX,-IAA,-3,-rep2

description: Library name: UTX-IAA-3-rep2


title: UTX,-IAA,-0,-rep1

description: Library name: UTX-IAA-0-rep1


title: UTX,-IAA,-6,-rep2

description: Library name: UTX-IAA-6-rep2


title: A375_Epic_MED23KO_day14_Vemu_rep3

description: Library name: Sample 9


title: A375_Epic_MED23KO_day14_DMSO_rep3

description: Library name: Sample 6


title: A375_Epic_MED12KO_day0_rep1

description: Library name: Sample 10


title: A375_Epic_MED23KO_day14_DMSO_rep1

description: Library name: Sample 4


title: A375_Epic_MED23KO_day0_rep3

description: Library name: Sample 3


title: UTX,+IAA,-6,-rep2

description: Library name: UTX+IAA-6-rep2


title: A375_Epic_MED23KO_day14_DMSO_rep2

description: Library name: Sample 5


title: A375_Epic_MED12KO_day8_Vemu_rep2

description: Library name: Sample 17


title: UTX,+IAA,-3,-rep2

description: Library name: UTX+IAA-3-rep2


title: UTX,+IAA,-6,-rep1

description: Library name: UTX+IAA-6-rep1


title: A375_MED23_Vemu_rep2.gz

description: Library name: Sample 16

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: A375 control and Mediator knockout (KO) cells were treated with either DMSO or 1 μM vemurafenib for 24 h.

value: 1 uM Vemurafenib


title: A375_Epic_MED23KO_day0_rep1

description: Library name: Sample 1


title: UTX,+IAA,-0,-rep2

description: Library name: UTX+IAA-0-rep2


title: UTX,+IAA,-3,-rep1

description: Library name: UTX+IAA-3-rep1


title: A375_MED23_Vemu_rep1.gz

description: Library name: Sample 15


title: A375_Epic_MED23KO_day0_rep2

description: Library name: Sample 2


title: A375_MED23_DMSO_rep1.gz

description: Library name: Sample 13

value: DMSO


title: RA,24,EZH2,rep2

description: Library name: RA-24-EZH2-rep2

data_processing:
Raw data underwent quality evaluation with Fastqc (v0.12.1) and Multiqc (v1.19). Adapters were removed with Trim-galore (v0.6.10).
Clean reads were aligned to the mm39 reference genome using Bowtie2 (v2.5.3) with the following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --no-unal.Only uniuqe mapping reads with at most two mismatches were retained.
Duplicates removed with Sambamba (v1.0), and Bigwig files were generated using deepTools(v3.5.4), then was normalized by RPKM.
Peak calling was conducted with Macs2 (v2.2.9.1).
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a BioRuptor sonicator (Diagenode).
The DNA Library of ChIP were prepared with a TruePrep DNA Library Prep Kit according to the manufacturer’s instructions (TD503, Vazyme).


title: UTX,+IAA,-0,-rep1

description: Library name: UTX+IAA-0-rep1


title: A375_MED23_DMSO_rep2.gz

description: Library name: Sample 14


title: RA,24,EZH2,rep1

description: Library name: RA-24-EZH2-rep1


title: A375_MED19_DMSO_rep1.gz

description: Library name: Sample 9

value: MED19 KO


title: A375_MED19_Vemu_rep1.gz

description: Library name: Sample 11


title: RA,12,EZH2,rep2

description: Library name: RA-12-EZH2-rep2


title: RA,12,EZH2,rep1

description: Library name: RA-12-EZH2-rep1


title: RA,3,EZH2,rep1

description: Library name: RA-3-EZH2-rep1


title: A375_MED12_Vemu_rep2.gz

description: Library name: Sample 8


title: A375_MED19_DMSO_rep2.gz

description: Library name: Sample 10


title: RA,3,EZH2,rep2

description: Library name: RA-3-EZH2-rep2


title: A375_MED19_Vemu_rep2.gz

description: Library name: Sample 12


title: A375_MED12_DMSO_rep1.gz

description: Library name: Sample 5


title: UTX,+IAA,FA,dMT,K4me1,rep2

description: Library name: UTX+IAA-FA-dMT-K4me1-2


title: A375_MED12_Vemu_rep1.gz

description: Library name: Sample 7


title: A375_MED12_DMSO_rep2.gz

description: Library name: Sample 6


title: RA,0,EZH2,rep2

description: Library name: RA-0-EZH2-rep2


title: A375_GFP_Vemu_rep2.gz

description: Library name: Sample 4

value: WT


title: RA,0,EZH2,rep1

description: Library name: RA-0-EZH2-rep1


title: UTX,+IAA,FA,dMT,K4me1,rep1

description: Library name: UTX+IAA-FA-dMT-K4me1-1


title: A375_GFP_Vemu_rep1.gz

description: Library name: Sample 3


title: UTX,+IAA,FA,WT,K4me1,rep2

description: Library name: UTX+IAA-FA-WT-K4me1-2


title: UTX,+IAA,FA,WT,K4me1,rep1

description: Library name: UTX+IAA-FA-WT-K4me1-1


title: UTX,-IAA,FA,K4me1,rep2

description: Library name: UTX-IAA-FA-K4me1-2


title: UTX,+IAA,FA,K4me1,rep2

description: Library name: UTX+IAA-FA-K4me1-2


title: A375_dKO_H3K27ac_rep2

description: Library name: Sample 53

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 and Mediator- or HDAC3-knockout cells were either left untreated or treated with DMSO or 1 μM vemurafenib for 24 hours prior to chromatin immunoprecipitation (ChIP) experiments.

value: HDAC3 MED23 dKO

tag: batch


title: UTX,-IAA,FA,K4me1,rep1

description: Library name: UTX-IAA-FA-K4me1-1


title: A375_dKO_H3K27ac_rep3

description: Library name: Sample 54


title: A375_MED23KO_MED23_rep3

description: Library name: Sample 51


title: A375_dKO_H3K27ac_rep1

description: Library name: Sample 52


title: UTX,+IAA,FA,K4me1,rep1

description: Library name: UTX+IAA-FA-K4me1-1


title: A375_MED23KO_MED23_rep2

description: Library name: Sample 50


title: UTX,-IAA,2i,K4me1,rep2

description: Library name: UTX-IAA-2i-K4me1-2


title: A375_MED23KO_MED23_rep1

description: Library name: Sample 49


title: UTX,-IAA,2i,K4me1,rep1

description: Library name: UTX-IAA-2i-K4me1-1


title: A375_GFP_DMSO_rep1.gz

description: Library name: Sample 1


title: UTX,+IAA,2i,K4me1,rep2

description: Library name: UTX+IAA-2i-K4me1-2


title: UTX,+IAA,2i,K4me1,rep1

description: Library name: UTX+IAA-2i-K4me1-1


title: A375_MED23KO_HDAC3_rep3

description: Library name: Sample 48


title: A375_MED23KO_HDAC3_rep1

description: Library name: Sample 46


title: A375_MED23KO_HDAC3_rep2

description: Library name: Sample 47


title: A375_MED23KO_H3K27ac_rep3

description: Library name: Sample 45


title: UTX,-IAA,24,K27me3,rep2

description: Library name: UTX-IAA-24-K27me3-rep2


title: UTX,-IAA,24,K27me3,rep1

description: Library name: UTX-IAA-24-K27me3-rep1


title: UTX,-IAA,6,K27me3,rep1

description: Library name: UTX-IAA-6-K27me3-rep1


title: A375_HDAC3KO_MED23_rep3

description: Library name: Sample 42

value: HDAC3 KO


title: A375_MED23KO_H3K27ac_rep2

description: Library name: Sample 44


title: UTX,-IAA,6,K27me3,rep2

description: Library name: UTX-IAA-6-K27me3-rep2


title: A375_GFP_DMSO_rep2.gz

description: Library name: Sample 2


title: UTX,-IAA,3,K27me3,rep1

description: Library name: UTX-IAA-3-K27me3-rep1


title: A375_HDAC3KO_MED23_rep2

description: Library name: Sample 41


title: UTX,-IAA,3,K27me3,rep2

description: Library name: UTX-IAA-3-K27me3-rep2


title: A375_MED23KO_H3K27ac_rep1

description: Library name: Sample 43


title: UTX,-IAA,0,K27me3,rep1

description: Library name: UTX-IAA-0-K27me3-rep1


title: UTX,-IAA,0,K27me3,rep2

description: Library name: UTX-IAA-0-K27me3-rep2


title: A375_HDAC3KO_HDAC3_rep2

description: Library name: Sample 38


title: A375_HDAC3KO_HDAC3_rep3

description: Library name: Sample 39


title: A375_HDAC3KO_MED23_rep1

description: Library name: Sample 40


title: UTX,+IAA,24,K27me3,rep1

description: Library name: UTX+IAA-24-K27me3-rep1


title: UTX,+IAA,24,K27me3,rep2

description: Library name: UTX+IAA-24-K27me3-rep2


title: UTX,+IAA,3,K27me3,rep2

description: Library name: UTX+IAA-3-K27me3-rep2


title: UTX,+IAA,6,K27me3,rep1

description: Library name: UTX+IAA-6-K27me3-rep1


title: UTX,+IAA,3,K27me3,rep1

description: Library name: UTX+IAA-3-K27me3-rep1


title: A375_HDAC3KO_H3K27ac_rep2

description: Library name: Sample 35


title: UTX,+IAA,0,K27me3,rep2

description: Library name: UTX+IAA-0-K27me3-rep2


title: A375_HDAC3KO_HDAC3_rep1

description: Library name: Sample 37


title: A375_Ctrl_MED23_rep2

description: Library name: Sample 32


title: UTX,+IAA,6,K27me3,rep2

description: Library name: UTX+IAA-6-K27me3-rep2


title: BAP1,+IAA,FA,C91A,K4me1,rep1

description: Library name: BAP1+IAA-FA-C91A-K4me1-1


title: A375_HDAC3KO_H3K27ac_rep3

description: Library name: Sample 36


title: BAP1,+IAA,FA,C91A,K4me1,rep2

description: Library name: BAP1+IAA-FA-C91A-K4me1-2


title: A375_HDAC3KO_H3K27ac_rep1

description: Library name: Sample 34


title: BAP1,+IAA,FA,WT,K4me1,rep2

description: Library name: BAP1+IAA-FA-WT-K4me1-2


title: A375_Ctrl_HDAC3_rep3

description: Library name: Sample 30


title: A375_Ctrl_MED23_rep1

description: Library name: Sample 31


title: BAP1,+IAA,FA,WT,K4me1,rep1

description: Library name: BAP1+IAA-FA-WT-K4me1-1


title: A375_Ctrl_MED23_rep3

description: Library name: Sample 33


title: A375_Crl_H3K27ac_rep3

description: Library name: Sample 27


title: A375_Ctrl_H3K27ac_rep2

description: Library name: Sample 26


title: BAP1,-IAA,FA,K4me1,rep2

description: Library name: BAP1-IAA-FA-K4me1-2


title: A375_Ctrl_HDAC3_rep1

description: Library name: Sample 28


title: UTX,+IAA,0,K27me3,rep1

description: Library name: UTX+IAA-0-K27me3-rep1


title: BAP1,-IAA,FA,K4me1,rep1

description: Library name: BAP1-IAA-FA-K4me1-1


title: A375_Ctrl_H3K27ac_rep1

description: Library name: Sample 25


title: BAP1,+IAA,FA,K4me1,rep2

description: Library name: BAP1+IAA-FA-K4me1-2


title: A375_Ctrl_HDAC3_rep2

description: Library name: Sample 29


title: A375_MED23sg_Vemu_H3K27ac_rep3

description: Library name: Sample 24


title: BAP1,+IAA,FA,K4me1,rep1

description: Library name: BAP1+IAA-FA-K4me1-1


title: A375_MED23sg_Vemu_H3K27ac_rep2

description: Library name: Sample 23


title: A375_MED23sg_Vemu_H3K27ac_rep1

description: Library name: Sample 22


title: A375_MED23sg_DMSO_H3K27ac_rep3

description: Library name: Sample 21


title: BAP1,-IAA,24,119ub1,rep2

description: Library name: BAP1-IAA-24-119ub1-rep2


title: BAP1,+IAA,2i,K4me1,rep1

description: Library name: BAP1+IAA-2i-K4me1-1


title: A375_MED23sg_DMSO_H3K27ac_rep1

description: Library name: Sample 19


title: A375_MED19sg_Vemu_H3K27ac_rep1

description: Library name: Sample 16


title: A375_MED19sg_Vemu_H3K27ac_rep3

description: Library name: Sample 18


title: BAP1,-IAA,24,119ub1,rep1

description: Library name: BAP1-IAA-24-119ub1-rep1


title: BAP1,-IAA,6,119ub1,rep2

description: Library name: BAP1-IAA-6-119ub1-rep2


title: BAP1,-IAA,3,119ub1,rep2

description: Library name: BAP1-IAA-3-119ub1-rep2


title: A375_MED19sg_DMSO_H3K27ac_rep3

description: Library name: Sample 15


title: A375_MED19sg_DMSO_H3K27ac_rep2

description: Library name: Sample 14


title: A375_MED19sg_Vemu_H3K27ac_rep2

description: Library name: Sample 17


title: BAP1,-IAA,3,119ub1,rep1

description: Library name: BAP1-IAA-3-119ub1-rep1


title: BAP1,-IAA,2i,K4me1,rep2

description: Library name: BAP1-IAA-2i-K4me1-2


title: BAP1,-IAA,2i,K4me1,rep1

description: Library name: BAP1-IAA-2i-K4me1-1


title: BAP1,-IAA,0,119ub1,rep2

description: Library name: BAP1-IAA-0-119ub1-rep2


title: BAP1,-IAA,6,119ub1,rep1

description: Library name: BAP1-IAA-6-119ub1-rep1


title: A375_MED23sg_DMSO_H3K27ac_rep2

description: Library name: Sample 20


title: A375_MED19sg_DMSO_H3K27ac_rep1

description: Library name: Sample 13


title: BAP1,+IAA,2i,K4me1,rep2

description: Library name: BAP1+IAA-2i-K4me1-2


title: A375_MED12sg_Vemu_H3K27ac_rep2

description: Library name: Sample 11


title: BAP1,-IAA,0,119ub1,rep1

description: Library name: BAP1-IAA-0-119ub1-rep1


title: A375_MED12sg_Vemu_H3K27ac_rep3

description: Library name: Sample 12


title: A375_MED12sg_Vemu_H3K27ac_rep1

description: Library name: Sample 10


title: BAP1,+IAA,6,119ub1,rep2

description: Library name: BAP1+IAA-6-119ub1-rep2


title: A375_MED12sg_DMSO_H3K27ac_rep3

description: Library name: Sample 9


title: BAP1,+IAA,24,119ub1,rep2

description: Library name: BAP1+IAA-24-119ub1-rep2


title: BAP1,+IAA,24,119ub1,rep1

description: Library name: BAP1+IAA-24-119ub1-rep1


title: A375_MED12sg_DMSO_H3K27ac_rep1

description: Library name: Sample 7


title: BAP1,+IAA,6,119ub1,rep1

description: Library name: BAP1+IAA-6-119ub1-rep1


title: BAP1,+IAA,3,119ub1,rep1

description: Library name: BAP1+IAA-3-119ub1-rep1


title: A375_GFP_Vemu_H3K27ac_rep3

description: Library name: Sample 6


title: UTX, dMT, MLL4, rep2, CUT&Tag

description: Library name: UTX-dMT-MLL4-rep2

data_processing:
Raw data underwent quality evaluation with FastQC (v0.12.1) and MultiQC (v1.19).
Adapters were removed with Trim-galore (v0.6.10).
Clean reads were aligned to the mm39 reference genome using Bowtie2 (v2.5.3)
Duplicates removed with Sambamba (v1.0), and Bigwig files were generated using deepTools (v3.5.4)
Peak calling was conducted with Macs2 (v2.2.9.1)
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Cells were washed and harvested by wash buffer and incubated with activated conA beads. Then primary antibody was added, followed by Guinea Pig anti-Rabbit IgG antibody. After incubation, pA-Tn5 adapter complex was added. The purified DNA was amplified, then 200-1,000bp fragments were enriched for sequencing.
CUT&Tag libraries were prepared by Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyem, TD904)


title: A375_GFP_DMSO_H3K27ac_rep2

description: Library name: Sample 2


title: BAP1,+IAA,0,119ub1,rep2

description: Library name: BAP1+IAA-0-119ub1-rep2


title: A375_GFP_DMSO_H3K27ac_rep3

description: Library name: Sample 3


title: BAP1,+IAA,0,119ub1,rep1

description: Library name: BAP1+IAA-0-119ub1-rep1


title: A375_dKO_rep2

description: Library name: Sample 65

treatment_protocol: A375 control cells, Mediator- or HDAC3-knockout cells, and SOX10-overexpressing cells were either untreated or treated with DMSO or 1 μM vemurafenib for 24 hours prior to RNA extraction.


title: UTX, WT, MLL4, rep1, CUT&Tag

description: Library name: UTX-WT-MLL4-rep1


title: UTX, -IAA, MLL4, rep2, CUT&Tag

description: Library name: UTX-IAA-MLL4-rep2


title: A375_dKO_rep3

description: Library name: Sample 66


title: A375_GFP_Vemu_H3K27ac_rep2

description: Library name: Sample 5


title: A375_GFP_Vemu_H3K27ac_rep1

description: Library name: Sample 4


title: UTX, WT, MLL4, rep2, CUT&Tag

description: Library name: UTX-WT-MLL4-rep2


title: A375_GFP_DMSO_H3K27ac_rep1

description: Library name: Sample 1


title: BAP1,+IAA,3,119ub1,rep2

description: Library name: BAP1+IAA-3-119ub1-rep2


title: A375_MED23KO_rep3

description: Library name: Sample 63


title: UTX, +IAA, MLL4, rep2, CUT&Tag

description: Library name: UTX+IAA-MLL4-rep2


title: A375_MED12sg_DMSO_H3K27ac_rep2

description: Library name: Sample 8


title: BAP1, C91A, MLL4, rep2, CUT&Tag

description: Library name: BAP1-C91A-MLL4-rep2


title: A375_HDAC3KO_rep3

description: Library name: Sample 60


title: UTX, -IAA, MLL4, rep1, CUT&Tag

description: Library name: UTX-IAA-MLL4-rep1


title: BAP1, C91A, MLL4, rep1, CUT&Tag

description: Library name: BAP1-C91A-MLL4-rep1


title: A375_MED23KO_rep1

description: Library name: Sample 61


title: A375_MED23KO_rep2

description: Library name: Sample 62


title: A375_HDAC3KO_rep2

description: Library name: Sample 59


title: UTX, +IAA, MLL4, rep1, CUT&Tag

description: Library name: UTX+IAA-MLL4-rep1


title: BAP1, WT, MLL4, rep2, CUT&Tag

description: Library name: BAP1-WT-MLL4-rep2


title: A375_Ctrl_rep2

description: Library name: Sample 56


title: A375_Ctrl_rep3

description: Library name: Sample 57


title: BAP1, -IAA, MLL4, rep2, CUT&Tag

description: Library name: BAP1-IAA-MLL4-rep2


title: BAP1, WT, MLL4, rep1, CUT&Tag

description: Library name: BAP1-WT-MLL4-rep1


title: BAP1, +IAA, MLL4, rep2, CUT&Tag

description: Library name: BAP1+IAA-MLL4-rep2


title: A375_MED23sg1_EV_rep3

description: Library name: Sample 51


title: BAP1, +IAA, MLL4, rep1, CUT&Tag

description: Library name: BAP1+IAA-MLL4-rep1


title: A375_HDAC3KO_rep1

description: Library name: Sample 58


title: A375_MED23sg1_SOX10OE_rep2

description: Library name: Sample 53

value: MED23 KO/SOX10 OE


title: BAP1, -IAA, MLL4, rep1, CUT&Tag

description: Library name: BAP1-IAA-MLL4-rep1


title: UTX, dMT, MLL4, rep1, CUT&Tag

description: Library name: UTX-dMT-MLL4-rep1


title: A375_MED23sg1_SOX10OE_rep3

description: Library name: Sample 54


title: A375_MED23sg1_SOX10OE_rep1

description: Library name: Sample 52


title: Bmal1KO_RAW264.7_ChIP

city: Fukuoka

first: Akito

last: Tsuruta

department: Pharmaceutics

country: Japan

institute: Kyushu university

description: Library name: Bmal1KO_RAW264.7_ChIP

data_processing:
Raw sequencing reads were quality-checked and trimmed using fastp v1.0.1. The quality-filtered reads were aligned to the mouse reference genome (mm39) using BWA-MEM v0.7.19-r1273. SAM/BAM processing was performed using samtools v1.23. Duplicate reads were removed using Picard v3.4.0.. Peaks were identified from the aligned reads using MACS3 v3.0.3 and HOMER v5.1 with the mm39 reference genome. For each IP sample, the corresponding Input sample was used as a control for peak calling. Broad peaks were called using MACS3.
Assembly: mm39
Supplementary files format and content: Peak files in broadPeak format containing genomic coordinates of enriched regions identified by MACS3.
Supplementary files format and content: Signal tracks in bigWig format representing normalized ChIP-seq signal across the genome.

growth_protocol: DMEM, 5% fetal bovine serum. Cells were cultured at 37℃ and 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature. After quenching and cell lysis, chromatin was sonicated with Bioruptor UCD-300 (CosmoBio).
ChIP libraries were prepared for sequencing using NEBNext Ultra II DNA Library Prep Kit  according to the manufacturer's protocol.

value: Macrophage like

value: Bmal1 knockout

tag: chip antibodies

value: H3K27ac (Abcam, #ab4729)


title: Mfp2KO_RAW264.7_Input

description: Library name: Mfp2KO_RAW264.7_Input

value: Mfp2 knockout


title: Mfp2KO_RAW264.7_ChIP

description: Library name: Mfp2KO_RAW264.7_ChIP


title: A375_MED23sg1_EV_rep2

description: Library name: Sample 50


title: A375_MED23sg1_EV_rep1

description: Library name: Sample 49


title: Naive_RAW264.7_Input

description: Library name: Naive_RAW264.7_Input

value: wild-type


title: A375_Ctrl_rep1

description: Library name: Sample 55


title: Bmal1KO_RAW264.7_Input

description: Library name: Bmal1KO_RAW264.7_Input


title: A375_GFPsg_SOX10OE_rep1

description: Library name: Sample 46

value: SOX10 OE


title: Naive_RAW264.7_ChIP

description: Library name: Naive_RAW264.7_ChIP


title: A375_dKO_rep1

description: Library name: Sample 64


title: A375_GFPsg_SOX10OE_rep2

description: Library name: Sample 47


title: A375_GFPsg_EV_rep3

description: Library name: Sample 45


title: mT23-2D, Input

city: Davis

first: Suyakarn

last: Archasappawat

state: California

address: 241 Briggs Hall

department: Microbiology and Molecular Genetics

institute: University of California, Davis

description: Library name: Sample 6

data_processing:
All analyses were performed on the Galaxy platform. Raw reads were quality-trimmed with Trim Galore! (Galaxy Version 0.6.10+galaxy0) to remove adapter sequences and low-quality bases. Trimmed reads were aligned to the Mus musculus mm9 reference genome using Bowtie2 (Galaxy Version 2.5.3+galaxy1), then filtered with SAMtools (Galaxy Version 2.5.2+galaxy3) to retain only properly paired reads with a mapping quality ≥ 30 while excluding mitochondrial reads (chrM). PCR and optical duplicates were removed with MarkDuplicates (Galaxy Version 3.1.1.0), and coverage tracks (BigWig files) were generated from the resulting unique, high-quality reads using bamCoverage (Galaxy Version 3.5.4+galaxy0).
Assembly: mm9
Supplementary files format and content: BigWig file for each sample except input

growth_protocol: All cells (mT3-2D, mT23-2D) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
For ChIP-seq, approximately 1 × 10⁷ cells were harvested per sample using TrypLE Express Enzyme (Gibco, 12605028) and resuspended in PBS to generate a single-cell suspension. Chromatin immunoprecipitation was carried out using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology, #9003) according to the manufacturer’s protocol with minor modifications. Briefly, cells were fixed in 1% formaldehyde at room temperature for 10 minutes to crosslink protein-DNA interactions. Crosslinking was quenched with glycine (final concentration 125 mM) for 5 minutes at room temperature. Cells were then washed twice with ice-cold PBS and lysed in lysis buffer to isolate nuclei. Chromatin was enzymatically digested with 1 µl of micrococcal nuclease (MNase) at 37°C for 20 minutes to achieve partial digestion, followed by mechanical shearing using a Bioruptor (Diagenode) set to high power for 3 rounds of 10 cycles (30 seconds on, 30 seconds off). Shearing was performed in 1.5 ml TPX microtubes (Diagenode, C30010010) to generate DNA fragments ranging from 150 to 500 bp. DNA fragmentation was verified by 1.8-2% agarose gel electrophoresis. For immunoprecipitation, 10 µl of antibody was used per reaction: BRD2 (Cell Signaling Technology, 5848S) or BRD4 (Bethyl Laboratories, A301-985A100). Chromatin and protein G magnetic beads were incubated overnight at 4°C with antibodies under constant agitation using a tube rotator to promote optimal antigen-antibody interaction. Beads were then washed sequentially with low salt, high salt, and LiCl wash buffers, followed by TE buffer. Crosslinks were reversed by incubating with Proteinase K at 65°C for 2 hours. DNA was purified using spin columns included in the kit according to the manufacturer’s instructions (Cell Signaling Technology, 14209S).
Library preparation and sequencing for ChIP-seq was carried out by Novogene Co., LTD. Sample quality was assessed prior to library construction. DNA fragments were end-repaired, A-tailed, and ligated to Illumina adapters, followed by size selection, PCR amplification, and quantification.

treatment_protocol: Cells (mT3-2D, mT23-2D) were treated with JQ1 (1 µM; MedChemExpress, Cat. No. HY-13030) or DMSO for 24 hours prior to ChIP-seq preparation.

value: Pancreatic cancer cells

tag: chip antibody


title: A375_MED23sg2_Vemu_rep2

description: Library name: Sample 41

value: Melanoma cell line


title: A375_GFPsg_EV_rep1

description: Library name: Sample 43


title: A375_MED23sg2_Vemu_rep3

description: Library name: Sample 42


title: mT23-2D, DMSO, BRD4

description: Library name: Sample 8


title: mT23-2D, JQ1, BRD2

description: Library name: Sample 9


title: A375_GFPsg_EV_rep2

description: Library name: Sample 44


title: A375_MED23sg2_Vemu_rep1

description: Library name: Sample 40


title: A375_MED23sg2_DMSO_rep1

description: Library name: Sample 37


title: mT3-2D, Input

description: Library name: Sample 1


title: A375_MED23sg2_DMSO_rep2

description: Library name: Sample 38


title: mT23-2D, DMSO, BRD2

description: Library name: Sample 7


title: mT23-2D, DMSO

description: Library name: Sample 5

data_processing:
Raw reads were quality-trimmed with Trim Galore! (Galaxy Version 0.6.7+galaxy0) to remove adapter sequences and low-quality bases. Clean reads were aligned to the Mus musculus mm9 reference genome using HISAT2 (Galaxy Version 2.2.1+galaxy1), and gene-level counts were obtained with featureCounts (Galaxy Version 2.0.3+galaxy2). Normalizationanalysis was performed with DESeq2 (Galaxy Version 2.11.40.8+galaxy0).
Assembly: mm9
Supplementary files format and content: Tabular file includes normalized counts for each sample
Supplementary files format and content: Tabular files include raw counts for each sample

growth_protocol: All cells (mT3-2D, mT19-2D, mT23-2D) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were lysed in 1 ml of TRIzol reagent (Thermo Fisher Scientific, 15596026) at room temperature for 5 minutes with gentle agitation, followed by the addition of 200 µl of chloroform (Reagents, C755N59), according to the manufacturer’s protocol. RNA was extracted using the PureLink RNA Mini Kit (Invitrogen, 12183018A) and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific) prior to sequencing submission.
Library preparation and sequencing for RNA-seq was carried out by Novogene Co., LTD. Total RNA quality was assessed using 1% agarose gel electrophoresis, NanoDrop spectrophotometry (for RNA quantity and purity), and an Agilent 2100 Bioanalyzer (for RNA Integrity Number, RIN). Poly(A) mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, and reverse-transcribed to synthesize first-strand cDNA with random primers. Second-strand cDNA synthesis was performed using a dUTP-incorporation protocol to maintain strand specificity. The resulting double-stranded cDNA was end-repaired, A-tailed, and ligated to Illumina adapters, followed by size selection and PCR amplification. Libraries were quantified and quality-checked prior to sequencing.

treatment_protocol: Cells (mT3-2D, mT19-2D, mT23-2D) were treated with JQ1 (1 µM; MedChemExpress, Cat. No. HY-13030) or DMSO for 24 hours prior to RNA extraction.


title: mT3-2D, JQ1, BRD4

description: Library name: Sample 5


title: A375_GFPsg_SOX10OE_rep3

description: Library name: Sample 48

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


title: A375_MED23sg1_Vemu_rep1

description: Library name: Sample 34


title: mT23-2D, JQ1

description: Library name: Sample 6


title: A375_MED23sg2_DMSO_rep3

description: Library name: Sample 39


title: mT19-2D, JQ1

description: Library name: Sample 4


title: A375_MED23sg1_Vemu_rep2

description: Library name: Sample 35


title: mT23-2D, JQ1, BRD4

description: Library name: Sample 10


title: A375_MED23sg1_DMSO_rep3

description: Library name: Sample 33


title: mT3-2D, JQ1

description: Library name: Sample 2


title: A375_MED23sg1_DMSO_rep2

description: Library name: Sample 32


title: mT3-2D, JQ1, BRD2

description: Library name: Sample 4


title: mT3-2D, DMSO, BRD2

description: Library name: Sample 2


title: A375_MED23sg1_Vemu_rep3

description: Library name: Sample 36


title: mT19-2D, DMSO

description: Library name: Sample 3


title: mT3-2D, DMSO, BRD4

description: Library name: Sample 3


title: mT3-2D, DMSO

description: Library name: Sample 1


title: A375_MED23sg1_DMSO_rep1

description: Library name: Sample 31


title: A375_MED19sg2_Vemu_rep3

description: Library name: Sample 30


title: ChIPseq_InputH3K27me3_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep3_BC126_R1

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_28
Input DNA for associated H3K27me3 sample replicate

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 ChIP-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. For 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). Then, R1 reads FASTQ sequencing files were mapped to the mouse GRCm38 - mm10 reference genome using STAR (2.7.0f) with default parameters. HOMER was used to convert aligned reads into “tag directories” for further analyses.
ChIP-seq – H3K27me3 analysis Regions positive for H3K27me3 in adult male homeostatic microglia were first identified with HOMER’s getDiffPeakReplicate.pl program, using two independent biological replicates and their associated input HOMER’s (command: -genome mm10 -DESeq2 -size 1250 -L 0 -F 2 -region). To that file, the Bhlhe40 gene body coordinates were appended (chr6 108660629 108666925). Then, to quantify and compare H3K27me3 abundance in homeostatic vs CPZ inflammatory microglia subsets, H3K27me27+ regions identified above were annotated with sequencing reads from H3K27me3 ChIP-seq tag directories from 3 independent replicates generated from homeostatic, CPZ CD229-CD11c-, CPZ CD229+CD11c- and CPZ CD229+CD11c+ microglia (n = 3), using HOMER’s annotatePeak.pl program with mm10 -noadj parameters. Then, regions with differential H3K27me3 abundance were identified using HOMER’s getDiffExpression.pl program, which leveraged R/DESeq2 to assess differential enrichment (-AvsA -simpleNorm), using threshold of FDR 0.05. The 3 homeostatic files used for differential abundance were distinct from the 2 homeostatic files used to identify H3K27me3+ regions.
ChIP-seq data visualization: The UCSC genome browser was used to visualize ChIP-seq sequencing data. Bedgraph.gz files were generated using HOMER's makeUCSCfile.pl. For H3K27me3 UCSC data visualization, original tag directories were downsampled, randomly, to 20 million tags using HOMER?s getRandomReads.pl; tags.tsv file were then converted to tag directories and used for makeUCSCfile.pl. Lastly, for visualization of H3K27me3+ regions, region.bed files were generated using called regions.txt files using HOMER?s pos2bed.pl. H3K4me3 files used for UCSC data visualization were previously generated. UCSC genome browser visualization of H3K4me3 ChIP-seq data from adult male mouse microglia was performed using the makeUCSCfile.pl command, using ChIP-seq sequencing files from Belhocine et al. 2022 (GEO accession GSM5066662 and GSM5066664).
Assembly: mm10
Supplementary files format and content:
H3K27me3_Basal_regions.txt: Tab-delimited text files of H3K27me3+ regions identified in basal, homeostatic adult male microglia
H3K27me3_Basal_regions.bed: bed file of H3K27me3+ regions identified in basal, homeostatic adult male microglia
H3K27me3_Basal_regions_BasalvsCuprizone_DE_RawData.txt: Tab-delimited text files of raw read counts at H3K27me3+ regions, first identified in basal/homeostatic adult male microglia, for homeostatic and inflammatory microglia subsets
H3K27me3_Basal_regions_BasalvsCuprizone_DE_simpleNorm.txt: Tab-delimited text files of normalized read counts at H3K27me3+ regions, first identified in basal/homeostatic adult male microglia, for homeostatic and inflammatory microglia subsets (10 million reads/sample). Results from differential enrichment analyses are also annotated.

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).
Chromatin immunoprecipitation Following sorting, aliquots of 400,000 to 600,000 microglia were centrifuge (1000 RCF at 4°C for 10 min), and cell pellet were snap-frozen in liquid nitrogen and stored at -80°C. When ready, chromatin immunoprecipitation for histone modification H3K27me3 was performed as follows, using microglia 400,000 to 600,000 per replicates. First microglia were briefly thawed on ice and lysed by incubation in 1 ml of lysis buffer (0.5% IGEPAL CA-630, 10 mM HEPES pH 7.9, 85 mM KCl, 1 mM EDTA pH 8.0, in molecular grade water) for 10 min on ice. Lysates were centrifuged at 800 RCF for 5 min at 4°C, and pellets were resuspended in 200 µl of sonication/ immunoprecipitation buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.5 mM EGTA, 0.1% Deoxcycholate, 0.5% Sarkosyl, in molecular grade water). Sonication was performed with a Bioruptor Standard Sonicator (Diagenode) and consisted of two rounds of 10 cycle of 30 sec “sonication-on”, 90 sec “sonication-off”.  Twenty-two microliters of 10% Triton-X were then added to samples (1% final concentration) on ice, and lysates were cleared by centrifugation for 5 min at 18,000 RCF at 4°C. Two microliters of supernatant were then set aside for input library sequencing controls. Each sample supernatants were then immunoprecipitated with 5.0 µg H3K27me3 antibody (Active Motif 39155) pre-bound to 17 µl Protein A Dynabeads (Thermo Fisher Scientific 10001D), on a rotator for three hours at 4°C.  Immunoprecipitates were washed three times each on ice with ice-cold wash buffer I (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA pH 8.0 in molecular grade water), wash buffer III (10 mM Tris-HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Deoxycholate, 1mM EDTA in water) and TET (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 0.1% Tween-20, in molecular grade water) and eluted with 1% SDS/TE at RT in a final volume of 100 µl.  Reverse-crosslinking was then performed on immunoprecipitates and saved input aliquots. First, 6.38 µl of 5 M NaCl (final concentration 300 mM; Thermo Fisher Scientific AM9759) was added to each sample immersed in 100 µl SDS/TE. Crosslinking was then reversed by overnight incubation at 65-68°C in a hot air oven. Potentially contaminating RNA was then digested for one hour at 37°C with 0.33 mg/ml RNase A, proteins were digested for one hour at 55°C with 0.5 mg/ml proteinase K (NEB P8107S), and DNA was extracted using Sera-Mag SpeedBeads (Thermo Fisher Scientific 6515205050250).  DNA was then purified by addition of 1.5 µl Sera-Mag SpeedBeads Carboxyl Magnetic Beads (Cytivia 45152105050250), resuspended in 150 µl 20% PEG 8000/2.5 M NaCl (PEG 8000 from Sigma-Aldrich P2139; NaCl 5M 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).  ChIP-seq final library preparation Sequencing libraries were prepared from recovered DNA (ChIP) 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).  ChIP-seq libraries were single- or 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 ChIP-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

tag: read length


title: A375_MED19sg2_Vemu_rep2

description: Library name: Sample 29

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

value: 1 uM Vemurafenib


title: ChIPseq_H3K27me3_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep3_BC120_R1

description:
Library name: Sample_27
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: ChIPseq_InputH3K27me3_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep1_BC111_PE150_R1

description:
Library name: Sample_24
Input DNA for associated H3K27me3 sample replicate


title: A375_MED19sg2_DMSO_rep3

description: Library name: Sample 27

value: DMSO


title: ChIPseq_H3K27me3_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep2_BC118_PE150_R1

description:
Library name: Sample_25
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: A375_MED19sg2_Vemu_rep1

description: Library name: Sample 28

value: MED19 KO


title: A375_MED19sg1_Vemu_rep2

description: Library name: Sample 23


title: ChIPseq_H3K27me3_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep1_BC104_PE150_R1

description:
Library name: Sample_23
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt

value: WT


title: ChIPseq_InputH3K27me3_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC123_PE150_R1

description:
Library name: Sample_20
Input DNA for associated H3K27me3 sample replicate


title: A375_MED19sg1_Vemu_rep3

description: Library name: Sample 24


title: ChIPseq_H3K27me3_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC117_PE150_R1

description:
Library name: Sample_19
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: A375_MED19sg2_DMSO_rep2

description: Library name: Sample 26


title: A375_MED19sg1_DMSO_rep1

description: Library name: Sample 19


title: A375_MED19sg2_DMSO_rep1

description: Library name: Sample 25


title: A375_MED12sg2_Vemu_rep2

description: Library name: Sample 17

value: MED12 KO


title: A375_MED12sg2_Vemu_rep3

description: Library name: Sample 18


title: ChIPseq_H3K27me3_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC119_R1

description:
Library name: Sample_21
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: ChIPseq_H3K27me3_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC118_R1

description:
Library name: Sample_15
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: A375_MED19sg1_Vemu_rep1

description: Library name: Sample 22


title: ChIPseq_InputH3K27me3_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC125_R1

description:
Library name: Sample_22
Input DNA for associated H3K27me3 sample replicate


title: A375_MED19sg1_DMSO_rep2

description: Library name: Sample 20


title: ChIPseq_InputH3K27me3_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC110_PE150_R1

description:
Library name: Sample_18
Input DNA for associated H3K27me3 sample replicate


title: A375_MED19sg1_DMSO_rep3

description: Library name: Sample 21


title: ChIPseq_InputH3K27me3_Microglia_CD229PositiveCD11cPositive_WT_Male_Adult_Cuprizone_4w_rep2_BC124_PE150_R1

description:
Library name: Sample_26
Input DNA for associated H3K27me3 sample replicate


title: ChIPseq_InputH3K27me3_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep3_BC124_R1

description:
Library name: Sample_16
Input DNA for associated H3K27me3 sample replicate


title: ChIPseq_H3K27me3_Microglia_CD229PositiveCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC103_PE150_R1

description:
Library name: Sample_17
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: ChIPseq_InputH3K27me3_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC122_PE150_R1

description:
Library name: Sample_14
Input DNA for associated H3K27me3 sample replicate


title: A375_MED12sg2_Vemu_rep1

description: Library name: Sample 16


title: ChIPseq_H3K27me3_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep2_BC116_PE150_R1

description:
Library name: Sample_13
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: A375_MED12sg2_DMSO_rep3

description: Library name: Sample 15


title: ChIPseq_InputH3K27me3_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC107_PE150_R1

description:
Library name: Sample_12
Input DNA for associated H3K27me3 sample replicate


title: A375_MED12sg2_DMSO_rep2

description: Library name: Sample 14


title: ChIPseq_H3K27me3_Microglia_WT_Male_Adult_Basal_rep5_BC115_PE150_R1

description:
Library name: Sample_9
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt

value: None; Regular diet


title: A375_MED12sg1_Vemu_rep2

description: Library name: Sample 11


title: A375_MED12sg2_DMSO_rep1

description: Library name: Sample 13


title: ChIPseq_InputH3K27me3_Microglia_WT_Male_Adult_Basal_rep5_BC121_PE150_R1

description:
Library name: Sample_10
Input DNA for associated H3K27me3 sample replicate


title: ChIPseq_H3K27me3_Microglia_CD229NegativeCD11cNegative_WT_Male_Adult_Cuprizone_4w_rep1_BC102_PE150_R1

description:
Library name: Sample_11
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: A375_MED12sg1_Vemu_rep1

description: Library name: Sample 10


title: ChIPseq_H3K27me3_Microglia_WT_Male_Adult_Basal_rep3_BC102_R1

description:
Library name: Sample_5
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: ChIPseq_H3K27me3_Microglia_WT_Male_Adult_Basal_rep4_BC101_PE150_R1

description:
Library name: Sample_7
ChIP-seq
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_RawData.txt
H3K27me3_Basal_regions_BasalvsCuprizone_SamplesAnnotated_DifferentialEnrichment_simpleNorm.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep3_BC19_R1

description:
Library name: Sample_42
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_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

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.

value: 0.2% Cuprizone diet for 5 weeks prior sacrifice


title: ChIPseq_InputH3K27me3_Microglia_WT_Male_Adult_Basal_rep3_BC105_R1

description:
Library name: Sample_6
Input DNA for associated H3K27me3 sample replicate


title: A375_MED12sg1_DMSO_rep2

description: Library name: Sample 8


title: ChIPseq_InputH3K27me3_Microglia_WT_Male_Adult_Basal_rep4_BC106_PE150_R1

description:
Library name: Sample_8
Input DNA for associated H3K27me3 sample replicate


title: A375_MED12sg1_DMSO_rep1

description: Library name: Sample 7


title: A375_GFPsg_Vemu rep1

description: Library name: Sample 4


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep2_BC17_R1

description:
Library name: Sample_39
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: A375_MED12sg1_DMSO_rep3

description: Library name: Sample 9


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep1_BC15_R1

description:
Library name: Sample_38
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: A375_GFPsg_Vemu rep2

description: Library name: Sample 5


title: A375_GFPsg_Vemu rep3

description: Library name: Sample 6


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep2_BC17_R1

description:
Library name: Sample_41
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229Positive_Cx3cr1Mef2aKO_Male_Adult_Basal_rep2_BC13_PE150_R1

description:
Library name: Sample_37
Peaks_ATACseq_Microglia_Cx3cr1Mef2a_Basal_CD229Subset_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229Positive_Cx3cr1Mef2aKO_Male_Adult_Basal_rep1_BC9_PE150_R1

description:
Library name: Sample_36
Peaks_ATACseq_Microglia_Cx3cr1Mef2a_Basal_CD229Subset_SamplesAnnotated_RawData.txt


title: A375_GFPsg_DMSO rep3

description: Library name: Sample 3


title: A375_GFPsg_DMSO rep2

description: Library name: Sample 2


title: A375_TADA2Bsg_CRISPRa1_day14_Vemu_rep3

description:
Library name: Sample 33
htseq_count_CRISPRa1.txt

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

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.

value: TADA2B KO


title: A375_MED12sg1_Vemu_rep3

description: Library name: Sample 12


title: A375_TADA2Bsg_CRISPRa1_day14_Vemu_rep2

description:
Library name: Sample 32
htseq_count_CRISPRa1.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Mef2aKO_Male_Adult_Cuprizone_5w_rep1_BC16_R1

description:
Library name: Sample_40
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: A375_GFPsg_DMSO rep1

description: Library name: Sample 1


title: ATACseq_Microglia_CD229Negative_Cx3cr1Mef2aKO_Male_Adult_Basal_rep1_BC8_PE150_R1

description:
Library name: Sample_34
Peaks_ATACseq_Microglia_Cx3cr1Mef2a_Basal_CD229Subset_SamplesAnnotated_RawData.txt


title: A375_TADA2Bsg_CRISPRa1_day14_Vemu_rep1

description:
Library name: Sample 31
htseq_count_CRISPRa1.txt


title: ATACseq_Microglia_Cx3cr1Mef2aKO_Male_Adult_Basal_rep1_BC8_R1

description:
Library name: Sample_32
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_Cx3cr1Mef2aKO_Male_Adult_Basal_rep2_BC19_R1

description:
Library name: Sample_33
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_CD229Negative_Cx3cr1Mef2aKO_Male_Adult_Basal_rep2_BC12_PE150_R1

description:
Library name: Sample_35
Peaks_ATACseq_Microglia_Cx3cr1Mef2a_Basal_CD229Subset_SamplesAnnotated_RawData.txt


title: A375_TADA2Bsg_CRISPRa1_day14_DMSO_rep3

description:
Library name: Sample 30
htseq_count_CRISPRa1.txt


title: A375_TADA2Bsg_CRISPRa1_day14_DMSO_rep2

description:
Library name: Sample 29
htseq_count_CRISPRa1.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep4_BC10_PE150_R1

description:
Library name: Sample_31
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: A375_TADA2Bsg_CRISPRa1_day14_DMSO_rep1

description:
Library name: Sample 28
htseq_count_CRISPRa1.txt


title: A375_TADA2Bsg_CRISPRa1_day0_rep3

description:
Library name: Sample 27
htseq_count_CRISPRa1.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep1_BC8_R1

description:
Library name: Sample_28
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep3_BC3_PE150_R1

description:
Library name: Sample_30
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cPositive_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep2_BC4_R1

description:
Library name: Sample_29
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep1_BC3_R1

description:
Library name: Sample_25
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: A375_TADA2Bsg_CRISPRKO_day7_Vemu_rep2

description:
Library name: Sample 23
htseq_count_CRISPRKO.txt

value: 2 uM Vemurafenib


title: A375_TADA2Bsg_CRISPRa1_day0_rep1

description:
Library name: Sample 25
htseq_count_CRISPRa1.txt


title: A375_TADA2Bsg_CRISPRa1_day0_rep2

description:
Library name: Sample 26
htseq_count_CRISPRa1.txt


title: ATACseq_Microglia_Cx3cr1Cre_Male_Adult_Basal_rep3_BC13_R1

description:
Library name: Sample_23
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep3_BC6_PE150_R1

description:
Library name: Sample_27
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: ATACseq_Microglia_Clec7aPositiveCD229PositiveCD11cNegative_Cx3cr1Cre_Male_Adult_Cuprizone_5w_rep2_BC2_PE150_R1

description:
Library name: Sample_26
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Cuprizone5w_SamplesAnnotated_RawData.txt


title: A375_TADA2Bsg_CRISPRKO_day7_DMSO_rep3

description:
Library name: Sample 21
htseq_count_CRISPRKO.txt


title: ATACseq_Microglia_Cx3cr1Cre_Male_Adult_Basal_rep4_BC1_R1

description:
Library name: Sample_24
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_SamplesAnnotated_RawData.txt


title: A375_TADA2Bsg_CRISPRKO_day7_Vemu_rep1

description:
Library name: Sample 22
htseq_count_CRISPRKO.txt


title: A375_TADA2Bsg_CRISPRKO_day7_DMSO_rep1

description:
Library name: Sample 19
htseq_count_CRISPRKO.txt


title: ATACseq_Microglia_CD229PositiveCD11cNegative_Trem2KO_Male_Adult_Cuprizone_4w_rep2_BC7_R1

description:
Library name: Sample_19
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_rep3

description:
Library name: Sample 15
htseq_count_epic.txt


title: ATACseq_Microglia_Cx3cr1Cre_Male_Adult_Basal_rep1_BC5_R1

description:
Library name: Sample_21
Peaks_ATACseq_Microglia_Cx3cr1CreERT2WT_Cx3cr1Mef2a_Basal_WholePopulation_SamplesAnnotated_RawData.txt


title: A375_TADA2Bsg_CRISPRKO_day0_rep3

description:
Library name: Sample 18
htseq_count_CRISPRKO.txt


title: A375_Epic_day8_Vemu_rep2

description:
Library name: Sample 14
htseq_count_epic.txt